Systems, apparatuses, devices for microbiome monitoring and methods of operation and use

Abstract

Embodiments of the present disclosure relates to systems, apparatuses, devices and methods for rapid and automated analysis of the microbiome in a portable apparatus. In some embodiments, regular profiling of a user's microbiome without the need for extensive laboratory infrastructure can be performed.

Description

SYSTEMS, APPARATUSES, DEVICES FOR MICROBIOME MONITORING AND METHODS OF OPERATION AND USERelated Applications

[0001] The disclosure claims the benefit of and priority to European patent application no. EP2025300005.3, filed February 20, 2025, the entire disclosure of which is herein incorporated by reference.Technical Field

[0002] The disclosure relates to systems, methods, apparatuses and devices for at least one of determining and tracking a microbiome of a user. In particular, embodiments described herein relate to a portable device for monitoring a gut microbiome of a user.Background

[0003] Gastrointestinal conditions, such as diarrhea, irritable bowel syndrome (IBS), and dysbiosis (imbalance of gut bacteria), are some of the most common ailments affecting people today. These issues can be caused by changes in diet, stress, lack of sleep, exposure to pathogens, or antibiotics, and can lead to reduced quality of life and illness. Existing methods and systems for gut microbiome analysis and diagnostics are non-portable, costly, and time-consuming, requiring laboratory infrastructure and specialized expertise. These methods also incur logistic and temporal burdens including sample collection, removal of sample to the laboratory infrastructure, sample processing, sample analysis, and delivery of analysis back to the subject. Due to the dynamic natureof the microbiome, the results may be inaccurate by the time they are delivered to the subject. Further, existing methods may be infeasible for those in austere environments or in areas with limited resources.As such, there remains a need for a portable, compact, cost-effective and rapid analysis of the microbiome without requiring laboratory infrastructure or specialized expertise. The systems, methods, apparatuses and devices of the present disclosure enable the automated, routine, and rapid analysis of a user’s microbiome. In particular, embodiments of the present disclosure provide easy-to-understand, socialized, and gamified representations of user’s biological data. This may allow for longitudinal and hyper-personalized microbial profiling, allowing users to track microbial changes and link them to early illness detection or to optimize recovery from illness or injury, as well as wellness which can allow users to monitor their normal baseline and track microbial changes to optimize health, recovery, training and / or link them to early illness detection or to optimize recovery from illness or injury.Summary

[0004] Gastrointestinal indications such as, for example, diarrhea, irritable bowel syndrome (IBS), and dysbiosis (imbalance of gut bacteria) impact quality of life for many individuals. Existing gut microbiome monitoring methods often incur operative, logistic, and temporal burdens due to sampling, removal of the sample to a laboratory infrastructure, sample processing, and analysis. For these reasons, existing methods lack accessibility for users.

[0005] In contrast, embodiments described herein provide users with a cost-effective, rapid, and scalable solution for real-time microbiome monitoring. Embodiments described herein integrate advanced culturomics and automated imaging, enabling at-home detection of bacterial and viral threats, real-time monitoring of gut microbiome health (e.g., next-day insights without requiring laboratory infrastructure and specialized expertise), and individual gut health assessments. Embodiments described herein can include a system, apparatus / device including automated sample spreading, temperature-controlled incubation, high-resolution imaging, machine learning and / or artificial-intelligence analysis to enable unprecedented portability, accuracy, and speed for gut microbiome assessment and tracking. Embodiments according to the present disclosure can beused as a monitoring tool across “interventions,” including, for example, dietary changes and stress. For example, elite athletes can monitor their normal baseline across pre-competition season, adjusting training load, dietary interventions and competition / high stress events such as travel, races / competitions, which induce changes to microbiome profile.

[0006] In some embodiments of the disclosure, a microbiome monitoring apparatus is provided and includes a housing, a cartridge configured to be removably disposed in a portion of the housing, the cartridge including a growth medium disposed therein configured to receive at least one spreading element on a surface thereof, at least one spreading element configured to spread a sample on the surface of the growth medium, a heating element configured to supply heat to the cartridge to incubate the sample for a period of time, and an imaging device disposed within the housing and configured to capture image data of the sample at the very least after the sample has been incubated for the period of time.

[0007] Some embodiments may further include one and / or another of (and, if not mutually exclusive, in some embodiments, a plurality of, in some embodiments, a majority of, in some embodiments, substantially all of, and in some embodiments, all of) the following structures, functions, functionality, steps, elements, or clarifications:the cartridge is configured to be removably disposed in the portion of the housing at a predetermined angle from horizontal;the cartridge comprises or includes a sample dish for containing the growth medium; an actuation mechanism configured to couple with the cartridge when the cartridge is disposed in the housing and configured to rotate the cartridge at a predetermined angular velocity such that the at least one spreading element spreads a sample over the surface of the growth medium;a light source configured to illuminate the growth medium as the imaging device captures the image data;o such illumination may be merely used to capture image data, and one or more images can be taken at any time, and / or for general illumination for any period of time, including being kept on (e.g., all day, hours, and the like);after the sample is spread over the surface of the growth medium, a / the actuation mechanism is configured to stop rotation of the cartridge such that the at least one spreading element moves to a periphery of the growth medium before the imaging device captures the imaging data so as to move the spreading element out of a field of view of the imaging device;the predetermined angle of the cartridge causes at least one of (i) the at least one spreading element to move to a / the periphery of the growth medium before the imaging device captures the imaging data, and / or (ii) prevention of condensation build up on the growth medium;electronics (singular or plural) disposed within the housing, the electronics configured to control at least one of the heating element and the actuation mechanism;a / the growth medium is suitable for culturing one or more microorganisms;a / the growth medium comprises chromogenic agar;the apparatus is sized and shaped for portability;the apparatus is configured to automatically spread, incubate and capture image data of the sample following disposition of the cartridge in the housing;a / the imaging device disposed in an inner volume of the housing;a / the heating element configured to supply heat to the cartridge for a period of time to incubate the sample;a / the growth medium is configured to receive the at least one spreading element on the surface;the at least one spreading element comprises a bead, a ball, or an otherwise spherical object; a roulette structure including a plurality of pockets spaced along a periphery thereof; each pocket of a / the roulette structure being configured to receive a spreading element so as to rotationally receive and carry a / the spreading element(s) from a first portion of the cartridge to a second portion of the cartridge whereby the spreading element(s) exits the pocket so as to cross a / the surface of the growth medium;each pocket of a / the roulette structure includes at least one inclined base wall upon which the at least one spreading element is received;each pocket includes at least one inclined base wall, or a pair of inclined base walls upon which the at least one spreading element is received;a first of a / the pair of inclined base walls is arranged closer to a central axis of the roulette and is configured to aid in a spreading element existing a pocket when arriving at the second portion of the cartridge;a second of a / the pair of inclined base walls is arranged closer to the periphery of the roulette is configured to aid in receiving a spreading element within a pocket at the first portion of the cartridge;the at least one spreading element comprises a plurality of spreading elements, where the spreading elements can be beads, and the plurality may be between 4-30 beads, 5-25 beads, 5-20 beads, 5-15 beads, 5-10 beads, and ranges therebetween;a / the angular velocity of a / the cartridge and / or a / the sample dish having a diameter of between 50 mm and 100 mm and an RPM of between 5 and 300;a / the diameter of a / the sample dish is selected from the group consisting of between 50-90 mm, 50-80mm, 50-70 mm, 50-60 mm, 50-55mm, and ranges therebetween;an RPM for rotating a / the cartridge and / or a / the sample dish is selected from the group consisting of between 5-250 RPM, 5-200 RPM, 5-150 RPM, 5-100 RPM, 5-50 RPM, 5-40 RPM, 5-30 RPM, 5-20 RPM, 5-10 RPM, 5-9 RPM, 8-10 RPM and ranges therebetween; rotation of a / the cartridge and / or a / the sample dish corresponds to a continuous, single direction, 360-degree rotation over a period of time;rotation of a / the cartridge and / or a / the sample dish corresponds to a continuous, two-direction back and forth movement, each directional movement being a single 360-degree rotation, and where the overall two-direction rotation is performed over a period of time; rotation of a / the cartridge and / or a / the sample dish corresponds to a continuous, two-direction back and forth movement, each directional movement being a single, less than360-degree rotation, and where the overall two-direction rotation is performed over a period of time;rotation of a / the cartridge and / or a / the sample dish corresponds to a continuous, two- direction back and forth movement, each directional movement being a single, 180 degrees of less rotation, and where the overall two-direction rotation is performed over a period of time;anda / the angular velocity corresponds to between 300 degrees / s and 600 degrees / s, and ranges therebetween.

[0008] In some embodiments, a microbiome monitoring apparatus is provided including a cartridge configured to receive a growth medium, where the cartridge is configured to be removably disposed within a housing at a predetermined angle from horizontal, when disposed in the housing, the cartridge engages an actuation mechanism configured to rotate the cartridge such that at least one spreading element comprising a bead spreads a biological sample across the surface of the growth medium, and after the sample is spread across the growth medium, the actuation mechanism stops rotation of the cartridge such that the at bead rolls to the periphery of the solid or semi-solid growth medium. These embodiments may further include the cartridge is configured to receive one or more beads on the surface of the growth medium, the growth medium is suitable for culturing one or more microorganisms, and / or the growth medium comprises chromogenic agar.

[0009] In some embodiments, a method of characterizing a microbiome is provided and includes (i) contacting a sample comprising one or more microorganisms with the cartridge of the apparatus according to any of the disclosed apparatus / device / system embodiments, (ii) spreading the sample on the surface of growth medium contained by the cartridge using a / the at least one spreading element, (iii) culturing the sample under conditions for the one or more microorganisms to grow on the growth medium, (iv) capturing at least one image of the sample using the imaging device; and (v) identifying one or more microorganisms in the at least one image for characterizing the microbiome.

[0010] In some embodiments, a method of characterizing a microbiome is provided and includes (i) supplying a sample comprising one or more microorganisms of a microbiome to a cartridge of a microbiome monitoring apparatus, with the apparatus including a housing, the cartridge configured to be removably disposed in a portion of the housing at a predetermined angle from horizontal, the cartridge including a growth medium disposed therein and including a surface for which the sample is disposed thereon and receives at least one spreading element, an actuation mechanism coupled to the cartridge when the cartridge is disposed in the housing and configured to rotate the cartridge at a predetermined angular velocity such that the at least one spreading element spreads the sample over the surface of the growth medium, a heating element for supplying heat to the cartridge to incubate the sample for at least a first period of time, and an imaging device disposed in the housing and configured to capture image data of the cartridge at least one of during and after the sample has incubated for the period of time; the method further including (ii) spreading the sample over the surface of the growth medium using the at least one spreading element, (iii) culturing the sample for the at least first period of time under conditions for the one or more microorganisms to grow on the growth medium, (iv) capturing at least one image of the cartridge using the imaging device after culturing the sample for at least the first period of time; and (v) identifying one or more microorganisms in the at least one image so as to characterize the microbiome.

[0011] Some embodiments may further include one and / or another of (and, if not mutually exclusive, in some embodiments, a plurality of, in some embodiments, a majority of, in some embodiments, substantially all of, and in some embodiments, all of) the following structures, functions, functionality, steps, elements, or clarifications:the sample comprises an environmental sample, a human sample, or an animal sample; the one or more microorganisms comprise bacteria;the bacteria comprise aerobic bacteria;the sample comprises one or more of stool, saliva, skin, blood, plasma, serum, urine, sputum, mucus, pleural fluid, nipple aspirates, lymph fluid, respiratory fluid, stomach contents, lachrymal fluid, breast milk, semen or vaginal secretions;the growth medium including a single type of growth medium, or a plurality of different types of growth media suitable for culturing different types of microorganisms;the growth medium comprises chromogenic agar;identifying the one or more microorganisms in the at least one image comprises characterizing size, color, shape and / or growth rate of colonies grown on the surface of the growth medium after culturing the biological sample for at least the first period of time; identifying the one or more microorganisms in the at least one image comprises quantifying a number of colonies of the one or more microorganisms;identifying of the one or more microorganisms in the at least one image is via a computer vision algorithm;anddiluting the sample in a buffer prior to supplying the sample, whereby the one or more microorganisms in the sample are diluted so as to produce single colonies on the surface of the growth medium after culturing;

[0012] In some embodiments, a method of characterizing changes in a microbiome of a subject is provided, and includes (i) supplying a first sample from a subject comprising one or more microorganisms with the cartridge of the apparatus according to any one of the apparatus / device / system embodiments disclosed herein, (ii) spreading the first sample over the surface of the growth medium using at least one spreading element, (iii) culturing the first sample under conditions for the one or more microorganisms to grow on the growth medium, (iv) capturing at least one image of the sample using the imaging device, (v) identifying one or more microorganisms in the at least one image so as to characterize the microbiome of the first sample, (vi) repeating steps (i)-(v) at least once with at least a second sample from the subject, so as to characterize the microbiome present in the second sample, and (vii) comparing the microbiome present in the first sample with the microbiome present in the second sample so as to characterize changes in the microbiome of the subject.

[0013] Such embodiments may further include collection of the first sample, and the second sample are separated by a period of time, changes in the microbiome are associated with an illnessand / or wellness of the subject, and / or changes in the microbiome are associated with recovery from an illness by the subject.

[0014] In some embodiments, a non-transitory, processor-readable medium storing instructions that, when executed by a processor, cause the processor to: cause display, via a graphical user interface (GUI) of a computing device, of a user-selectable object configured to trigger establishment of a wireless connection with an apparatus of any of the apparatuses / devices / systems disclosed herein, cause display, at a first time, via the GUI and in response to receiving first microbiome data from the apparatus, of a first graphic feature representing a microbiome of a user of the apparatus, the first graphic feature including an arc-shaped health score indicator, cause display, at a second time after the first time, via the GUI and in response to receiving second microbiome data from the apparatus, of a second graphic feature representing the microbiome of the user of the apparatus, the second graphic feature including a modified version of the arc-shaped health score indicator and a modified version of the array of representations of microorganisms from the plurality of microorganisms, and at least one of generating a health score represented by at least one of the first graphic feature and the second graphic feature and identifying at least some of the microbiome of the sample via a computer vision algorithm.

[0015] Some embodiments may further include one and / or another of (and, if not mutually exclusive, in some embodiments, a plurality of, in some embodiments, a majority of, in some embodiments, substantially all of, and in some embodiments, all of) the following structures, functions, functionality, steps, elements, or clarifications:at least one of the first microbiome data or the second microbiome data includes a representation of at least one microorganism from the plurality of microorganisms of the microbiome;storing instructions to cause the processor to cause display, via the GUI, of a third graphic feature that includes a representation of a time-lapse progression associated with the microbiome of the user of the apparatus;a / the representation of the time-lapse progression includes an animation sequence; the representation of the time-lapse progression is associated with an overnight period;storing instructions to cause the processor to: cause display, via the GUI, of a third graphic feature that includes an animation sequence associated with the microbiome of the user of the apparatus, and / or cause display, via the GUI, of an interactive object that, when interacted with by the user of the apparatus, causes the animation sequence to advance between a start point thereof and an end point thereof;storing instructions to cause the processor to transmit a signal to cause illumination of at least one indicator light of the apparatus to indicate at least one of: powering on the apparatus, powering off the apparatus, connecting the apparatus to Bluetooth®, a beginning of a sample processing procedure, a completion of a sample processing procedure, and a reminder to the user of the apparatus to provide a sample;storing instructions to cause the processor to transmit a signal to cause a modification to at least one incubation setting of the apparatus;storing instructions to cause the processor to initiate a cartridge reorder in response to at least one of (i) a user interaction with the GUI, and / or (ii) receiving a signal from the apparatus indicating that the cartridge requires replacement;storing instructions to cause the processor to generate a recommendation for the user based on at least one of the first microbiome data, the second microbiome data, and data received via an application programming interface (API) of a wearable fitness tracker;at least one of the first microbiome data or the second microbiome data includes at least one of image data, data generated by analyzing a biological sample received by the apparatus, and data generated by analyzing the image data;andthe first graphic feature also includes an arc-shaped health score indicator and an array of representations of developmental stages from a plurality of developmental stages.Brief Description of the Drawings

[0016] FIG. 1A is a block diagram of a microbiome monitoring device, according to some embodiments of the disclosure.

[0017] FIG. IB is a block diagram of a cartridge assembly of a microbiome monitoring device, according to some embodiments of the disclosure.

[0018] FIG. 1C is a schematic diagram of at least a portion of electronics of a microbiome monitoring device, according to some embodiments of the disclosure.

[0019] FIG. 2A shows a predetermined angle at which a cartridge assembly is configured to be disposed in a housing of a microbiome monitoring device, according to some embodiments of the disclosure.

[0020] FIG. 2B is a cross-section of a cartridge assembly at the predetermined angle, according to some embodiments of the disclosure.

[0021] FIGS. 3A-3H show a variety of external views of a microbiome monitoring device according to some embodiments of the disclosure which includes a left side view (3A), a rightside view (3B), a top view (3C), a bottom view (3D), a front perspective view (3E), a back perspective view (3F), a front view (3G), and a back view (3H).

[0022] FIG. 4 is a cross-sectional side view of a microbiome monitoring device according to some embodiments of the disclosure.

[0023] FIG. 5A shows an illustration of a cartridge holder according to some embodiments of the disclosure.

[0024] FIG. 5B is an illustration of a cartridge holder fitting into a housing of the microbiome monitoring device according to some embodiments of the disclosure.

[0025] FIG. 6 is an illustrations showing a front perspective view of a path of rotation of the cartridge relative to the housing and a travel path of a spreading element during sample spreading, according to some embodiments of the disclosure.

[0026] FIGS. 7A-7C2 show various views of a cartridge holder including a motor and gear system and heating element coupled thereto, according to some embodiments of the disclosure.

[0027] FIGS. 7D1-7D4 show various views of a cartridge holder including a motor and one more gears of a gear system, according to some embodiments of the disclosure.

[0028] FIGS. 7D5-7D8 show various views of a cartridge / rotation portion, including a motor and one or more gears of a gear system, according to some embodiments of the disclosure.

[0029] FIGS. 7E-7K show various views of a, depending upon the view, a cartridge, cartridge assembly, and cartridge holder, providing a bearing assembly, according to some embodiments of the disclosure.

[0030] FIGS.7L-7S2 show various views of a roulette / spreading element system, and / or elements thereof, according to some embodiments of the disclosure.

[0031] FIG. 8A is a cross-sectional side view of a microbiome monitoring device according to some embodiments of the disclosure.

[0032] FIG. 8B is a cross-sectional, perspective view of some internal components of a microbiome monitoring device according to some embodiments of the disclosure.

[0033] FIG. 8C is a perspective view of a light diffusing element for diffusing light generated by a light source (e.g., one more LEDs), for a microbiome monitoring device, according to some embodiments of the disclosure.

[0034] FIG. 9 is an exploded perspective view of a microbiome monitoring device according to some embodiments of the disclosure.

[0035] FIGS. 10A-10C are cross-sectional side views of a housing of a microbiome monitoring device showing, inter aha, a cartridge assembly disposed therein, according to some embodiments of the disclosure.

[0036] FIG. 11 shows the rotation mechanism of a microbiome monitoring device, according to some embodiments of the disclosure.

[0037] FIG. 12 shows a cross-sectional side / perspective view of, inter alia, a heating element coupled to the cartridge of a microbiome monitoring device, according to some embodiments of the disclosure.

[0038] FIG. 13 shows a bottom, perspective view of a gear system of a cartridge of a microbiome monitoring device, according to some embodiments of the disclosure.

[0039] FIGS. 14A show a bottom perspective view of an actuation mechanism to rotate a cartridge of a microbiome monitoring apparatus, according to some embodiments of the disclosure.

[0040] FIG. 15A is an image of a cartridge of a microbiome monitoring apparatus, according to some embodiments of the disclosure.

[0041] FIG. 15B is an image illustrating a plurality of spreading elements covered in dye prior to a sample spreading process, according to some embodiments of the disclosure.

[0042] FIG. 15C is an image of the cartridge of FIGs. 15A-B after a sample spreading process, according to some embodiments of the disclosure.

[0043] FIGS. 16A-16B show views of a heating element(s) configured to be coupled to a cartridge of a microbiome monitoring apparatus, according to some embodiments of the disclosure.

[0044] FIGS. 17A-17B show an inner volume of a housing of a microbiome monitoring apparatus configured to hold electronics according to some embodiments of the disclosure.

[0045] FIG. 18 is a side, cross-section view of an imaging device of a microbiome monitoring device for imaging of the growth media, according to some embodiments of the disclosure.

[0046] FIG. 19A is an image of a cartridge / sample dish for a microbiome monitoring apparatus (w / o lighting) provided to a cartridge, according to some embodiments of the disclosure.

[0047] FIG. 19B is an image of a cartridge / sample dish for a microbiome monitoring apparatus (w / lighting) provided to a cartridge for improved contrast, according to some embodiments of the disclosure.

[0048] FIGS. 20A-20B show perspective views of a cartridge / sample dish divider for a cartridge for a microbiome monitoring apparatus, according to some embodiments of the disclosure.

[0049] FIGS. 20C-20D are images of a cartridge / sample dish configured to hold a plurality of different growth mediums thereon, for a cartridge for a microbiome monitoring apparatus, according to some embodiments of the disclosure.

[0050] FIG. 21 is a flow chart of an example method of operation of a microbiome monitoring apparatus, according to some embodiments of the disclosure.

[0051] FIG. 22 is a flow diagram of a software-implemented method for communicating with a cartridge-bearing microbiome monitoring apparatus and causing display, via GUI, of a graphic feature representing a health score, according to some embodiments of the disclosure.

[0052] FIGS. 23A-23B are exemplary wireframe diagrams of GUIs in a mobile software application for operating a microbiome monitoring apparatus, according to some embodiments of the disclosure.Detailed DescriptionMicrobiome Monitoring Device

[0053] In some embodiments, the microbiome monitoring device may be configured to receive a biological sample (hereinafter, “sample”) from a user (e.g., a human sample such as a fecal sample, collection from tissue paper, sample swabbed from perinium, and the like, or an environmental sample or animal sample). The device may be configured to automatically spread the sample across a growth medium disposed in a cartridge (e.g., a disposable cartridge). The microbiome monitoring device may be configured to heat the cartridge and sample thereon such that microorganisms (e.g., bacteria and / or yeast) in the sample multiply to a level sufficient for detection. In some embodiments, the microbiome monitoring device may be configured to capture images of the incubated sample (and / or capture images of the sample before and / or during incubation). The microbiome monitoring device may include a light source configured to apply light to the cartridge and the sample thereon during image capture. In some embodiments, the microbiome monitoring device may be configured to analyze the image data of the sample (e.g., using imaging processing algorithms) to detect and / or identify one or more bacteria and / or yeast in the sample. Alternatively or additionally, the microbiome monitoring device may send the image data to an external device (e.g., a user device, an external computer, a server, a database, etc., which may be remote and communicating through a computer network), and the external device(s) may be configured to analyze the image data of the sample to detect and / or identify one or more microorganisms (e.g., bacteria and / or yeast) in the sample. In some embodiments, the microbiome monitoring device and / or the external device(s), may be configured to display results to the user (e.g., within 24 hours or less). In some embodiments, a microbiome monitoring system can be configured to execute one or more algorithms (e.g., machine learning algorithms) trained on datasets and / or personalized datasets to enable accurate and scalable analysis of microbial compositions while comparing results against genomic, phenotypic, and taxonomic standards. Combining these systems allows simultaneous bacterial and viral profiling, unprecedented speed, and portability — all without requiring extensive reagents or laboratory infrastructure.

[0054] FIG. 1A is a block diagram of a microbiome monitoring device 100 (hereinafter, “the device 100”), according to some embodiments of the disclosure. In some embodiments, the device 100 may be configured to receive a biological sample, spread the biological sample, heat (e.g.,incubate) the biological sample, and image the biological sample. In some embodiments, the device may be configured to analyze the image data of the biological sample and produce diagnostics of the biological sample. In some embodiments, the device 100 may be configured to perform at least one of spreading the sample, heating the sample, imaging the sample, and analyzing the sample without user intervention (e.g., automatically). In some embodiments, the device 100 may be configured to communicate data collected to an external device(s) 180 to present results (and / or analyze results) to a user regarding the biological sample.

[0055] The device 100 may include a housing 150 defining an inner volume configured to at least partially house or receive an imaging device 140 (e.g., camera such as a red-green-blue (RGB) camera, complementary metal-oxide semiconductor (CMOS) camera, charge-coupled device (CCD) camera, etc.), a light source 142 (e.g., light emitting diode(s) (LED), ultraviolet (UV) light, etc.), a cartridge 112, an actuation mechanism 130, and electronics 160. In some embodiments, the cartridge 112 may be configured to hold a sample dish (which may be a removable and / or disposable) for holding the growth medium and sample accordingly instead of directly by the cartridge. The camera may include between 2 and 48 megapixels and may include a pixel size of between 1 micro to 10 micros (for example). The housing may be manufactured from any durable material that can be formed by plastic injection molding, 3D printing, and the like (for example). Such materials can include, for example, aUV-stable Polycarbonate (PC) and Acrylonitrile styrene acrylate (ASA), as well as ABS or PP. Note, some materials can also be made of metal as well.

[0056] The cartridge / sample dish may include a growth medium (e.g., a solid and / or semi-solid growth medium) thereon configured to receive a biological sample on a surface thereof. In some embodiments, the cartridge 112 may not hold a sample dish, and the growth medium may be disposed directly in the cartridge 112. In some embodiments, the sample dish may be the cartridge which holds the growth medium for receiving a sample on the surface thereof. The growth medium may include agar and nutrient required for growth of microorganisms (e.g., bacteria and / or yeast), including, without limitation carbon, glucose, dextrose, salts, amino acids, peptone, meat extract, and / or yeast extract and combinations thereof. Exemplary growth medium may comprise, without limitation, nutrient broth / agar, tryptose soy broth / agar, brain heart infusion broth / agar, Sabouraud dextrose broth / agar, enriched broth / agar, selenite broth / agar, or gram-negative broth / agar. In some embodiments, the growth medium may include chromogenic agar.

[0057] In some embodiments, the housing 150 can include a portion configured to receive the cartridge 112. For example, the housing 150 can define an opening (e.g., slot, chamber, cavity, shelf, etc.) configured to receive the cartridge 112 in a specific configuration. The cartridge 112 may be removably disposed in the portion of the housing 150 such that a surface of the cartridge 112 configured to receive the sample thereon faces towards the imaging device 140. The portion of the housing 150 may hold or position the cartridge 112 such that at least a portion of the cartridge 112 is in a field of view of the imaging device 140. In some embodiments, the cartridge 112 may be removably disposed in the portion of the housing 150 at a predetermined angle (e.g., a non-zero angle) from horizontal. In some embodiments, the cartridge 112 may be configured to be disposed in a cartridge holder 120, and the cartridge holder 120 may be disposed (e.g., slidably disposed) in the portion of the housing 150. In some embodiments, the opening of the housing 150 may be angled such that the cartridge 112 (and the cartridge holder 120) when disposed in the opening is held at the predetermined angle, as described in further detail in FIGS. 2A-2B. In some embodiments, the cartridge 112 may be disposable such that a new cartridge is used for each sample. In some embodiments, a portion of the cartridge 112 may be reusable (as well as a sample dish held therein, in some embodiments). In some embodiments, the cartridge holder 120 may be reusable and configured to receive a disposable cartridge 112 with each use.

[0058] In some embodiments, the cartridge holder 120 may include a stationary portion (e.g., a frame) configured to remain stationary relative to the housing 150 during a sample spreading process and a rotating portion configured to rotate relative to the stationary portion and the housing 150 during the sample spreading process. In some embodiments, when the cartridge holder 120 and the cartridge 112 are disposed in the housing 150, the rotating portion of the cartridge holder 120 may be configured to engage with the actuation mechanism 130. For example, the rotating portion of the cartridge holder 120 may include one or more gears (e.g., a gear mechanism on a bottom surface thereof) configured to engage with a motor and / or one or more gears of the actuation mechanism 130. Once engaged, the actuation mechanism 130 can be activated to cause the rotating portion of the cartridge holder 120 to rotate. In some embodiments, the cartridge 112 may be configured to be disposed in the rotating portion of the cartridge holder 120 such that cartridge 112 is rotated with the rotating portion of the cartridge holder 120. In some embodiments, the stationary portion of the cartridge holder 120 may at least partially enclose or encompass the rotating portion or act as a frame to stabilize the rotating portion as the rotating portion rotates. Insome embodiments, the actuation mechanism 130 may be configured to engage directly to the cartridge 112 to rotate the cartridge 112. For example, the stationary portion of the cartridge 112 may define an opening on a bottom side thereof through which the cartridge 112 and the actuation mechanism 130 can be coupled to one another. In some embodiments, the motor allows for a continuous 360-degree rotation of the rotating portion of the cartridge; in some embodiments, the motor can be controlled to provide less than 360-degree rotation intermittently, in some embodiments, controlled back and forth rotation of 360-degree rotation, and / or 180 degrees or less rotation, and in some embodiments, intermittent rotation of 180 degrees or less.

[0059] In some embodiments, the actuation mechanism 130 may include at least one of a gear mechanism (which can include one or more gears), a motor (e.g., a rotary motor), a hand crank, an electromagnetic actuator, or a combination thereof. In some embodiments, the actuation mechanism 130 may include a motor configured to rotate the rotating portion of the cartridge holder 120 and / or the cartridge 112 via a gear mechanism (or via direct connection to a shaft of the motor - e.g., which can be at the center, periphery, or anywhere in between, of the cartridge). In some embodiments, the actuation mechanism 130 may be configured to be controlled by the electronics 160, and / or powered by the electronics 160. In some embodiments, the electronics 160 may include a controller (which can be referred to as a processor, a master-control-unit or MCU, such terms and acronyms being used interchangeably throughout the disclosure) configured to control a starting / stopping of the actuation mechanism 130, a velocity (e.g., an angular velocity), and / or an acceleration of the actuation mechanism 130. In some embodiments, the actuation mechanism may optionally be actuated by a user (e.g., hand crank mechanism with gears). In some embodiments, the electronics can include a plurality of processors, and in some embodiments, such processors can be designated to control and / or power one and / or another specific structure, e.g., the actuation mechanism, the imaging device, etc., can each have an independent or share a separate processor, and in some embodiments, such separate processors can be controlled by an MCU.

[0060] In some embodiments, the motor is a DC motor inside a typical 360-degree micro servo (such as the SG90 360 or FS90R), which can provide an RPM ranging from 0 to 130 RPM (rotations per minute). Such a motor can also include: - an operating voltage of 4.8V to 6.0V, a maximum RPM at 6V of about 130 RPM, a maximum RMP at 4.8V of 100 RPM, a stall torque at 6V of 1.5kg / m, and a stall torque at 4.8V of 1.3 kg / m.

[0061] In some embodiments, when not providing continuous rotation, standard SG90 corresponds to a positional servo (0-180°). In some embodiments, if modified for continuous rotation, the DC motor can spin constantly, although torque is impacted (lower). Accordingly, in some embodiments, approximate angular Velocity is 500° / s (at 4.8V) to 600% (at 6.0V), and RPM ~8.3-10 RPM (based on 60° in 0.1 s-0.12s). In some embodiments, angular rotation range is 0° to 180° (which may be limited by internal potentiometer and mechanical stops).

[0062] In some embodiments, the cartridge holder 120 may include or be coupled to the heating element 122. Therefore, when the cartridge holder 120 and the cartridge 112 are disposed in the housing 150, the heating element can apply heat to (e.g., incubate) the cartridge 112, and therefore the growth medium and sample thereon. In some embodiments, the heating element 122 may be configured to supply heat to the cartridge 112 within a predetermined temperature range and / or for a predetermined period of time to cause sufficient growth of microorganisms (e.g., bacteria and / or yeast) in the sample for detection and / or identification, as described in further detail below. In some embodiments, the heating element 122 may be configured to supply heat to the cartridge 112 such that the cartridge 112 is at of a temperature of about 20°C to about 42°C, about 25°C to about 41°C, about 35°C to about 40°C, or about 36°C to about 38°C or any range therebetween. In some embodiments, the cartridge 112 is at a temperature of about 20°C to about 42°C, about 25°C to about 41°C, about 35°C to about 40°C, or about 36°C to about 38°C for a period of between about 1 hour and about 96 hours, about 5 hours and about 72 hours, about 12 hours and about 48 hours, about 15 hours and about 36 hours, or about 20 hours and about 24 hours or any range therebetween. In some embodiments, the device 100 may be configured to monitor the temperature of the heating element 122 and / or the cartridge 112 via, for example, a temperature sensor / thermistor and / or the like, the output of which may be used by the MCU or other processor to adjust the temperature of the heating element 122 to maintain the temperature within the predetermined range.

[0063] In some embodiments, the imaging device 140 may be configured to capture imaging data of the cartridge 112 (and / or sample dish) during and / or after the cartridge 112 is rotated (e.g., the sample has been spread across the cartridge 112) and / or heated by the heating element 122. In some embodiments, the imaging device 140 may be configured to capture imaging data after the cartridge 112 has been incubated for a predefined period of time. In some embodiments, the imaging device 140 may be configured to capture images at any time either before the samplebeing provided, after the sample has been provided, during incubation, and after incubation. In some embodiments the field of view of the imaging device can be configured to be between about 5 mm and about 500 mm, inclusive of all ranges and subranges therebetween. In some embodiments, the imaging device 140 may be configured to capture images having a radius between about 30 mm and about 100 mm, inclusive of all ranges and subranges therebetween. In some embodiments, the imaging device 140 may capture images having a radius of about 90 mm, and in some embodiments, about 60 mm. In some embodiments, a size of the cartridge 112 and a radius captured by the imaging device 140 may correspond to one another.

[0064] In some embodiments, the light source 142 may be configured to provide light to illuminate at least a surface of the growth medium and / or at least a portion of the cartridge and / or sample dish (and therefore the sample thereon) to change a contrast, signal -to-nose ratio, and / or resolution of the image data collected by the imaging device 140. In some embodiments, the light source 142 may provide illumination from underneath, and / or around the cartridge 112, upon the light source being on a periphery of cover 452 (see below), onto, for example, a bottom surface of the cartridge 112. In some embodiments, the light source 142 (or a separate light sterilization light source) may be configured to sterilize the device 100 (e.g., via ultraviolet light, via sample runs). In some embodiments, the light source 142 may be configured to indicate to a user a state of the device 100. For example, the light source 142 may light up (including, for example, a series of pulses) to indicate at least one of a stage of the monitoring process, a completion of one or more steps of the monitoring process (e.g., completion of spreading, heating, and / or imaging), and / or a successful connection to an external device (e.g., wireless connection to the external device 180).

[0065] In some embodiments, the electronics 160 may be coupled to the imaging device 140, the light source 142, the heating element 122, and / or the actuation mechanism 130. As noted above, the electronics 160 may include at least one controller or processor (see above, such terms can be used interchangeably) configured to control the heating element 122, the actuation mechanism 130, the imaging device 140, and the light source 142. The controller can be configured to control the actuation mechanism 130 to rotate the cartridge 112 according to one or more parameters (e.g., velocity, time period, acceleration, direction, etc.). The controller may be configured to activate the heating element 122 (e.g., after the cartridge 112 has been rotated and / or after the sample has been sufficiently spread) to heat the cartridge 112. The controller may be configured tosimultaneously activate the light source 142 to illuminate the sample and the imaging device 140 to image the sample.

[0066] The controller may include any suitable processing device(s) configured to run and / or execute a set of instructions or code. For example, the controller or processor can be and / or can include one or more data processors, image processors, graphics processing units (GPU), physics processing units, digital signal processors (DSP), analog signal processors, mixed-signal processors, machine learning processors, compression processors (e.g., data compression to reduce data rate and / or memory requirements), encryption processors (e.g., for secure wireless data and / or power transfer), and / or the like. The controller or processor can be, for example, a general-purpose processor, central processing unit (CPU), microprocessor, microcontroller, Field Programmable Gate Array (FPGA), an Application Specific Integrated Circuit (ASIC), a processor board, a virtual processor, and / or the like. The controller or processor can be configured to run and / or execute or implement software application processes and / or other modules, processes and / or functions related to the function of the imaging device 140, the light source 142, the heating element 122, and / or the actuation mechanism 130. The underlying device technologies may be provided in a variety of component types, for example, metal-oxide semiconductor field-effect transistor (MOSFET) technologies like complementary metal-oxide semiconductor (CMOS), bipolar technologies like generative adversarial network (GAN), polymer technologies (e.g., silicon-conjugated polymer and metal-conjugated polymer-metal structures), mixed analog and digital, and / or the like.

[0067] The electronics 160 can include a communication device and / or interface configured to communicate signals between the device 100 and the external device(s) 180 and / or between the controller (or in some embodiments, between other processors if included) and imaging device 140, the light source 142, the heating element 122, and / or the actuation mechanism 130. The communication interface can be any suitable device(s) and / or interface(s) that can communicate with the imaging device 140 and a network (e.g., a local area network (LAN), a wide area network (WAN), or the cloud) and / or an external device(s) (e.g., a cell phone, tablet, a laptop, or a desktop computer, etc.). Moreover, the communication interface can include one or more wired and / or wireless interfaces, such as, for example, Ethernet interfaces, optical carrier (OC) interfaces, and / or asynchronous transfer mode (ATM) interfaces. In some embodiments, the communication interface can be, for example, a network interface card and / or the like that can include at least an Ethernet port and / or a wireless radio (e.g., a WI-FI® radio, a BLUETOOTH® radio, cellular suchas 3G, 4G, 5G, etc., 802.1 IX Zigbee, etc.). In some embodiments, the communication interface can include one or more satellite, WI-FI, BLUETOOTH, or cellular antenna. In some embodiments, the communication interface can be communicably coupled to an external device(s) (e.g., an external processor) that includes one or more satellite, WI-FI, BLUETOOTH, or cellular antenna, or a power source such as a battery. In some embodiments, the communication interface can be a near-field communication (NFC) device such that information can be exchanged with nearby electronics. In some embodiments, the communication interface can be BLUETOOTH low energy (BLE) audio. In some embodiments, the communication interface may be configured to communicate information to and / or receive information from an external device including, for example, a cell phone, tablet, laptop, desktop computer, etc. In some embodiments, the communication interface may be configured to communicate information to and / or receive information from an additional external device including, for example, an ingestible smart pill with sensors collected data directly from the gastrointestinal tract. In some embodiments, one or more UBS ports (any size) may be provided for use in at least one of supply power, data communication, and the like, and can be arranged on along a portion of the housing of the devices and apparatus disclosed herein.

[0068] In some embodiments, the communication interface can be configured to receive image data from the imaging device 140 and to communicate those signals to the external device(s) 180, e.g., for further processing and / or analysis or presentation to a user. In some embodiments, the communication interface may also be configured to communicate signals to the imaging device 140 or other components of the device 100. The system (e.g., the device 100 and / or the external device 180) may be configured to analyze the image data of the sample (e.g., using imaging processing algorithms) to detect and / or identify one or more microorganisms (e.g., bacteria and / or yeast) in the sample. The microbiome monitoring system may be configured to detect specific microbes including, but not limited to, pathogens such as Salmonella, Campylobacter, Listeria monocytogenes, Staphylococcus aureus (e.g, methicillin resistant S. aureus), Coliforms and E. coli, as well as non-pathogens.

[0069] The electronics 160 can be configured to power the imaging device 140, the light source 142, the heating element 122, and / or the actuation mechanism 130, via, for example, a battery or external power. The device 100 may be battery-powered and / or powered wirelessly. In some embodiments, the device 100 may include a power cord extending therefrom and configured toreceive power from a wall plug. In some embodiments, the device 100 may optionally include one or more speakers configured to output sounds to the user. For example, the speakers may output sounds indicating a connection to Bluetooth, notifications, a progress of the analysis, etc. In some embodiments, the housing 150 may include one or more supports or legs. In some embodiments, the speakers may be disposed in the supports or legs of the housing 150.

[0070] In some embodiments, the cartridge 112 may be provided to the user such that the user disposes a biological sample on the growth medium (e.g., via an application such as a syringe, a pipette, an eye dropper, a swab, or the like). The user may dispose the spreading element(s) on the surface of the growth medium and / or around the periphery of the growth medium before disposing the cartridge 112 into the cartridge holder 120. In some embodiments, the spreading element(s) may be pre-positioned around the periphery. In some embodiments, the user may be provided with a kit to be used with the device 100 to analyze a respective sample. The kit can be a cartridge kit may include a cartridge, and preferably a plurality of cartridges (e.g., any of the cartridges described herein) with growth medium therein, a spreading element (and preferably a plurality of spreading elements for one or more uses), and an applicator (and preferably a plurality of applicators). In some embodiments, the kit may include a covering (e.g., a cover, a film, a casing, a protector, etc.) configured to protect a surface of the growth medium prior to use. In some embodiments, the user may be provided with dilution elements (or kit) configured for diluting the sample prior to disposing the cartridge 112 in the housing 150. In some embodiments, the user may be provided with one or another of the kits identified about. An exemplary dilution kit comprises a suitable swab(s) to collect the sample(s), a vial(s) of a dilution medium (e.g., sterile buffer or water, and the like), and a syringe(s), pipette(s) and / or eye dropper(s) to apply the diluted sample to the growth medium. In some embodiments, a cartridge kit and a dilution kit may be provided together (as earlier indicated). In some embodiments, the cartridge kit and the dilution kit may be provided separately. In some embodiments, the user may be provided with a plurality of cartridge kits such that the user can analyze a plurality of samples to track a microbiome over time (e.g., gut, oral, vaginal, skin, and the like).

[0071] FIG. IB is a block diagram of a cartridge assembly 210 of a microbiome monitoring device (hereinafter, “the device”), according to some embodiments of the disclosure. In some embodiments, the cartridge assembly 210 includes a cartridge 212 configured to be coupled to or at least partially disposed in a cartridge holder 220. In some embodiments, the cartridge 212 mayinclude a growth medium 214 (e.g., a solid or semi-solid growth medium) disposed therein. For example, the cartridge 212 may have an indented central portion configured to receive the growth medium 214. Alternatively, the cartridge 212 may be configured to hold a sample dish which includes the growth medium 214 thereon. For example, the sample dish may be disposed in the central portion of the cartridge 212. The growth medium 214 may be configured to receive a biological sample thereon. In some embodiments, the cartridge 212 (and / or the sample dish) may be configured to receive a plurality of different types growth media 214 therein. For example, the cartridge 212 (and / or sample dish) may be divided into one or more sections, each section configured to receive a respective type of growth medium 214. In some embodiments, the cartridge 212 (and / or sample dish) may be configured to receive a divider including a plurality of sections such that a different growth medium 214 can be placed in each section from the plurality of sections. In some embodiments, the divider may be removed before being provided to the user. Including multiple types of growth media 214 in a cartridge can maximize a number or type of microorganisms (e.g., bacteria and / or yeast) that can be detected within a single sample run.

[0072] In some embodiments, the growth medium 214 may be configured to receive one or more spreading elements 216 on a surface thereof configured to spread the biological sample during an automated spreading process. The spreading element(s) 216 may include an element configured to roll or slide across the growth medium 214 to spread the sample across the surface of the growth medium 214. In some embodiments, the spreading element(s) 216 may include any suitable structure configured to spread material across the growth medium 214 such as, for example, a bead, a ball, sphere, cylindrical element, a pill-shaped element, rod, etc. The spreading element(s) 216 may include any suitable material such as, for example, glass, plastic, metal, or a suitable combination thereof. In some embodiments, the spreading element(s) 216 may include a diameter between about 0.1 mm to about 10 mm, inclusive of all ranges and subranges therebetween. In some embodiments, the spreading element(s) 216 may include a diameter between about 1 mm to about 5 mm, inclusive of all ranges and subranges therebetween. In some embodiments, the spreading element(s) 216 may have a diameter between about 2 mm and about 4 mm, inclusive of all ranges and subranges therebetween. In some embodiments, the spreading elements) 216 may have a diameter of about 3 mm.

[0073] In some embodiments, the cartridge 212 may be configured to rotate when the cartridge 212 is disposed in the housing. In some embodiments, when the cartridge holder 220 including thecartridge 212 is disposed in the housing, the cartridge holder 220 (or the cartridge 212) may be configured to engage with an actuation mechanism disposed in the housing. In some embodiments, the cartridge holder 220 may include a gear system 224 configured to engage with the actuation mechanism. For example, a rotating portion of the cartridge holder 220 (e.g., similar to the rotating portion of cartridge holder 120) may include one or more gears disposed on a bottom side thereof. The cartridge holder 220 may include a number of gears between 1 gear and 4 gears, inclusive of all ranges and subranges therebetween. In some embodiments, the cartridge holder 220 may include a pair of gears. The actuation mechanism may include a motor or the like, and in some embodiments, a shaft of the motor may be directly coupled to the cartridge without use of any gears. As such, when the motor and / or gear(s) of the actuation mechanism are actuated, the motor and / or gear(s) of the actuation mechanism may rotate the rotating portion of the cartridge holder 220 and the cartridge 212 disposed therein.

[0074] Rotation of the cartridge 212 may cause the spreading element(s) 216 to move over the surface of the growth medium 214. In some embodiments, one or more parameters of the rotation such as a speed (or angular velocity), acceleration, and / or direction of rotation may impact a path of the spreading element(s) 216 across the growth medium 214. In some embodiments, the cartridge 212 may rotate at a predetermined constant speed for a predetermined duration of time (e.g., less than one minute). For example, the cartridge 212 may start from 0 to 100% the maximum speed and back to 0 after the predetermined duration of time. In some embodiments, the speed may be variable over the predetermined duration of time (e.g., from 0 to 30% maximum speed and back down to 25% maximum speed and so on). In some embodiments, the speed may change (e.g., stepwise) monotonically. In some embodiments, the speed may change (e.g., stepwise) non-monotonically. In some embodiments, the cartridge 212 may be configured (e.g., the controller may cause the cartridge) to abruptly change speed of the cartridge 212 (e.g., stepwise, with high acceleration) for a predetermined duration of time (e.g., in the range of 10 seconds to 30 seconds, in a range of under a minute, etc.). In some embodiments, the cartridge 212 may rotate at a speed in a range between 1 and 50 rotations per minute (RPM), and in some embodiments, between 50 RPM and 300 RPM, inclusive of all ranges and subranges therebetween. In some embodiments, the speed may be in a range of about 110 RPM to about 130 RPM, inclusive of all ranges and subranges therebetween. In some embodiments, the cartridge may may have a stall torque in a range between about 1.3 kg / cm and about 1.5 kg / cm, inclusive of all ranges and subrangestherebetween. In some embodiments, the cartridge 212 may rotate with a continuous 360-degree rotation. In some embodiments, the cartridge 212 may rotate with a combination of clockwise and counterclockwise rotation.

[0075] In some embodiments, the controller may store a plurality of rotation protocols. In some embodiments, the rotation protocols may be “fail-safes” for one another. For example, if a first rotation protocol is not causing the spreading elements to sufficiently spread the sample (e.g., due to non-ideal environments of the cartridge when the user receive the kit), a second rotation protocol may be initiated.

[0076] In some embodiments, one or more parameters of the rotation of the cartridge 212 may be in a predetermined range to cause a path of the spreading element(s) that results in substantially uniform spreading of the sample across the growth medium 214. In some embodiments, the rotation of the cartridge 212 may cause the spreading element(s) 216 to spread the sample sufficiently uniformly or evenly across the surface of the growth medium. In some embodiments, the cartridge 212 may have a circular shape such as when the cartridge 212 is rotated, the spreading element(s) 216 evenly spread the sample across the surface of the growth medium 214. In some embodiments, the spreading element(s) 216 may follow a linear path as the cartridge 212 spins. In some embodiments, the spreading element(s) 216 may follow a circular or spiral path as the cartridge 212 spins. In some embodiments, the actuation mechanism may be configured to rotate the cartridge 212 for a predetermined period of time between about 10 seconds to about 5 minutes, inclusive of all ranges and subranges therebetween. In some embodiments, the cartridge 212 may be rotated for less than one minute. In some embodiments, the predetermined period of time for rotating the cartridge 212 may be sufficient to evenly spread the sample over at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or substantially all of the surface of the growth medium 214.

[0077] While the cartridge 212 is described as configured to rotate, it should be appreciated that the cartridge 212 and actuation mechanism may be configured for any suitable motion to cause the spreading element(s) 216 to spread the sample. For example, the actuation mechanism may be configured to vibrate the cartridge 212, move the cartridge 212 linearly (e.g., back and forth in various directions), shake the cartridge 212, cause random motion of the cartridge 212, or any suitable motion to cause the spreading element(s) 216 to spread the sample.

[0078] In some embodiments, once the spreading element 216 reaches a peak point along the rotation (e.g., a high-point within a circular path the spreading element 216 follows), the spreading element 216 may roll from the peak point, through the sample, towards the bottom of the cartridge 212. This process may be repeated with each revolution of the cartridge 212 to spread the sample across the growth medium 214. In some embodiments, a plurality of spreading elements(s) 216 may follow a similar path to spread the sample more efficiently.

[0079] In some embodiments, the cartridge holder 220 may include a heating element 222. In some embodiments, the heating element 222 may include a heating plate (or, for example, any DC powered heating device) coupled to a bottom of the cartridge holder 220. In some embodiments, the heating element 222 may be configured to radiate heat from a surface thereof facing the cartridge 212. In some embodiments, when the cartridge 212 is disposed in the cartridge holder 220, a bottom surface of the cartridge 212 may be disposed near a top surface of the heating element 222, the heating element 222 configured to radiate heat toward the growth medium in the cartridge 212. In some embodiments, the heating element 222 may have dimensions corresponding to the cartridge 212 such that the heating element 222 provides heat substantially uniformly across the growth medium 214 in the cartridge 212. In some embodiments, the heating element 222 may be positioned such that the cartridge 212 and the heating element 222 have a center point along the same axis. In some embodiments, a single axis may extend through a center point of the cartridge 212, the heating element 222, and optionally at least one gear from the gear system 224 and / or motor shaft. In some embodiments, the heating element 222 may have a diameter smaller than a diameter of the cartridge 212 such that the heating element 222 occupies less space in the housing. In some embodiments, the heating element 222 may heat a portion of the cartridge 212. In some embodiments, the heating element 222 may heat the cartridge 212 while the cartridge 212 rotates.

[0080] FIG. 1C is a schematic diagram of at least a portion of electronics of a microbiome monitoring device, according to some embodiments of the disclosure. In this figure, electronics 160 can include a camera module 226, which is associated with a designated processor 229 (here shown as a Raspberry Pi Zero 2), light elements 227 (e.g., LEDs), an MCU 228 (shown here as a ESP32 with BLE and Wi-Fi) which is shown in communication with or otherwise connected to motor 230, LED(s) (e.g., light elements 227), heater 234 and / or temperature sensor 236 (indicated as a thermistor for example). The acronym “CSI” corresponds to common-system-interface,“UART” to universal-asynchronous-receiver-transceiver, “GPIO” to general-purpose input / output, and “ADC” to analog-to-digital converter and provide such functionality between the noted elements of FIG. 1C.

[0081] It is worth noting that while FIGS. 1A-C show components connected, powered and / or in communication, such connections can be any of parallel, serial, or a combination to be functionally connected, powered and / or in communication.

[0082] FIG. 2A shows a predefined angle a at which the cartridge assembly 310 is configured to be disposed in a housing of a microbiome monitoring device, according to some embodiments of the disclosure. The predetermined angle a may be in a range between about 5 degrees to about 60 degrees, inclusive of all ranges and subranges therebetween. In some embodiments, the predetermined angle a may be in a range between about 45 degrees to about 50 degrees, inclusive of all ranges and subranges therebetween. An axis Z may extend perpendicular to the cartridge through a center point of the cartridge assembly 310. In some embodiments, the cartridge may be configured to rotate about the axis Z. FIG. 2B shows a schematic diagram of the cartridge assembly 310 at the predetermined angle a. The cartridge assembly 310 includes a cartridge holder 320 including a heating element 322 and a gear system (not shown; note, the gear system can be one more gears, a hand crank, and / or a motor and motor shaft). The cartridge holder 320 can be configured to hold a cartridge 312 therein (can also hold a sample dish, although in some embodiments, the cartridge 312 can be the sample dish containing the growth medium and sample). The cartridge 312 may define a portion including a growth medium 314 disposed therein. A spreading element 316 (or a plurality of spreading elements 316) may be configured to spread a biological sample across a top surface of the growth medium 314. The gear system 324 may be configured to cause rotation of at least a portion of the cartridge holder 320 and the cartridge 312 disposed therein.

[0083] As shown, the cartridge assembly 310 is positioned at the predetermined angle a such that the top surface of the growth medium 314 aligns with a field of view FOV of an imaging device 340. Therefore, once the sample is spread across the top surface of the growth medium 314, and the heating element 322 can provide heat to the cartridge 312 for a period of time sufficient to allow microorganisms to grow, the imaging device 340 can capture image data of the top surface of the growth medium 314. In some embodiments, the predetermined angle of the cartridgeassembly 310 may clear the field of view FOV of the imaging device 340 (e.g., the one or more spreading elements can be cleared from the growth medium, or at least from a majority of the growth medium). As shown, the predetermined angle of the cartridge assembly 310 may cause the spreading element 316 to move (e.g., fall, roll, slide, etc.) out of the field of view after the sample has been sufficiently spread and / or before the imaging device 340 captures image data of the growth medium 314. Therefore, the spreading element 316 may be moved out of the field of view FOV of the imaging device 340 such that the spreading element 316 does not obstruct a view of the sample. In some embodiments, the predetermined angle can also prevent condensation from building up on the top surface of the growth medium 314. For example, the predetermined angle of the cartridge 312 may be such a gravitational force causes condensation to move down the surface of the growth medium 314 towards a bottom edge of the cartridge 312 and out of the field of view FOV of the imaging device 340. In some embodiments, gradual changes in temperature (e.g., via the heating element) may also be operable to prevent or reduce condensation build up. In some embodiments where cartridge 310 (which can include either additionally or alternatively, a sample dish which can be disposable) with enclosed spreading elements 316 and including a cap coupled thereto (i.e., not exposed growth medium), condensation can trickle down the cap (instead of the solid or semi-solid growth medium itself). In some embodiments, condensation build up on the imaging device can be reduced or prevented by heat (applied to or from the imaging device), from an anti-fogging agent, and / or from an angle of the imaging device relative to horizontal.

[0084] In some embodiments, the opening of the housing may be configured to receive the cartridge holder 320 in a specific orientation. In some embodiments, the cartridge holder 320 may be configured to receive the cartridge 312 in a specific orientation (e.g., with a top surface of the growth medium 314 facing towards the imaging device 340). In some embodiments, the predetermined angle of the cartridge assembly 310 may enable uniform spreading of the sample by the spreading element 316. Although not shown, a light source may be disposed near the cartridge assembly 310 and configured to supply light to the growth medium 314 to improve an image quality (e.g., image contrast, signal-to-noise ratio, etc.) of the image data captured by the imaging device 340.

[0085] FIGS. 3A shows a left side view, FIG. 3B shows a right side view, FIG. 3C shows a top view, FIG. 3D shows a bottom view, FIG. 3E shows a front perspective view, FIG 3F shows a back perspective view, FIG.3G shows a front view, and FIG. H shows a back view, respectively,of a microbiome monitoring device 400 (hereinafter, “the device 400”), according to some embodiments of the disclosure. In some embodiments, all components of the microbiome monitoring device may be fully contained in the housing 450. As shown, device 400 may include a housing 450. In some embodiments, the device 400 may include a first end portion 450a (e.g., a front end) defining a first volume (e.g., substantially spherical volume) and a second end portion 450b (e.g., a back end) defining a second volume (e.g., substantially spherical volume). In some embodiments, the housing 450 may define an opening between the first volume and the second volume in which the cartridge assembly 410 is configured to be disposed. In some embodiments, the user may only be able to engage or remove the cartridge assembly 410 from the device 400. In some embodiments, the cartridge assembly 410 may include an engagement portion 402 (e.g., a tab, grip, etc.) configured to be engaged by the user to remove the cartridge assembly 410 from the housing 450 and / or to dispose the cartridge assembly 410 into the housing 450. In some embodiments, the first volume may hold an imaging device (not shown). Therefore, the first volume may have dimensions (e.g., a diameter) such that the imaging device can be disposed a predetermined distance from the surface of the growth medium of the cartridge assembly 410. The second volume may be configured to house the actuation mechanism (not shown) and / or the electronics (not shown).

[0086] In some embodiments, the main housing 450 may be configured to be coupled to a first cover 452 (e.g., a cap, lens, a window, etc.) to enclose and / or protect the cartridge (not shown). In some embodiments, the cap 452 may be configured to be opaque to prevent light from entering or exiting the device 400. In some embodiments, the cap 452 may be at least partially transparent to allow the user to see inside the housing 450 (e.g., the cartridge and analysis process) and / or to allow the user to see the changes of light emitted from the light source (e.g., 142 in FIG. 1A) of the device 400. The housing 450 may be configured to be coupled to a second cover 454. The second cover 454 may enclose the electronics disposed in the second volume and protect the electronics from an external environment. In some embodiments, the device 400 may include one or more support members 456 (e.g., feet, legs, etc.) configured to stabilize the device 400, In some embodiment, the support members 456 may extend from the first end portion 450a of the housing 450. In some embodiments, the support members 456 and the second end portion 450b of the housing 450 may be configured to rest on a surface to stabilize the device 400 (e.g., by forming a tripod).

[0087] As shown in FIGS.3B, 3C, 3D, 3G, and 3H, the device 400 may optionally include a hand crank 438 extending from a side thereof. The hand crank 438 may be configured to be actuated by the user to in turn actuate an actuation mechanism inside the housing 450. In some embodiments, the hand crank 438 may be rotated by the user to cause the actuation mechanism to rotate a gear system of the cartridge assembly 410, thereby causing rotation of the cartridge (not shown). As shown in FIG. 3H, the device 400 may include an opening 458 at a second end (e.g., back end) thereof through which one or more cords (e.g., cord to transmit power and / or information).

[0088] FIG.4 is a cross-sectional side view of the device 400, according to some embodiments of the disclosure. The device 400 includes the housing 450 including the first end portion 450a and the second end portion 450b. The cartridge assembly 410 may be configured to be disposed in a central portion of the housing 450 between the first end portion 450a and the second end portion 450b. When the cartridge assembly 410 is disposed in the central portion of the housing 450, the cartridge 412 may align with an opening of the light source 442 and at least partially face towards the imaging device 440. In some embodiments, an axis extending through a center point of the cartridge assembly 410 is disposed at a non-zero angle from the x-axis.

[0089] The first end portion 450a includes the cap 452 configured to cover the first end portion 450a. The cartridge holder 420 includes a stationary portion 423a, 423b disposed around a rotating portion 421. A heating element 422 may be coupled to the stationary portion 423b such that the heating element 422 is positioned under the cartridge 412. The stationary portion 423a, 423b may be configured to secure the cartridge assembly 410 relative to the housing 450, and the rotating portion 421 may be coupled to a gear system (e.g., a 2-gear system) including a first gear 424a and a second gear 424b. The second gear 424b may be coupled to the actuation mechanism including a motor 434 configured to rotate (e.g., automatically) the second gear 424b, which in turn rotates the first gear 424a. The first gear 424a may be fixed relative to the rotating portion 421 of the cartridge holder 420 such that the rotating portion 421 and the cartridge 412 rotate with the first gear 424a.

[0090] In some embodiments, the second end portion 451b of the housing 450 may define an inner volume configured to hold electronics. The second end portion 450b may be coupled to a second cover 454 configured to enclose the electronics. The electronics may be structurally and / orfunctionally similar to the electronics 160, and therefore, the details of the electronics are not described herein with respect to FIG. 4.

[0091] FIG.5A shows the cartridge holder 420 including the cartridge 412 disposed therein. FIG.5B shows how the cartridge assembly 410 including the cartridge holder 420 and the cartridge disposed therein fits into the housing 450.

[0092] FIG. 6 shows a front view of a path of rotation of the cartridge relative to the housing of the device 400, according to some embodiments of the disclosure. The cartridge may rotate counterclockwise. In some embodiments, the cartridge may rotate clockwise and / or may change direction during the spread process. As the cartridge rotates along a first path Me, the spreading element may roll (e.g., linearly) along path Msfrom near a top of the cartridge (e.g., a peak point that is a first height) towards a bottom of the cartridge (e.g., a low point that a second heigh lower than the first height). The spreading element may move into the periphery at the bottom edge of the cartridge. In some embodiments, while the cartridge is rotating, the spreading element may be carried from the low point to the peak point (e.g., toward a top of the housing in which the cartridge is disposed). Once the spreading element reaches the peak point along the rotation the spreading element may roll (e.g., linearly or substantially linearly) along path back towards the low point. This process may be repeated with each revolution of the cartridge. Although shown with a single spreading element, the cartridge may include a plurality of spreading elements configured to roll from the peak point (or set of peak points), through a portion of sample, and towards the bottom of the cartridge until the sample has been spread across the surface.

[0093] FIGS. 7A-7C2 show a cartridge holder 420 of a cartridge assembly 410 configured to be disposed in a housing of a microbiome monitoring device, according to some embodiments of the disclosure. As shown in FIG 7A, the cartridge holder 420 includes a stationary portion 423 (generally the outer periphery / housing thereof) and a rotating portion 421. The rotating portion 421 may be disposed within the stationary portion 423. The rotating portion 421 may define a cavity configured to receive a cartridge (not shown). FIG.7B shows a bottom view of the cartridge assembly 410 with a heating element 422 coupled thereto (left) and the heating element 422 removed (right). The heating element 422 may be fastened to a bottom side of the stationary of the cartridge holder 420 (see FIGS. 7D1-4) such that the heating element 422 can supply heat to the cartridge. The rotating portion 421 may include or be coupled to a first gear 424a. The first gear424a may be configured to engage a second gear 424b. In some embodiments, the second gear 424b may be coupled to a motor 434 (not shown in image). Therefore, when the motor 434 is activated, the motor 434 may cause the second gear 424b to rotate, thereby causing the first gear 424a (and rotating portion 421 coupled thereto) to rotate. In some embodiments, the motor 434 may be positioned to extend upward from the cartridge holder 420, as shown in FIG.7A and 7C1.Alternatively, the motor 434 may be configured to extend below the cartridge holder 420 (see FIGS. 7D1-4). In some embodiments, the motor 434 may not be fixed directly to the cartridge holder 420 and may instead be disposed in the second end portion 450b of the housing (not shown) and configured to rotate a gear system of the cartridge holder 420 via one or more connectors. The cartridge holder 420 may be structurally and / or functionally similar to the cartridge holders 120, 220, and 320, and therefore certain details of the cartridge holder 420 are not described herein with respect to FIGS. 7A-7C2.

[0094] FIGS.7D1-7D4, which show a cartridge holder 420 of a cartridge assembly 410, according to some embodiments of the disclosure, configured to be disposed in a housing of a microbiome monitoring device. As shown, the cartridge holder 420 includes a stationary portion (generally the outer periphery / housing thereof), when inserted into the device housing, and a rotating portion 421, which may be disposed within the stationary portion. Here, the motor 434 is smaller and includes a single gear 425a (in some embodiments, directly mounted on a shaft of the motor), which transmits rotational energy from the motor to a gear 425b The rotating portion 421 may define a cavity configured to receive, inter alia, a cartridge (not shown). The perspective view in FIG. 7D3 illustrates an inner, circumferential ring-structure 429 arranged along the periphery of the rotating portion 421. The structure, which can be referred to at least in some embodiments, as a roulette wheel, which includes a plurality of pockets to capture at least one spreading element (e.g., bead), during rotation of the rotating portion. Specifically, at least a portion of the roulette above the surface of the growth medium, and given the angle of the cartridge holder to the horizontal, the bead is captured by one of the pockets when the bead is located on a lower part of the cartridge, and carried by rotation to near or at the top of the rotation of the cartridge where it falls from the pocket and across the growth medium (and sample contained thereon), resulting in the spreading of sample over the growth medium. In some embodiments, a plurality of spreading elements can speed the spreading of the sample over the surface of the growth medium. FIGs.7D5-7D6 illustrates the rotating portion 421, gears 425a and 425b, and motor 434. FIGs. 7D7-7D8 illustrate rotating portion 421 gears 425a and 425b, as well as a perimeter recess 433 (which can be referred to as an inner-race) which corresponds to a portion of bearing for the rotating portion. The recess 433 is a guide for a plurality of balls (which can be referred to as ball-bearings) for such a bearing; in some embodiments, three or more balls (as shown, in FIG. 7H, six balls can be used given the six areas of the cage). As shown in FIG. 7K, the cartridge holder 420 can include a recess 431 around the inner (which can be referred to as an outer -race of the bearing) which corresponds in location to the recess 433. The bearing also includes a cage 435 with openings 437 for retaining the balls 439 of the bearing in a specific, spaced apart arrangement. Accordingly, the cage 435 in some embodiments is sized so that it captures the plurality of balls in openings 437 and remains in place when assembled onto, for example, the rotating portion 421. In some embodiments, a coating of a lubricant within the recesses and / or on the balls is provided. Accordingly, recesses 431 and 433, cage 435 with openings 437, and balls 439 form the bearing for allowing smooth rotation of the rotating portion with relatively little friction.

[0095] .

[0096] FIGs. 7E-7K illustrate the rotating portion 421 which is configured to house the cartridge / sample dish, according to some embodiments, which can include a background 421a at the center to the growth medium for improved imaging and analysis. Such a background may be a solid structure which does not provide any light transmission, or a background which provides minimal transmission.

[0097] FIGs. 7L-7R illustrate a roulette structure (see above with reference to FIG. 7D3), according to some embodiments. As earlier noted, roulette 429 includes a plurality of pockets 441 which are used to capture a spreading element(s), in some embodiments, a plurality (preferably) of beads 439 (in some embodiments, glass beads). In some embodiments, the roulette 429 can be placed within a cartridge / sample dish (in some embodiments, a cartridge and / or sample dish; in some embodiments, the cartridge can be the sample dish), such that, the growth medium is either below the roulette, or at least a portion of the roulette is placed below the surface of the growth medium. In this way, the spreading element(s) can easily cross the surface of the growth medium during rotation of the rotation portion / cartridge / sample dish. In some embodiments, the height of one or more walls of the pockets is such that it does not greatly interact with the growth medium so as to avoid splitting / cracking the growth medium.

[0098] FIGs. 7P-7S2 correspond to a roulette 429 according to some embodiments. In these embodiments, the roulette 429 can be an integral member of the cartridge (and / or sample dish) such that the growth medium 445a is provided therein (e.g., in area 453), the surface 445b of which may be arranged proximate or immediately adjacent to the edge of each of the plurality of pockets (e.g., see FIG. 7S2). Roulette 429 includes the plurality of pockets 441 for receiving a spreading element(s) 439 (e.g., a bead). As shown in FIG. 7S1, each pocket 441 may be sized and shaped to capture enough of a spreading element(s) 439 so as to retain it from a bottom of the cartridge (when receiving the spreading element) to carry it a sufficient rotational distance to arrive and be expelled from a pocket at or near the top / peak of rotation. Upon existing, the spreading element / bead rolls across the surface 445b of the grown medium 445a so as to spread any sample previously provided on the surface 445b. Accordingly, in such a design of at least a plurality of the pockets (either all the pockets or a subset thereof), angles 447 and 449 are arranged to allow easy ingress and egress of a spreading element, as well as allowing for the sufficient rotational distance. To this end, in some embodiments, such angles may be between 5 degrees and 45 degrees, and all ranges therebetween. In some embodiments, such angled walls may not be provided, and / or may be provided with at least corner radii to allow the spreading element to enter and released from a pocket . FIG. 7R is a cross-section of roulette 429 taken via B-B of FIG. 7Q.

[0099] FIG. 8A a cross-sectional side view of a microbiome monitoring device 500 (hereinafter, “the device 500”) including an imaging device 540, a cartridge holder 520, electronics 560, motor 522, according to some embodiments of the disclosure. The device 500 includes the housing 550 including the first end portion 550a and the second end portion 550b. The cartridge assembly 510 may be configured to be disposed in a central portion of the housing 550 between the first end portion 550a and the second end portion 550b.

[0100] The cartridge holder 520 includes a stationary portion 523a, 523b disposed around a rotating portion 521. A heating element 522 may be coupled to the stationary portion 523b such that the heating element 522 is positioned under the cartridge. The stationary portion 523a, 523b may be configured to secure the cartridge assembly 510 relative to the housing 550, and the rotating portion 521 may be coupled to a gear system (e.g., a 2-gear system) including a first gear 524a and a second gear 524b. The second gear 524b may be coupled to the actuation mechanism including a motor (not shown). The first gear 524 may be fixed relative to the rotating portion 521 of the cartridge holder 520 such that the rotating portion 521 and the cartridge 512 rotate with thefirst gear 524a. As shown, the imaging device 540 may be coupled to the stationary portion 523a of the cartridge holder 520. The device 500 may be structurally and / or functionally similar to the devices 100, 400 and therefore, the details of the electronics are not described herein with respect to FIG. 8A.

[0101] FIG. 8B is a cross-section of some of the components of the microbiome apparatus, according to some embodiments. As shown, cartridge 420 (which may also be or contain a sample dish housing the growth medium and / or roulette), rotating portion 421, gears 425a and 425b, motor 434, imaging device 840 having wired connection 842 to electronics 160 (in some embodiments, the camera may be wirelessly connected to other components), one more LEDs 844 to provide illumination to the surface of the growth medium, a light diffusing element 846 arranged proximate (in some embodiments) for diffusing the light from the one more LEDs 844 so as to substantially eliminate (and preferably eliminate) reflection of light off the surface of the growth medium, and heating element 844. FIG. 8C is an enlarged perspective image of the light diffusing element 846 having an inner opening 847 for placement / receiving the imaging device, and openings 848 each for receiving a screw to affix the light diffusing element to a structural component and / or the camera (in some embodiments, the light diffusing element may include a snap-fit component in place of the openings which allow for a frictional fit with a corresponding element of the imaging device and / or adjacent structure element of the apparatus. The light-diffusing element can be made of a plastic which is translucent so as to provide diffuse light (i.e., instead of being transparent).

[0102] As noted earlier, as one of skill in the art will appreciate, in some embodiments, the apparatus includes a temperature sensor (e.g., a thermistor) placed adjacent the growth medium (and / or the cartridge) to monitor the temperature of the growth medium. The sensor can provide signals to a processor(s) of the apparatus to help with temperature regulation (i.e., turning of the heating element on or off).

[0103] FIG. 9 is an exploded view of the microbiome monitoring device 600 (hereinafter, “the device 600”), according to some embodiments of the disclosure. As shown, the device includes a housing 650 defining a first end portion configured to couple to a first cap 652 and a second end portion configured to couple to a second cap 654. The cartridge holder 620 may be configured to fit in a central portion 649 of the housing 650. The cartridge holder 620 is configured to hold a cartridge 612. The first end portion of the housing 650 may include an imaging device 640configured to capture image data of the cartridge 612. The device 600 may include a heating element 622 configured to heat the cartridge 612. As shown, the heating element 622 may have a smaller area than the cartridge 612 in order to be space efficient within the housing 650. The cartridge 612 may be coupled to a first gear 624a, and the first gear 624a may be configured to engage a second gear 624b. The first gear 624a and the second gear 624b may be coupled to a first actuation mechanism 634 (e.g., an automatic motor) and / or optionally a second actuation mechanism 635, 638 (e.g., a hand crank 638 and manually driven gear 635). The second end portion of the housing may define an inner volume configured to receive electronics (not shown). The second cap 654 when coupled to the housing 650 may protect the electronics.

[0104] FIG. 10A is a transparent side view of the device 600 with the cartridge holder 620 shown as opaque. The cartridge holder 620 may be configured to slide into an opening defined in the central portion of the device 600 such that the cartridge holder 620 sits at a nonzero angle in the device 600. When the cartridge holder 620 is disposed in the device 600, an engagement portion 602 may extend from a top of the device 600 such that the user can easily actuate (e.g., pull, push, grab) the cartridge holder 620. FIG. 10B is a cross-sectional side view of the device 600 with the rotating portion 621 of the cartridge holder shown as opaque. FIG. 10C shows a transparent view of the device 600 with the cartridge 612 shown as opaque. As shown in FIGS. 10B-10C, the cartridge 612 is configured to sit in the rotating portion 621 of the cartridge holder 620.

[0105] FIG. 11 shows the cartridge relative to the housing and a side view of the actuation mechanism for rotating the cartridge about an axis an axis of rotation (see 601, FIG. 12), according to some embodiments of the disclosure. The cartridge may be configured to rotate about the axis Z while a portion of the cartridge holder 620 is stationary. As shown, the cartridge is coupled to an actuation mechanism 630 including a motor 634.

[0106] The cartridge holder 620 includes a stationary portion disposed around a rotating portion 621. A heating element may be coupled to the stationary portion such that the heating element is positioned under the cartridge. The imaging device 640 may be positioned to capture images of the cartridge assembly 610. The rotating portion 621 may be coupled to a gear system (e.g., a 3-gear system) including a first gear 624a, a second gear 624b, and a third gear 624c. The first gear 624a and the second gear 624b may be coupled to the cartridge holder 620, and the third gear 624c may be included in the actuation mechanism 630 fixed in the housing 650. The actuationmechanism 630 may include a motor 634 configured to rotate the third gear 624c, which in turn causes rotation of the first gear 624a and the second gear 624b. The device 600 may be structurally and / or functionally similar to the devices 100, 400, 500, described and illustrated earlier.

[0107] FIG. 12 shows a cross-sectional view of a heating element 622 disposed below a portion of the cartridge 612. As shown, the cartridge assembly 610 is configured to be disposed in a portion of the housing at a predetermined angle. In some embodiments, the heating element 622 may be positioned relative to the cartridge 612 via a pin holder 627 extending from an inner surface of the housing 650 (see circled area 621a). The cartridge holder 620 includes an inner rotating portion 621 configured to receive the cartridge 612. The rotating portion 621 may include the first gear 624a coupled to a bottom surface thereof and may rotate (according to some embodiments) along axis 601. The first gear 624a may be configured to engage the second gear 624b, which in turn engages the third gear 624c. The third gear 624c may be coupled to the actuation mechanism 634 (e.g., a motor) via a connector 636. FIG. 13 shows a bottom view of a cartridge assembly 610 including the first gear 624a affixed to a bottom of a rotating portion 621 and configured to engage the second gear 624b. One or more components of the device 600 may be structurally and / or functionally similar to the devices 100, 400, 500 and therefore certain details of the device 600 are not described herein with respect to FIGS. 12-13.

[0108] FIGS. 14A-14B show an actuation mechanism including a first gear 724 coupled to the cartridge 712 disposed in a cartridge holder 720. The first gear 724 may be configured to engage to a second gear 735 (e.g., non-parallel to the first gear 724). The second gear 735 may be driven by a hand-actuated mechanism 738 (e.g., a hand crank). One or more components of the device 700 may be structurally and / or functionally similar to the devices 100, 400, 500, 600, and therefore certain details of the device 700 are not described herein with respect to FIGS. 14A-14B. The first gear 724, in addition to a bevel gear component, may also include another gear component for engagement with a motor 734 (either directly with a motor shaft of the motor or via another gear 724b).

[0109] FIG. 15A is an image of a cartridge 812 including a growth medium therein. FIG. 15B shows a plurality of spreading elements 816 covered in dye prior to a self-spreading process. FIG.15C shows the cartridge 812 after the self-spreading process with the sample 801 spread sufficiently uniformly across a surface of the growth medium.

[0110] FIGS. 16A shows a heating element 922, according to some embodiments of the disclosure. The heating element 922 may be configured to supply heat to the cartridge, The heating element may include a plurality of openings 923 configured to be fastened to a bottom surface of the cartridge holder to hold the heating element 922 relative to the cartridge. The heating element 922 may have a diameter equivalent to a diameter of the cartridge to evenly heat a growth medium and sample therein. FIG. 16B shows a heating element 1022 configured to supply heat to a portion of a cartridge, according to some embodiments of the disclosure. The heating element 1022 may have a diameter smaller than a diameter of the cartridge such that the heating element 1022 occupies lower space within a housing of a microbiome monitoring device.

[0111] FIGS. 17A-17B show an inner volume 1151 of the housing of a microbiome monitoring device configured to hold electronics, according to some embodiments of the disclosure. As shown, the housing of the microbiome monitoring device may define an opening 1158 to allow one or more cables or connectors to extend from the inner volume 1151 of the housing to outside the housing. The opening 1158 may provide access for power cables and / or to connect the electronics within the housing to one or more external devices.

[0112] FIG. 18 shows an imaging device 1240 disposed in the housing of the microbiome monitoring device for collecting images of the cartridge (and / or sample dish), which includes the growth medium (imaging may only be of the growth medium according to some embodiments), according to some embodiments of the disclosure. In some embodiments, the imaging device 1240 may include a camera such as a RGB camera, CMOS camera, CCD camera, or the like. In some embodiments, the imaging device 1240 may include a plurality of cameras having different parameters and / or configured to capture different image data (e.g., different angles, colors, contrast level, etc.) The imaging device 1240 may be positioned to capture an entirety of the growth medium. In some embodiments, the imaging device 1240 may be angled according to an angle of the cartridge such that the images captured by the imaging device 1240 are not skewed or warped. The imaging device 1240 may be structurally and / or functionally similar to the imaging device 140, and therefore, certain details of the imaging device 1240 are not described herein with respect to FIG. 18. FIG. 19 A shows an image of a cartridge 1312 without lighting directed at the cartridge 1312. FIG. 19B shows an image of a cartridge 1412 after incubation with lighting directed at the cartridge (i.e., lighter background illustrated).

[0113] FIGS. 20A-20C show a cartridge divider 1513, according to embodiments. The cartridge divider 1513 may be configured to be disposed in a portion of the cartridge (e.g., the indented central portion) before growth medium is disposed therein. In some embodiments, the cartridge divider 1513 may be configured to divide the cartridge into one or more sections. As shown, the cartridge divider 1513 may have a plurality of extensions (prongs, arms, dividers, etc.). When the divider 1513 is disposed in the cartridge, the extensions may divide the cartridge into a plurality of sections, each section configured to receive a growth medium (e.g., a different type of growth medium) therein. FIG.20D shows an example of a cartridge including a plurality of sections with at least a subset of the plurality of sections including different types of growth media therein. The cartridge / sample dish can include a plurality of types of growth media may enable detection of a larger range of microorganisms using a single sample.

[0114] FIG.21 is a flow chart diagram of an example method 1700 of operation of a microbiome monitoring device (e.g., any of the microbiome monitoring devices 100, 400, 500, 600 described herein). One of skill in the art will appreciate that, prior to initiating operation of the device, the device is powered (e.g., plugged in or via internal battery if configured as such). While the device, in some embodiments, can be configured to be completely automated (via a start button on the device, not shown), in some embodiments, operation of the device (starting, stopping, processing, etc.) is via a smart device (e.g., smartphone) in communication with the device. In some embodiments, the method 1700 may include receiving a cartridge at a predetermined angle, the cartridge including a growth medium and spreading element(s) disposed therein, at 1702. In some embodiments, the method may include rotating the cartridge at a predetermined speed such that a spreading element disposed on the growth medium spreads the sample across the surface of the growth medium, at 1704. In some embodiments, the spreading element(s) may be configured to roll linearly from a high point in the housing to a low point in the housing with each revolution of the cartridge. In some embodiments, the cartridge may be configured to rotate such that the sample is spread across the surface of the growth medium substantially uniformly or evenly. At 1706, the method may include heating, with a heating element, the cartridge for a period of time to culture one or more microorganisms. In some embodiments, the heating element may heat the cartridge during rotation. In some embodiments, the heating element may heat the cartridge after rotation. In some embodiments, the cartridge may be heated for a period of time and / or within a predetermined temperature range as described herein. In some embodiments the period of timemay depend on the temperature range. In some embodiments, the heating element may be positioned under the cartridge and configured to uniformly heat the growth medium such that the colonies of microorganisms are cultured substantially evenly across the growth medium. In some embodiments, the method may include capturing, with an imaging device, imaging data of the cartridge during or after the period of time for which the heating element heats the cartridge, at 1708. In some embodiments, the method may include capturing, with an imaging device, a plurality of images of the cartridge during or after the period of time for which the heating element heats the cartridge, at 1708. In some embodiments, the method may further include analyzing the imaging data (e.g., on the microbiome monitoring device and / or an external device) to detect and / or identify one or more microorganisms (e.g., bacteria and / or yeast). In some embodiments, the method can include executing an Al and / or machine learning algorithm to determine a microbiome profile for a user. The method may include displaying the results of the analysis to the user. In some embodiments, the results of the analysis may be provided to the user within about 1 hour to about 24 hours of collecting the sample. In some embodiments, the results of the analysis may be provided to the user after 24 hours of collecting the sample, e.g., within 36 hours, within 48 hours, or within 72 hours of collecting the sample.Methods of Using Microbiome Monitoring Devices

[0115] The present disclosure provides methods of characterizing a microbiome. These methods can be rapid, routine, and portable using consumer-facing microbiome monitoring devices described herein.

[0116] In some embodiments, the method of characterizing a microbiome comprises: (i) contacting a sample comprising one or more microorganisms with the cartridge of the microbiome monitoring device of the present disclosure; (ii) spreading the sample on the surface of the solid or semi-solid growth medium disposed in the cartridge using a spreading element; (iii) culturing the sample under conditions sufficient for the one or more microorganisms to grow on the solid or semi-solid growth medium; (iv) capturing at least one image of the cartridge / sample dish (or just the growth medium) using the imaging device; and (v) identifying one or more microorganisms in the at least one image, thereby charactering the microbiome.

[0117] In some embodiments, the sample comprises an environmental sample. Exemplary environmental samples include, without limitation, swabs of environmental surfaces (counters, floors, cabinets) from homes or institutions, environmental water samples, soil samples and the like.

[0118] In some embodiments, the sample comprises a human sample. In some embodiments the human is a juvenile (e.g., an infant, a child or an adolescent). In some embodiments, the human is an adult.

[0119] In some embodiments, the sample comprises an animal sample. Exemplary animals include agricultural animals (horses, sheep, pigs, cows, chickens, turkeys and the like), pets (dogs, cats, gerbils, hamsters, and the like), and research animals (monkeys, rats, mice, and the like).

[0120] The sample collected may be a biological sample. In some embodiments, the biological sample can comprise one or more of stool, cecal samples, saliva, skin, blood, plasma, serum, urine, sputum, mucus, pleural fluid, nipple aspirates, lymph fluid, respiratory fluid, stomach contents, lachrymal fluid, breast milk, menstrual blood, semen or vaginal secretions, or supernatants isolated therefrom. In some embodiments, the biological sample is collected directly from the subject. In some embodiments, the biological sample is collected indirectly by swabbing using an absorbent device such as a cotton swab. In some embodiments, the sample comprises a surface swab (e.g., of skin, hair or nails). In some embodiments, the sample is collected directly or indirectly using an inoculating loop or needle.

[0121] In some embodiments, the sample comprises one or more microorganisms. In some embodiments, the one or more microorganisms comprise bacteria. In some embodiments, the bacteria comprises aerobic bacteria. In some embodiments, the bacteria comprises anaerobic bacteria. In some embodiments, the one or more microorganisms comprise yeast. In some embodiments, the one or more microorganisms comprise viruses. In some embodiments, the one or more microorganisms comprise fungi.

[0122] In some embodiments, the sample comprises a solid, or semi-solid sample. In some embodiments, the solid or semi-solid sample is dissolved or diluted into a suitable volume of a buffer. In some embodiments, the sample comprises a liquid. In some embodiments, the liquid is diluted in a suitable volume of buffer. Suitable volumes for dissolving or diluting a sample will be apparent to persons of ordinary skill in the art. Suitable volumes include volumes wherebyapplication to the growth medium followed by spreading produces colonies of microorganisms that are sufficiently spaced on the surface the growth medium that such colonies can be readily imaged, identified and quantified.

[0123] In some embodiments, the sample has a volume of less than about 0.001 ml, less than about 0.01, less than about 0.1 ml, less than about 0.2 ml, less than about 0.3 ml, less than about 0.4 ml, less than about 0.5 ml, less than about 0.6 ml, less than about 0.7 ml, less than about 0.8 ml, less than about 0.9 ml, less than about 1.0 ml, less than about 1.1 ml, less than about 1.2 ml, less than about 1.3 ml, less than about 1.4 ml, less than about 1.5 ml, less than about 1.6 ml, less than about 1.7 ml, less than about 1.8 ml, less than about 1.9 ml, less than about 2.0 ml, less than about 3 ml, less than about 4 ml, less than about 5 ml, less than about 6 ml, less than about 7 ml, less than about 8 ml, less than about 9 ml, or less than about 10 ml.

[0124] In some embodiments, the biological sample has a volume of at least about 0.001 ml, at least about 0.01 ml, at least about 0.1 ml, at least about 0.2 ml, at least about 0.3 ml, at least about 0.4 ml, at least about 0.5 ml, at least about 0.6 ml, at least about 0.7 ml, at least about 0.8 ml, at least about 0.9 ml, at least about 1.0 ml, at least about 1.1 ml, at least about 1.2 ml, at least about 1.3 ml, at least about 1.4 ml, at least about 1.5 ml, at least about 1.6 ml, at least about 1.7 ml, at least about 1.8 ml, at least about 1.9 ml, at least about 12.0 ml, at least about 3 ml, at least about 4 ml, at least about 5 ml, at least about 6 ml, at least about 7 ml, at least about 8 ml, at least about 9 ml, or at least about 10 ml.

[0125] In some embodiments, the biological sample has a volume between about 0.001 ml and 5 ml, between about 0.01 ml and 4 ml, or between about 0.1 ml and 1 ml.

[0126] In some embodiments, the biological sample is dissolved or diluted in a buffer prior to contacting the sample with the growth medium. In some embodiments, the sample is diluted such that the one or more microorganisms in the sample are sufficiently diluted to produce single colonies on the surface of the solid or semisolid growth medium after culturing. Suitable buffers are known to the person of ordinary skill in the art and can include, without limitation, saline, phosphate buffered saline (PBS), Ringers, phosphate buffer, water and the like.

[0127] In some embodiments, the sample is dissolved or diluted into a volume of less than about 0.5 ml, less than about 0.6 ml, less than about 0.7 ml, less than about 0.8 ml, less than about 0.9 ml, less than about 1.0 ml, less than about 1.1 ml, less than about 1.2 ml, less than about 1.3 ml,less than about 1.4 ml, less than about 1.5 ml, less than about 1.6 ml, less than about 1.7 ml, less than about 1.8 ml, less than about 1.9 ml, less than about 2.0 ml, less than about 3 ml, less than about 4 ml, less than about 5 ml, less than about 6 ml, less than about 7 ml, less than about 8 ml, less than about 9 ml, or less than about 10 ml.

[0128] In some embodiments, the sample is dissolved or diluted into a volume of at least about at least about 0.2 ml, at least about 0.3 ml, at least about 0.4 ml, at least about 0.5 ml, at least about 0.6 ml, at least about 0.7 ml, at least about 0.8 ml, at least about 0.9 ml, at least about 1.0 ml, at least about 1.1 ml, at least about 1.2 ml, at least about 1.3 ml, at least about 1.4 ml, at least about 1.5 ml, at least about 1.6 ml, at least about 1.7 ml, at least about 1.8 ml, at least about 1.9 ml, at least about 2.0 ml, at least about 3 ml, at least about 4 ml, at least about 5 ml, at least about 6 ml, at least about 7 ml, at least about 8 ml, at least about 9 ml, at least about 10 ml, at least about 20 ml, at least about 30 ml, at least about 40 ml or at least about 50 ml.

[0129] In some embodiments, the sample is dissolved or diluted into a volume of between about 0.5 ml and 50 ml, between about 1 ml and 10 ml, between about 5 ml and 25 ml, or between about 10 ml and 20 ml.

[0130] In some embodiments, the biological sample is diluted into about 1 ml, about 2 ml, about 3 ml, about 4 ml, about 5 ml, about 6 ml, about 7 ml, about 8 ml, about 9 ml, or about 10 ml of buffer. In some embodiments, the biological sample is diluted into 1 ml, 2 ml, 3 ml, 4 ml, 5 ml, 6 ml, 7 ml, 8 ml, 9 ml, or 10 ml of buffer. In some embodiments, the biological sample is diluted into 1 ml to 10 ml of buffer, 2 ml to 8 ml, 3 ml to 7 ml, or 4 ml to 6 ml of buffer.

[0131] In some embodiments, about 1 pm, about 5 pm, about 10 pm, about 50 pm, about 100 pm, about 200 pm, about 300 pm, about 400 pm, about 500 pm, about 600 pm, about 700 pm, about 800 pm, about 900 pm, about 1 ml, about 1.25 ml, about 1.5 ml, about 1.75 ml, or about 2 ml of the sample or the diluted sample is contacted with the cartridge (e.g., applied to the surface of the solid or semi-solid growth medium). In some embodiments, 1 pm, 5 pm, 10 pm, 50 pm, 100 pm, 200 pm, 300 pm, 400 pm, 500 pm, 600 pm, 700 pm, 800 pm, 900 pm, 1 ml, 1.25 ml, 1.5 ml, 1.75 ml, or 2 ml of the sample or the diluted sample is contacted with the cartridge. In some embodiments, between 1 pm and 2 ml, 500 pm and 1.75 ml, or 1 ml and 1.5 ml of the diluted biological sample is contracted with the cartridge.

[0132] In some embodiments, the cartridge including a solid or semi-solid growth medium comprises a single type of growth medium suitable for culturing microorganisms. In some embodiments, the cartridge includes a solid or semi-solid growth medium comprises a plurality of different types of growth media suitable for culturing different types of microorganisms (the cartridge may include a sample dish, see above). In some embodiments, the cartridge comprises 1 type of growth media, 2 types of growth media, 3 types of growth media, 4 types of growth media, 5 types of growth media, 6 types of growth media, 7 types of growth media, 8 types of growth media, 9 types of growth media, 10 types of growth media, 11 types of growth media, 12 types of growth media, 13 types of growth media, 14 types of growth media, or 15 or more types of growth media.

[0133] In some embodiments, the solid or semi-solid growth medium comprises agar. In some embodiments the solid or semi-solid growth medium comprises nutrients required for bacterial growth which may include, without limitation carbon, glucose, dextrose, salts, amino acids, peptone, meat extract, and / or yeast extract. Exemplary growth medium may comprise, without limitation, nutrient broth / agar, tryptose soy broth / agar, brain heart infusion broth / agar, Sabouraud dextrose broth / agar, enriched broth / agar, selenite broth / agar, or gram-negative broth / agar.

[0134] In some embodiments, solid or semi-solid growth medium comprises chromogenic agar. In some embodiments, the growth medium may be integrated with analyte-triggered cell-free transcription-translation (TXTL) biosensors (see, e.g., Lee, M.F., Lee, J.A., Biondo, J.R., Lux, J.E., Raig, R.M., Berger, P.N., Bernhards, C.B., Kuhn, D.L., Gupta, M.K. and Lux, M.W., (2023). Cell-Free Protein Expression in Polymer Materials. bioRxiv, pp.2023 -08; Liu, J., Pang, Y., Zhang, S., Cleveland, C., Yin, X., Booth, L., ... & Traverse, G. (2017). Triggerable tough hydrogels for gastric resident dosage forms. Nature communications, 8(1), 124.) and Elgabry, M. (2022). The future of biotechnology crime: are we prepared for it? (Doctoral dissertation, UCL (University College London)).

[0135] An exemplary chromogenic agar includes colorless chromogen molecules composed of a chromophore linked to an enzyme substrate specific to a target organism. If the target organism is present on the agar, the enzyme from in the target organism cleaves the chromogen releasing the chromophore from the substrate. The release of the chromophore results in a specific color change at the site of the target organism. The color change may be used to determine the presence and / orrelative abundance of the target organism by visualizing the number, shape, and size of the colonies. Non limiting examples of commercially available chromogenic agar include CHROMagar™ (Dr. A. Rambach), HardyCHROM™ (Hardy Diagnostics), Brilliance™ (ThermoFisher), Spectra™ (ThermoFisher), Rainbow® Agars (Biolog), CHROMID® Culture Media (bioMerieux), Select™ (Bio-Rad Laboratories), and BBL™ (BD).

[0136] The agars of the present disclosure may be used to identify, without limitation, the presence of Acinetobacter spp., Clostridioides difficile, beta-lactamase producing Enterobacteria, Campylobacter species (including C. ejuni and C. coli), Candida species (including C. albicans, C. tropicalis, C. glabrata, and C. krusei, C. auris, ), Colistin resistant Gram-negative bacteria, Gram-negative bacteria producing Extended Spectrum Beta-Lactamase, carbapenem-resistant Enterobacteria (CRE), Group A and / or Group B Streptococci, Bcc strains (including Burkholderia cepacia, B. cenocepacia and B. multivorans), Methicillin Resistant Staphylococcus aureus (MRSA), Enterobacteriaceae species (including E. cloacae and E. sakazakii), Escherichia coli, Enterococcus, Proteus species including P. mirabilis, Klebsiella species (including K. aerogenes, K. oxytoca, and K. pneumoniae), Serratia, Staphylococcus aureus, Citrobacter species, Staphylococcus saprophyticus, Streptococcus agalactiae, Pseudomonas species including P. aeruginosa, Salmonella species, Staphylococcus species, Enterococcus species including E. faecium and E. faecalis, Serratia species including S. marcescens, Shigella species (including S. sonnei, S. flexneri, S. boydii and S. dysenteriae), Vibro species (including V. cholerae, V. parahaemolyticus and V. vulnificus), Listeria species (including L. monocytogenes and L. ivanovii), Morganella, Providencia species, and Aeromonas species (including A. hydrophila, A.jandaei and A. tructi).

[0137] In some embodiments, the methods of the disclosure identify and / or quantify the abundance of one or more pathogenic organisms, including, but not limited to Salmonella, Campylobacter, Listeria monocytogenes, Staphylococcus aureus (e.g, methicillin resistant S. aureus), Coliforms and E. coli. As a non-limiting example, short bursts (“blooms”) of Escherichia coli in the human gut are known to be an indicator of illness and can be monitored using the methods described herein. See, for example, Han et al., J. Bacteriol. 2023 Dec 15;206(l):e00239-23. doi: 10.1128 / jb.00239-23; the contents of which are incorporated by reference herein in their entirety herein.

[0138] In some embodiments, the one or more microorganisms from the sample are identified in at least one image captured by an imaging device according to the present disclosure. In some embodiments, the one or more microorganisms from the sample are identified in a plurality of images captured by an imaging device according to the present disclosure. In some embodiments, 1 image, 2 images, 3 images, 4 images, 5 images, 6 images, 7 images, 8 images, 9 images, 10 images, 20 images, 30 images, 50 images, 75 images, 100 images, 200 images, 300 images, 500 images, or 1000 or more images are captured by the imaging device according to embodiments of the present disclosure. Without wishing to be bound by theory, it is thought that a plurality of images can be used to determine rate of growth of the one or more microorganisms and thereby aid in the identification or characterization thereof. For example, growth rate can be used to identify typically commensal bacteria that are pathogenic in the subject, or under specific circumstances. In some embodiments, a single image is captured at specified time points, for example, every second, every minute, every 10 minutes, every 20 minutes, every 30 minutes, every hour, every day, or every week. In some embodiments, an imaging device according to the present disclosure captures a series of images sufficient to produce a time lapse video.

[0139] In some embodiments, the one or more microorganisms in the image or plurality of images are identified by characterizing the morphology of their colonies, including size, color, and shape, and / or the growth rate of the colonies on the surface of the solid or semi-solid growth medium after culturing the sample (e.g., by incubating the cartridge) for at least a first period of time. In some embodiments, the one or more microorganisms in the image are identified by quantifying a number of colonies of the one or more microorganisms.

[0140] In some embodiments, the identifying of the one or more microorganisms in the at least one image comprises the use of a computer vision algorithm.

[0141] In some embodiments, the methods comprise culturing the sample (e.g., by incubating the cartridge) for at least a first period of time. In some embodiments, the first period of time comprises at least 30 minutes, at least 1 hour, at least 2 hours, at least 3 hours, at least 4 hours, at least 5 hours, at least 10 hours, at least 12 hours, at least 15 hours, at least 20 hours, at least 24 hours, at least 36 hours, at least 48 hours, at least 72 hours, at least 84 hours, at least 96 hours, at least 108 hours, at least 120 hours, at least 132 hours, at least 144 hours, at least 156 hours, or at least 168 hours.

[0142] In some embodiments, the first period of time comprises about 30 minutes, about 1 hour, about 2 hours, about 3 hours, about 4 hours, about 5 hours, about 10 hours, about 12 hours, about 15 hours, about 20 hours, about 24 hours, about 36 hours, about 48 hours, about 72 hours, about 84 hours, about 96 hours, about 108 hours, about 120 hours, about 132 hours, about 144 hours, about 156 hours, or about 168 hours.

[0143] In some embodiments, the first time period comprises between 1 hour and 168 hours, between 1 hour and 96 hours, between 5 hours and 72 hours, between 12 hours and 48 hours, between 15 hours and 36 hours, or between 20 hours and 24 hours.

[0144] In some embodiments, the first period of time comprises 5 hours. In some embodiments, the first period of time comprises 10 hours. In some embodiments, the first period of time comprises 12 hours. In some embodiments, the first period of time comprises 15 hours. In some embodiments, the first period of time comprises 24 hours. In some embodiments, the first period of time comprises 36 hours. In some embodiments, the first period of time comprises 48 hours. In some embodiments, the first period of time comprises 72 hours. In some embodiments, the first period of time comprises 84 hours. In some embodiments, the first period of time comprises 96 hours. In some embodiments, the first period of time comprises 108 hours. In some embodiments, the first period of time comprises 120 hours. In some embodiments, the first period of time comprises 144 hours. In some embodiments, the first period of time comprises 168 hours.

[0145] In some embodiments, the heating element maintains the cartridge, and the samples disposed on the surface of the solid or semi-solid growth medium, at a temperature of about 20°C, about 25°C, about 30°C, about 35°C, about 36°C, about 37°C, about 38°C, about 39°C, about 40°C, about 41 °C, or about 42°C. In some embodiments, the heating element maintains the cartridge, and the samples disposed on the surface of the solid or semi-solid growth medium, at a temperature of about 20°C, about 25°C, about 30°C, about 35°C, about 6°C, about 37°C, about 38°C, about 39°C, about 40°C, about 41 °C, or 42°C. In some embodiments, the cartridge is maintained at a temperature of between about 20°C to about 42°C, between about 25°C to about 41°C, between about 35°C to about 40°C, or between about 36°C to about 38°C. In some embodiments, the cartridge is maintained at a temperature of 37°C. In some embodiments, the cartridge is maintained at a temperature of 36°C. In some embodiments, the cartridge is maintained at a temperature of 38°C.

[0146] Also provided herein are methods of characterizing changes in the microbiome of a subject comprising (i) contacting a first sample from a subject comprising one or more microorganisms with the cartridge (e.g., the surface of the solid or semi-solid growth medium) according to the present disclosure; (ii) spreading the first sample on the surface of the solid or semi-solid growth medium using a spreading element; (iii) culturing the first sample under conditions sufficient for the one or more microorganisms to grow on the solid or semi-solid growth medium; (iv) capturing at least one image of the cartridge / sample dish (or only the growth medium according to some embodiments) using the imaging device; (v) identifying one or more microorganisms in the at least one image, thereby charactering the microbiome present in the first sample; (vi) repeating steps (i)-(v) at least once with at least a second sample from the subject, thereby characterizing the microbiome present in the second sample; and (vii) comparing the microbiome present in the first sample with the microbiome present in the second sample, thereby characterizing changes in the microbiome of the subject.

[0147] In some embodiments, the collection of the first sample and at least a second are separated by a period of time. In some embodiments, the period of time between the collection of the first sample and the at least second sample is about 12 hours, about 24 hours, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about 2 weeks, about 3 weeks, about 4 weeks, about 6 weeks, about 8 weeks, about 10 weeks, about 12 weeks, about 14 weeks, about 16 weeks, about 18 weeks, about 24 weeks, about 26 weeks, about 28 weeks, about 40 months, or about 52 weeks. In some embodiments, the period of time between the collection of the first sample and the at least second sample is the time between the subject’s bowel movements.

[0148] Many factors may influence the microbiome of a subject including, without limitation, diet, exercise, environmental exposures, and injuries. For example, a subject that is an athlete may experience a change in their microbiome after an injury. Additionally, an infant experiencing an illness or dietary intolerance may experience changes in their microbiome. In some embodiments, the changes in the microbiome are associated with an illness, infection, or injury in the subject. In some embodiments, the changes in the microbiome are associated with recovery from an illness, infection, or injury in a subject. The changes characterized by a method according to the present disclosure may inform lifestyle changes in the subject including, without limitation, dietary changes, activity level changes, or changes in drug regimens.Software / Mobile App

[0149] FIG. 22 is a flow diagram showing a software-implemented method for communicating with a cartridge-bearing apparatus and causing display, via a graphical user interface (GUI), of a graphic feature representing a health score, according to some embodiments of the disclosure. As shown in FIG. 22, the method 1800 (e.g., implemented via a non-transitory, processor-readable medium storing instructions that, when executed by a processor, cause the processor to perform the method) includes causing display, at 1802, via a GUI of a compute device (e.g., a mobile compute device), of a user-selectable object configured to trigger establishment of a wireless connection with an apparatus. The apparatus has a housing, an imaging device disposed in an interior of the housing, a cartridge removably disposed in a portion of the housing (which may include a sample dish which can hold the growth medium), and a heating element configured to supply heat to the cartridge. The method 1800 also includes causing display, at 1804, at a first time, via the GUI and in response to receiving first microbiome data from the apparatus, of a first graphic feature representing a microbiome of a user of the apparatus, the first graphic feature optionally including an arc-shaped health score indicator. The method 1800 also includes causing display, at 1806, causing display, at a second time after the first time, via the GUI and in response to receiving second microbiome data from the apparatus, of a second graphic feature representing the microbiome of the user of the apparatus. The second graphic feature includes a modified version of the arc-shaped health score indicator and a modified version of the array of representations of microorganisms from the plurality of microorganisms. A health score represented by at least one of the first graphic feature or the second graphic feature is generated based on contents of a sample received in the apparatus, the contents of the sample identified using computer vision.

[0150] In some implementations, at least one of the first microbiome data or the second microbiome data includes a representation of at least one microorganism from the plurality of microorganisms.

[0151] In some implementations, the method 1800 also includes causing the processor to cause display, via the GUI, of a third graphic feature that includes a representation of a time-lapse progression associated with the microbiome of the user of the apparatus.

[0152] In some implementations, the representation of the time-lapse progression includes an animation sequence.

[0153] In some implementations, the representation of the time-lapse progression is associated with an overnight period.

[0154] In some implementations, the method 1800 also includes causing display, via the GUI, of a third graphic feature that includes an animation sequence associated with the microbiome of the user of the apparatus, and causing display, via the GUI, of an interactive object that, when interacted with by the user of the apparatus, causes the animation sequence to advance between a start point thereof and an end point thereof.

[0155] In some implementations, the method 1800 also includes causing transmission of a signal to cause illumination of at least one indicator light of the apparatus, to indicate at least one of: powering on the apparatus, powering off the apparatus, connecting the apparatus to Bluetooth®, a beginning of a sample processing procedure, a completion of a sample processing procedure, or a reminder to the user of the apparatus to provide a sample.

[0156] In some implementations, the method 1800 also includes causing transmission of a signal to cause a modification to at least one incubation setting of the apparatus.

[0157] In some implementations, the method 1800 also includes initiating a cartridge reorder in response to at least one of (1) a user interaction with the GUI or (2) receiving a signal from the apparatus indicating that the cartridge should be replaced.

[0158] In some implementations, the method 1800 also includes generating a recommendation for the user based on at least one of the first microbiome data, the second microbiome data, or data received via an application programming interface (API) of a wearable fitness tracker.

[0159] In some implementations, at least one of the first microbiome data or the second microbiome data includes data generated by analyzing a biological sample received by the apparatus.

[0160] In some implementations, the first graphic feature also includes an arc-shaped health score indicator and an array of representations of developmental stages from a plurality of developmental stages.

[0161] In some embodiments, a software application configured to communicate with a cartridgebearing apparatus includes one or more of: a feature (e.g., displayed via a GUI) via which a user can share microbiome data with friends, a feed function, a leaderboard, an identification of gut bacteria that is associated with health, tracking health-related gut bacteria changes in response to nutrition and / or lifestyle changes, a feature that can be used to re-name, or that automatically renames, scientific names of bacteria to user-friendly and easy-to-remember names, and / or a feature via which a user can retrieve / pull up a feed of academic literature (e.g., recent literature) related to bacteria / microbes identified in a microbiome / sample, if the user desires to learn more.

[0162] FIGS.23A-23B are wireframe diagrams of GUIs in a mobile software application (“app”), according to some embodiments of the disclosure. As shown in FIG. 23A, the app can include a variety of GUI pages, including one or more of: a sign-up page, a sign-in page for a user, a home page, an overnight time-lapse animation page, a page showing gamified bacterial information and / or recommendations, a Bluetooth® connectivity page, a page for building a profile, a page showing sampling instructions, a page showing “buddies” (other participants / users who use another instance of the same app and can communicate with the user via the app), and a page showing a microbiome newsfeed. The home page can include an arc-shaped representation of a health score, and a selectable array of developmental stages (e.g., developmental stages of an infant / baby) each having their own associated health score. FIG. 23B shows a progression of health scores across a variety of developmental stages and also showing that the user can transition from the home page to a sampling instructions page. The overnight time-lapse page can include a slider bar that, in response to an interaction (sliding) by a user via the GUI, modifies the uppermost circular region, depicting / representing a variety of bacteria present / detected for that developmental stage.

[0163] In some embodiments, an automated script / software application (e.g., running on a mobile compute device) can include or be configured to perform computer vision to detect contents of a sample positioned in an apparatus of the present disclosure. The software application can link to a lookup table for identification of the sample, and / or calculate a health score (e.g., after / in response to sufficient data being input by a user of the software application and / or apparatus). Alternatively, or in addition, the software application can be configured to generate and present (e.g., via a GUI thereof) suggestions or recommendations to the user based on compiled data, for example with the goal or objective of increasing the health score. The generation and / or display of such suggestionsor recommendations can be implemented, for example, using gamification and / or socialization via the software application. In some embodiments, higher diversity may be considered desirable, and / or a higher content of pathogenic bacteria may be considered undesirable. Alternatively, or in addition, the generation and / or display of such suggestions or recommendations can be based on user-specific (e.g., on an individual, personalized basis) correlations and microbiome profile data for that user, leveraging the benefit of more frequent samples than are typically available using known techniques. As an example use case, the software application and apparatus can be used to track longitudinal profiles of elite athletes throughout a training season, to identify / encapsulate periods of health and of illness, with an objective of predicting when the athletes might get sick, and / or with an objective of predicting, when the athletes are ill, how to bring them to recovery faster, and / or with an objective of understanding why some athletes fall ill more / less than others, etc.ExamplesExample 1: Monitoring Athletic Performance

[0164] A portable microbiome incubator (according to one and / or another of the disclosed embodiments) was used to evaluate gut microbiome for 4-6 weeks for 10 athletes. Each test took less than 10 minutes and was conducted at home. Data collected included device readings (images, temperature logs), and anonymized sample data. The data can be used with additional data regarding training, sleep, mood, menstrual cycle tracking in women, stool frequency and Bristol type, and nutrition and supplement logs to understand how the body responds to load, recovery travel and cycle phase.

[0165] In one individual, across four usable stool samples (one additional sample showed no growth and was treated as a QC event), semi-quantitative chromogenic culture signals were tracked using CHROMagar™ Orientation, ECC, and Candida. These media are designed for presumptive differentiation, and are best interpreted as trend signals rather than confirmatory organism ID.

[0166] The largest shift in culture signature occurred during a travel / processed-food window and adjacent to a no-bowel-movement day, consistent with known rapid diet responsiveness andtransit-time effects on the gut microbial ecosystem. In addition, culture signature variability was observed across late luteal samples. Menstrual phase samples showed a stronger Enterococcus -group signal, while Candida remained negative across samples. This was consistent with known hormone-motility mechanisms (progesterone can reduce GI motility).

[0167] This indicates that one useful sampling regime for female athletes is to monitor the microbiome at various points in the menstrual cycle. For example, sample at both late / follicular / ovulation phases, the late luteal phase and on Day 2 of menses, as well as 48 hours pre-competition may be informative.Example 2: Wellness Center Monitoring

[0168] Trials can be conducted using a portable microbiome incubator (according to one and / or another of the disclosed embodiments) and at-home gut sampling and compared to Nanopore sequencing. Participants provide two stool samples per week. Each sample is loaded onto the portable incubator and run, then capped, labelled, dated and stored under refrigeration. Participants also provide data regarding sleep, nutrition and bowel movements. In parallel, a stool sample is collected for Nanopore sequencing. The trial runs for four weeks.Exemplary Enumerated EmbodimentsEmbodiment 1. A microbiome monitoring apparatus including a housing, a cartridge configured to be removably disposed in a portion of the housing, the cartridge including a growth medium disposed therein configured to receive at least one spreading element on a surface thereof, at least one spreading element configured to spread a sample on the surface of the growth medium, a heating element configured to supply heat to the cartridge to incubate the sample for a period of time; and an imaging device disposed within the housing and configured to capture image data of the sample at the very least after the sample has been incubated for the period of time.Embodiment 2. The apparatus of embodiment 1, where the cartridge configured to be removably disposed in the portion of the housing at a predetermined angle from horizontal, and / or the cartridge comprises or includes a sample dish for containing the growth medium.Embodiment 3. The apparatus of any of embodiments 1 -2, further comprising an actuationmechanism configured to couple with the cartridge when the cartridge is disposed in the housing and configured to rotate the cartridge at a predetermined angular velocity such that the at least one spreading element spreads a sample over the surface of the growth medium.Embodiment 4. The apparatus of any of embodiments 1-2, where the apparatus further includes a light source configured to illuminate the growth medium as the imaging device captures the image data.Embodiment 5. The apparatus of any of embodiments 1-4, where after the sample is spread over the surface of the growth medium, the actuation mechanism is configured to stop rotation of the cartridge such that the at least one spreading element moves to a periphery of the growth medium before the imaging device captures the imaging data so as to move the spreading element out of a field of view of the imaging device.Embodiment 6. The apparatus of any of embodiments 3-5, where the predetermined angle of the cartridge causes at least one of (i) the at least one spreading element to move to a / the periphery of the growth medium before the imaging device captures the imaging data, and (ii) prevention of condensation build up on the growth medium.Embodiment 7. The apparatus of any of embodiments 1-6, further comprising electronics disposed within the housing, the electronics configured to control at least one of the heating element and the actuation mechanism.Embodiment 8. The apparatus of any of embodiments 1-7, where the growth medium is suitable for culturing one or more microorganisms.Embodiment 9. The apparatus of any of embodiments 1-8, where the growth medium comprises chromogenic agar.Embodiment 10. The apparatus of any of embodiments 1-9, where the apparatus is sized and shaped for portability.Embodiment 11. The apparatus of any of embodiments 1-10, where the apparatus is configured to automatically spread, incubate and capture image data of the sample following disposition of the cartridge in the housing.Embodiment 12. The apparatus of any of embodiments 1-11, where the imaging device disposed in an inner volume of the housing.Embodiment 13. The apparatus of any of embodiments 1-12, where the heating element is configured to supply heat to the cartridge for a period of time to incubate the sample.Embodiment 14. The apparatus of any of embodiments 1-13, where the growth medium is configured to receive the at least one spreading element on the surface.Embodiment 15. The apparatus of any of embodiments 1-14, where the at least one spreading element comprises a bead.Embodiment 16. The apparatus of any of embodiments 1-15, further comprising roulette structure including a plurality of pockets spaced along a periphery thereof.Embodiment 17. The apparatus of embodiment 16, where each pocket of the roulette structure is configured to receive a spreading element so as to rotationally receive and carry a / the spreading element(s) from a first portion of the cartridge to a second portion of the cartridge whereby the spreading element(s) exits the pocket so as to cross a / the surface of the growth medium.Embodiment 18. The apparatus of embodiments 16 or 17, where each pocket includes at least one inclined base wall upon which the at least one spreading element is received.Embodiment 19. The apparatus of embodiments 16 or 17, where each pocket includes a pair of inclined base walls upon which the at least one spreading element is received.Embodiment 20. The apparatus of embodiment 19, where a first of the pair of inclined base walls is arranged closer to a central axis of the roulette and is configured to aid in a spreading element existing a pocket when arriving at the second portion of the cartridge.Embodiment 21. The apparatus of embodiments 19 or 20, where a second of the pair of inclined base walls is arranged closer to the periphery of the roulette is configured to aid in receiving a spreading element within a pocket at the first portion of the cartridge.Embodiment 22. The apparatus according to any of embodiments 1-21, where the at least one spreading element comprises a plurality of spreading elements.Embodiment 23. A microbiome monitoring apparatus comprising a cartridge configured to receive a growth medium, where the cartridge is configured to be removably disposed within a housing at a predetermined angle from horizontal, when disposed in the housing, the cartridge engages an actuation mechanism configured to rotate the cartridge such that at least one spreadingelement comprising a bead spreads a biological sample across the surface of the growth medium, and after the sample is spread across the growth medium, the actuation mechanism stops rotation of the cartridge such that the at bead rolls to the periphery of the solid or semi -solid growth medium.Embodiment 24. The apparatus of embodiment 23, where the cartridge is configured to receive one or more beads on the surface of the growth medium.Embodiment 25. The apparatus of any of embodiments 23-24, where the growth medium is suitable for culturing one or more microorganisms.Embodiment 26. The apparatus of any of embodiments 23-24, where the growth medium comprises chromogenic agar.Embodiment 27. The apparatus of embodiments 1 -26, where a / the angular velocity of rotation of a cartridge and / or sample dish having a diameter of between 50 mm and 100 mm and an RPM of between 5 and 300.Embodiment 28. The apparatus of embodiment 27, where the diameter of the sample dish is selected from the group consisting of: between 50-90 mm, 50-80mm, 50-70 mm, 50-60 mm, 50-55mm, and ranges therebetween.Embodiment 29. The apparatus of embodiment 27, where the RPM is selected from the group consisting of: between 5-250 RPM, 5-200 RPM, 5-150 RPM, 5-100 RPM, 5-50 RPM, 5-40 RPM, 5-30 RPM, 5-20 RPM, 5-10 RPM, 5-9 RPM, 8-10 RPM and ranges therebetween.Embodiment 30. The apparatus of embodiments 1-29, where rotation of a / the cartridge and / or a / the sample dish corresponds to a continuous, single direction, 360-degree rotation over a period of time.Embodiment 31. The apparatus of embodiments 1-29, where rotation of a / the cartridge and / or a / the sample dish corresponds to a continuous, two-direction back and forth movement, each directional movement being a single 360-degree rotation, and where the overall two-direction rotation is performed over a period of time.Embodiment 32. The apparatus of embodiments 1-29, where rotation of the cartridge and / or a sample dish corresponds to a continuous, two-direction back and forth movement, each directionalmovement being a single, less than 360-degree rotation, and where the overall two-direction rotation is performed over a period of time.Embodiment 33. The apparatus of embodiments 1-29, where rotation of a / the cartridge and / or a / the sample dish corresponds to a continuous, two-direction back and forth movement, each directional movement being a single, 180 degrees of less rotation, and where the overall two-direction rotation is performed over a period of time.Embodiment 34. The apparatus of embodiments 1-29, where a / the angular velocity of the cartridge and / or a / the sample dish corresponds to between 300 degrees / s and 600 degrees / s, and ranges therebetween.Embodiment 35. A method of characterizing a microbiome including contacting a sample comprising one or more microorganisms with the cartridge of the apparatus according to any one of embodiments 1-26, (ii) spreading the sample on the surface of growth medium contained by the cartridge using a / the at least one spreading element, (iii) culturing the sample under conditions for the one or more microorganisms to grow on the growth medium, (iv) capturing at least one image of the sample using the imaging device, and (v) identifying one or more microorganisms in the at least one image for characterizing the microbiome.Embodiment 36. A method of characterizing a microbiome including (i) supplying a sample comprising one or more microorganisms of a microbiome to a cartridge of a microbiome monitoring apparatus, the apparatus including a housing, the cartridge configured to be removably disposed in a portion of the housing at a predetermined angle from horizontal, the cartridge including a growth medium disposed therein and including a surface for which the sample is disposed thereon and receives at least one spreading element, an actuation mechanism coupled to the cartridge when the cartridge is disposed in the housing and configured to rotate the cartridge at a predetermined angular velocity such that the at least one spreading element spreads the sample over the surface of the growth medium, a heating element for supplying heat to the cartridge to incubate the sample for at least a first period of time, and an imaging device disposed in the housing and configured to capture image data of the cartridge at least one of during and after the sample has incubated for the period of time, the method further including (ii) spreading the sample over the surface of the growth medium using the at least one spreading element, (iii) culturing the sample for the at least first period of time under conditions for the one or more microorganisms togrow on the growth medium, (iv) capturing at least one image of the cartridge using the imaging device after culturing the sample for at least the first period of time, and (v) identifying one or more microorganisms in the at least one image so as to characterize the microbiome.Embodiment 37. The method of embodiment 36, where the sample comprises an environmental sample, a human sample, or an animal sample.Embodiment 38. The method of embodiments 37 or 37, where the one or more microorganisms comprise bacteria.Embodiment 39. The method of embodiment 38, where the bacteria comprise aerobic bacteria.Embodiment 40. The method of any of embodiments 36-39, where the sample comprises one or more of stool, saliva, skin, blood, plasma, serum, urine, sputum, mucus, pleural fluid, nipple aspirates, lymph fluid, respiratory fluid, stomach contents, lachrymal fluid, breast milk, semen or vaginal secretions.Embodiment 41. The method of any one of embodiments 36-40, where the growth medium comprises a single type of growth medium, or a plurality of different types of growth media suitable for culturing different types of microorganisms.Embodiment 42. The method of any one of embodiments 36-41, where the growth medium comprises chromogenic agar.Embodiment 43. The method of any one of embodiments 36-42, where identifying the one or more microorganisms in the at least one image comprises characterizing size, color, shape and / or growth rate of colonies grown on the surface of the growth medium after culturing the biological sample for at least the first period of time.Embodiment 44. The method of any one of embodiments 36-42, where identifying the one or more microorganisms in the at least one image comprises quantifying a number of colonies of the one or more microorganisms.Embodiment 45. The method of any one of embodiments 36-44, where identifying of the one or more microorganisms in the at least one image is via a computer vision algorithm.Embodiment 46. The method of any one of embodiments 36-45, further comprising diluting the sample in a buffer prior to supplying the sample, whereby the one or more microorganisms in thesample are diluted so as to produce single colonies on the surface of the growth medium after culturing.Embodiment 47. A method of characterizing changes in a microbiome of a subject including: (i) supplying a first sample from a subject comprising one or more microorganisms with the cartridge of the apparatus according to any one of embodiments 1 -26, (ii) spreading the first sample over the surface of the growth medium using at least one spreading element, (iii) culturing the first sample under conditions for the one or more microorganisms to grow on the growth medium, (iv) capturing at least one image of the sample using the imaging device, (v) identifying one or more microorganisms in the at least one image so as to characterize the microbiome of the first sample, (vi), repeating steps (i)-(v) at least once with at least a second sample from the subject, so as to characterize the microbiome present in the second sample; and (vii) comparing the microbiome present in the first sample with the microbiome present in the second sample so as to characterize changes in the microbiome of the subject.Embodiment 48. The method of embodiment 47, where collection of the first sample and the second sample are separated by a period of time.Embodiment 49. The method of embodiments 47 or 48, where changes in the microbiome are associated with an illness and / or wellness of the subject.Embodiment 50. The method of any of embodiments 47-49, where changes in the microbiome are associated with recovery from an illness by the subject.Embodiment 51. A non-transitory, processor-readable medium storing instructions that, when executed by a processor, cause the processor to: cause display, via a graphical user interface (GUI) of a computing device, of a user-selectable object configured to trigger establishment of a wireless connection with an apparatus of any of embodiments 1-26, cause display, at a first time, via the GUI and in response to receiving first microbiome data from the apparatus, of a first graphic feature representing a microbiome of a user of the apparatus, the first graphic feature including an arc-shaped health score indicator, and cause display, at a second time after the first time, via the GUI and in response to receiving second microbiome data from the apparatus, of a second graphic feature representing the microbiome of the user of the apparatus, the second graphic feature including a modified version of the arc-shaped health score indicator and a modified version of the array of representations of microorganisms from the plurality of microorganisms, and at leastone of generating a health score represented by at least one of the first graphic feature and the second graphic feature and identifying at least some of the microbiome of the sample via a computer vision algorithm.Embodiment 52. The non-transitory, processor-readable medium of embodiment 51, where at least one of the first microbiome data or the second microbiome data includes a representation of at least one microorganism from the plurality of microorganisms of the microbiome.Embodiment 53. The non-transitory, processor-readable medium of embodiments 51 or 52, further storing instructions to cause the processor to cause display, via the GUI, of a third graphic feature that includes a representation of a time-lapse progression associated with the microbiome of the user of the apparatus.Embodiment 54. The non-transitory, processor-readable medium of embodiment 53, where the representation of the time-lapse progression includes an animation sequence.Embodiment 55. The non-transitory, processor-readable medium of embodiment 54, where the representation of the time-lapse progression is associated with an overnight period.Embodiment 56. The non-transitory, processor-readable medium of embodiments 51 or 52, further storing instructions to cause the processor to: cause display, via the GUI, of a third graphic feature that includes an animation sequence associated with the microbiome of the user of the apparatus, and cause display, via the GUI, of an interactive object that, when interacted with by the user of the apparatus, causes the animation sequence to advance between a start point thereof and an end point thereof.Embodiment 57. The non-transitory, processor-readable medium of any of embodiments 51-56, further storing instructions to cause the processor to transmit a signal to cause illumination of at least one indicator light of the apparatus to indicate at least one of: powering on the apparatus, powering off the apparatus, connecting the apparatus to Bluetooth®, a beginning of a sample processing procedure, a completion of a sample processing procedure, and a reminder to the user of the apparatus to provide a sample.Embodiment 58. The non-transitory, processor-readable medium of any of embodiments 51-57, further storing instructions to cause the processor to transmit a signal to cause a modification to at least one incubation setting of the apparatus.Embodiment 59. The non-transitory, processor-readable medium of any of embodiments 51-58, further storing instructions to cause the processor to initiate a cartridge reorder in response to at least one of (i) a user interaction with the GUI, and (ii) receiving a signal from the apparatus indicating that the cartridge requires replacement.Embodiment 60. The non-transitory, processor-readable medium of any of embodiments 51-59, further storing instructions to cause the processor to generate a recommendation for the user based on at least one of the first microbiome data, the second microbiome data, and data received via an application programming interface (API) of a wearable fitness tracker.Embodiment 61. The non-transitory, processor-readable medium of any of embodiments 51 -60, where at least one of the first microbiome data or the second microbiome data includes at least one of image data, data generated by analyzing a biological sample received by the apparatus, and data generated by analyzing the image data.Embodiment 62. The non-transitory, processor-readable medium of any of embodiments 51-61, where the first graphic feature also includes an arc-shaped health score indicator and an array of representations of developmental stages from a plurality of developmental stages.Definitions & General Considerations

[0169] As used herein, the terms “about” and / or “approximately” when used in conjunction with numerical values and / or ranges generally refer to those numerical values and / or ranges near to a recited numerical value and / or range. In some instances, the terms “about” and “approximately” may mean within ± 10% of the recited value. For example, in some instances, “about 100 [units]” may mean within ± 10% of 100 (e.g., from 90 to 110). The terms “about” and “approximately” may be used interchangeably.

[0170] The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.” The terms “can” and “may” are used interchangeably in the present disclosure, and indicate that the referred to element, component, structure, function, functionality, objective, advantage, operation, step, process, apparatus, system, device, result, or clarification, has the ability to be used, included, or produced, or otherwise stand for the proposition indicated in the statement for which the term isused (or referred to) for a particular embodiment(s). Additionally, “any and all” of certain recited items including a part(s), a structure(s), a function(s) / functionality, a clarification(s) or a step(s) (and the like) corresponds to certain embodiments only including one of such item (and in some embodiments, only such item), certain embodiments including two or more of such items (and in some embodiments, only two or more of such items), certain embodiments including substantially all of the items (and in some embodiments, only substantial number of the items), and certain embodiments including all of such items (and in some embodiment, only all of such embodiments).

[0171] The phrase “and / or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with “and / or” should be construed in the same fashion, i.e., “one or more” of the elements so conjoined.

[0172] Other elements may optionally be present other than the elements specifically identified by the “and / or” clause, whether related or unrelated to those elements specifically identified.

[0173] As used herein in the specification and in the claims, “or” should be understood to have the same meaning as “and / or” as defined above. Thus, as a non-limiting example, a reference to “A and / or B”, when used in conjunction with open ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.

[0174] Moreover, when separating items in a list, “or” or “and / or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of’ or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e., “one or the other but not both”) when preceded by terms of exclusivity, such as “either,” “one of,” “only one of,” or “exactly one of.”

[0175] “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law.

[0176] As used herein in the specification and in the claims, the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, “at least one of A and B” (or, equivalently, “at least one of A or B,” or, equivalently “at least one of A and / or B”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc.

[0177] The terms “device” “apparatus” and “system” can be used interchangeably, and in some cases, a system can include two or devices / apparatuses.

[0178] In the claims, as well as in the specification above, all transitional phrases such as “comprising,” “including,” “carrying,” “having,” “containing,” “involving,” “holding,” “composed of,” and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases “consisting of’ and “consisting essentially of’ shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.

[0179] As used herein, the term “computer vision” or “computer vision algorithm" can be understood to mean a computational algorithm designed to process images and / or video by recognizing specified metrics, for example shapes, colors, and patterns, to capture, encode, and / or interpret information and / or data related the image or video (e.g. object detection, object tracking, object recognition, and / or object localization). Images and / or videos may be preprocessed before being analyzed by the computer vision algorithm. The computer vision algorithm may use statistical inference, artificial intelligence, and / or machine learning to inform analysis of the image and / or video. The computer vision algorithm may be implemented using continual and / orincremental learning using sparse training sets or trained using an annotated training set. The computer vision algorithm may be supervised or unsupervised. The computer vision algorithm may utilize feature-based approaches, Bayesian strategies, deep learning models including convolutional neural networks / deep neural networks or a deep Boltzmann machine. The computer vision algorithm may process images in real time or near real time.

[0180] As used herein, the term “microbiome” can be understood to mean the collection of all microbes / microorganisms (including bacteria, fungi, yeast and viruses) and their genetic material present in or on an organism or in a particular environment. The terms “microbes” and “microorganisms” can be used interchangeably herein. The microbiome may be dynamic and may change over time in response to various environmental factors including, without limitation, diet, exercise, medication (e.g. antibiotics, chemotherapeutics, steroids, antidepressants, statins, laxatives, proton pump inhibitors, immunotherapy, ACE inhibitors, alpha blockers, beta blockers, antihistamines, opioids, oral contraceptives, platelet aggregation inhibitors, and / or vitamins), illness (chronic or acute), infection, injury, amount of sleep, stress, pregnancy, hormonal cycles, environment and environmental exposures and / or weight.

[0181] ‘ ‘Microbiome data,” as used herein, refers to an image or plurality of images, e.g., timelapse or video, collected using the microbiome monitoring devices described herein.

[0182] While various inventive embodiments have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and / or structures for performing the function and / or obtaining the results and / or one or more of the advantages described herein, and each of such variations and / or modifications is deemed to be within the scope of the inventive embodiments described or illustrated herein. More generally, those skilled in the art will readily appreciate that all structure, parameters, dimensions, materials, functionality, and configurations described herein are meant to be an example and that the actual structure, parameters, dimensions, materials, functionality, and configurations will depend upon the specific application or applications for which the inventive teachings is / are used. Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific inventive embodiments described herein. It is therefore to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the claims supported by the present disclosure, and equivalents thereto, inventive embodimentsmay be practiced otherwise than as specifically described and claimed. Inventive embodiments of the present disclosure are also directed to each individual feature, system, article, structure, material, kit, functionality, step, and method described herein. In addition, any combination of two or more such features, systems, articles, structure, materials, kits, functionalities, steps, and methods, if such are not mutually inconsistent, is included within the inventive scope of the present disclosure. Moreover, some embodiments of this disclosure may be distinguishable from the prior art for specifically lacking one or more features / elements / functionality (i.e., claims directed to such embodiments can include negative limitations distinguishing said claim from the prior art).

[0183] Also, as noted, various inventive concepts may be embodied as one or more methods. The acts performed as part of a method may be ordered in any suitable way. Accordingly, embodiments may be constructed in which acts are performed in an order different than illustrated and described, which may include performing some acts simultaneously, even though shown as sequential acts in illustrative embodiments.

[0184] Any and all references to publications or other documents, including but not limited to, patents, patent applications, articles, webpages, books, etc., presented anywhere in the present application, are herein incorporated by reference in their entirety. Moreover, all definitions, as defined and used herein, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and / or ordinary meanings of the defined terms.

Claims

Claims:

1. A microbiome monitoring apparatus comprising:a housing;a cartridge configured to be removably disposed in a portion of the housing, the cartridge including a growth medium disposed therein configured to receive at least one spreading element on a surface thereof;at least one spreading element configured to spread a sample on the surface of the growth medium;a heating element configured to supply heat to the cartridge to incubate the sample for a period of time; andan imaging device disposed within the housing and configured to capture image data of the sample at the very least after the sample has been incubated for the period of time.

2. The apparatus of claim 1, wherein:the cartridge configured to be removably disposed in the portion of the housing at a predetermined angle from horizontal; and / orthe cartridge comprises or includes a sample dish for containing the growth medium.

3. The apparatus of any of claims 1, further comprising an actuation mechanism configured to couple with the cartridge when the cartridge is disposed in the housing and configured to rotate the cartridge at a predetermined angular velocity such that the at least one spreading element spreads a sample over the surface of the growth medium.

4. The apparatus of any of claims 1, wherein the apparatus further includes a light source configured to illuminate the growth medium as the imaging device captures the image data.

5. The apparatus of any of claims 3, wherein after the sample is spread over the surface of the growth medium, the actuation mechanism is configured to stop rotation of the cartridge such that the at least one spreading element moves to a periphery of the growth medium before the imaging device captures the imaging data so as to move the spreading element out of a field of view of the imaging device.

6. The apparatus of any of claims 2, wherein the predetermined angle of the cartridge causes at least one of (i) the at least one spreading element to move to a / the periphery of the growth medium before the imaging device captures the imaging data, and (ii) prevention of condensation build up on the growth medium.

7. The apparatus of any of claim 1, further comprising electronics disposed within the housing, the electronics configured to control at least one of the heating element and a / the actuation mechanism.

8. The apparatus of any of claim 1, wherein the growth medium is suitable for culturing one or more microorganisms.

9. The apparatus of any of claim 1, wherein the growth medium comprises chromogenic agar.

10. The apparatus of any of claim 1, wherein the apparatus is sized and shaped for portability.

11. The apparatus of any of claim 1, wherein the apparatus is configured to automatically spread, incubate and capture image data of the sample following disposition of the cartridge in the housing.

12. The apparatus of any of claim 1, wherein the imaging device disposed in an inner volume of the housing.

13. The apparatus of any of claim 1, wherein the heating element configured to supply heat to the cartridge for a period of time to incubate the sample.

14. The apparatus of any of claim 1, wherein the growth medium is configured to receive the at least one spreading element on the surface.

15. The apparatus of any of claim 1, wherein the at least one spreading element comprises a bead.

16. The apparatus of any of claim 1 , further comprising a roulette structure including a plurality of pockets spaced along a periphery thereof.

17. The apparatus of claim 16, wherein each pocket of the roulette structure is configured to receive a spreading element so as to rotationally receive and carry a / the spreading element(s) from a first portion of the cartridge to a second portion of the cartridge whereby the spreading element(s) exits the pocket so as to cross a / the surface of the growth medium.

18. The apparatus of claim 17, wherein each pocket includes at least one inclined base wall upon which the at least one spreading element is received.

19. The apparatus of claim 17, wherein each pocket includes a pair of inclined base walls upon which the at least one spreading element is received.

20. The apparatus of claim 17, wherein a first of the pair of inclined base walls is arranged closer to a central axis of the roulette and is configured to aid in a spreading element existing a pocket when arriving at the second portion of the cartridge.

21. The apparatus of claim 19, wherein a second of the pair of inclined base walls is arranged closer to the periphery of the roulette is configured to aid in receiving a spreading element within a pocket at the first portion of the cartridge.

22. The apparatus claim 1 , wherein the at least one spreading element comprises a plurality of spreading elements.

23. A microbiome monitoring apparatus comprising a cartridge configured to receive a growth medium, wherein:the cartridge is configured to be removably disposed within a housing at a predetermined angle from horizontal,when disposed in the housing, the cartridge engages an actuation mechanism configured to rotate the cartridge such that at least one spreading element comprising a bead spreads a biological sample across a surface of the growth medium, andafter the sample is spread across the growth medium, the actuation mechanism stops rotation of the cartridge such that the at bead rolls to a periphery of the growth medium.

24. The apparatus of claim 23, wherein the cartridge is configured to receive one or more beads on the surface of the growth medium.

25. The apparatus of claim 23, wherein the growth medium is suitable for culturing one ormore microorganisms.

26. The apparatus of claim 23, wherein the growth medium comprises chromogenic agar.

27. The apparatus of claim 3, wherein the angular velocity corresponds to a cartridge and / or sample dish having a diameter of between 50 mm and 100 mm and an RPM of between 5 and 300.

28. The apparatus of claim 27, wherein the diameter of the sample dish is selected from the group consisting of: between 50-90 mm, 50-80mm, 50-70 mm, 50-60 mm, 50-55mm, and ranges therebetween.

29. The apparatus of claim 27, wherein the RPM is selected from the group consisting of:between 5-250 RPM, 5-200 RPM, 5-150 RPM, 5-100 RPM, 5-50 RPM, 5-40 RPM, 5-30 RPM, 5-20 RPM, 5-10 RPM, 5-9 RPM, 8-10 RPM and ranges therebetween.

30. The apparatus of claim 3, wherein rotation of the cartridge and / or a sample dish corresponds to a continuous, single direction, 360-degree rotation over a period of time.

31. The apparatus of claim 3, wherein rotation of the cartridge and / or a sample dish corresponds to a continuous, two-direction back and forth movement, each directional movement being a single 360-degree rotation, and wherein the overall two-direction rotation is performed over a period of time.

32. The apparatus of claim 3, wherein rotation of the cartridge and / or a sample dishcorresponds to a continuous, two-direction back and forth movement, each directional movement being a single, less than 360-degree rotation, and wherein the overall two- direction rotation is performed over a period of time.

33. The apparatus of claim 3, wherein rotation of the cartridge and / or a sample dish corresponds to a continuous, two-direction back and forth movement, each directional movement being a single, 180 degrees of less rotation, and wherein the overall two- direction rotation is performed over a period of time.

34. The apparatus of claim 3, wherein the angular velocity corresponds to between 300 degrees / s and 600 degrees / s, and ranges therebetween.

35. A method of characterizing a microbiome comprising:(i) contacting a sample comprising one or more microorganisms with the cartridge of the apparatus according to any one of claims 1-34;(ii) spreading the sample on the surface of growth medium contained by the cartridge using a / the at least one spreading element;(iii) culturing the sample under conditions for the one or more microorganisms to grow on the growth medium;(iv) capturing at least one image of the sample using an imaging device; and(v) identifying one or more microorganisms in the at least one image for characterizing the microbiome.

36. A method of characterizing a microbiome comprising:(i) supplying a sample comprising one or more microorganisms of a microbiome to a cartridge of a microbiome monitoring apparatus, the apparatus comprising a housing;the cartridge configured to be removably disposed in a portion of the housing at a predetermined angle from horizontal, the cartridge including a growth medium disposed therein and including a surface for which the sample is disposed thereon and receives at least one spreading element;an actuation mechanism coupled to the cartridge when the cartridge is disposed in the housing and configured to rotate the cartridge at a predetermined angular velocity such that the at least one spreading element spreads the sample over the surface of the growth medium;a heating element for supplying heat to the cartridge to incubate the sample for at least a first period of time; andan imaging device disposed in the housing and configured to capture image data of the cartridge at least one of during and after the sample has incubated for the period of time;(ii) spreading the sample over the surface of the growth medium using the at least one spreading element;(iii) culturing the sample for the at least first period of time under conditions for the one or more microorganisms to grow on the growth medium;(iv) capturing at least one image of the cartridge using the imaging device after culturing the sample for at least the first period of time; and(v) identifying one or more microorganisms in the at least one image so as to characterize the microbiome.

37. The method of claim 36, wherein the sample comprises an environmental sample, a human sample, or an animal sample.

38. The method of claim 36, wherein the one or more microorganisms comprise bacteria.

39. The method of claim 38, wherein the bacteria comprise aerobic bacteria.

40. The method of claim 36, wherein the sample comprises one or more of stool, saliva, skin, blood, plasma, serum, urine, sputum, mucus, pleural fluid, nipple aspirates, lymph fluid, respiratory fluid, stomach contents, lachrymal fluid, breast milk, semen or vaginal secretions.

41. The method of claim 36, wherein the growth medium comprises a single type of growth medium, or a plurality of different types of growth media suitable for culturing different types of microorganisms.

42. The method of claim 36, wherein the growth medium comprises chromogenic agar.

43. The method of claim 36, wherein identifying the one or more microorganisms in the at least one image comprises characterizing size, color, shape and / or growth rate of colonies grown on the surface of the growth medium after culturing a biological sample for at least the first period of time.

44. The method of claim 36, wherein identifying the one or more microorganisms in the at least one image comprises quantifying a number of colonies of the one or more microorganisms.

45. The method of claim 36, wherein identifying of the one or more microorganisms in the at least one image is via a computer vision algorithm.

46. The method of claim 36, further comprising diluting the sample in a buffer prior to supplying the sample, whereby the one or more microorganisms in the sample are diluted so as to produce single colonies on the surface of the growth medium after culturing.

47. A method of characterizing changes in a microbiome of a subject comprising:(i) supplying a first sample from a subject comprising one or more microorganisms with the cartridge of the apparatus according to any one of claims 1-34;(ii) spreading the first sample over the surface of the growth medium using at least one spreading element;(iii) culturing the first sample under conditions for the one or more microorganisms to grow on the growth medium;(iv) capturing at least one image of the sample using an imaging device;(v) identifying one or more microorganisms in the at least one image so as to characterize the microbiome of the first sample;(vi) repeating steps (i)-(v) at least once with at least a second sample from the subject, so as to characterize the microbiome present in the second sample; and(vii) comparing the microbiome present in the first sample with the microbiome present in the second sample so as to characterize changes in the microbiome of the subject.

48. The method of claim 47, wherein collection of the first sample and the second sample are separated by a period of time.

49. The method of claim 47, wherein changes in the microbiome are associated with an illness and / or wellness of the subject.

50. The method of claim 47, wherein changes in the microbiome are associated with recovery from an illness by the subject.

51. A non-transitory, processor -readable medium storing instructions that, when executed by a processor, cause the processor to:cause display, via a graphical user interface (GUI) of a computing device, of a user- selectable object configured to trigger establishment of a wireless connection with an apparatus of any of claims 1-34;cause display, at a first time, via the GUI and in response to receiving first microbiome data from the apparatus, of a first graphic feature representing a microbiome of a user of the apparatus, the first graphic feature including an arc-shaped health score indicator; andcause display, at a second time after the first time, via the GUI and in response to receiving second microbiome data from the apparatus, of a second graphic feature representing the microbiome of the user of the apparatus, the second graphic feature including a modified version of the arc-shaped health score indicator and a modified version of an array of representations of microorganisms from a plurality of microorganisms,andat least one of generating a health score represented by at least one of the first graphic feature and the second graphic feature and identifying at least some of the microbiome of the sample via a computer vision algorithm.

52. The non-transitory, processor-readable medium of claim 51, wherein at least one of the first microbiome data or the second microbiome data includes a representation of at least one microorganism from the plurality of microorganisms of the microbiome.

53. The non-transitory, processor-readable medium of claim 51, further storing instructions to cause the processor to cause display, via the GUI, of a third graphic feature that includes a representation of a time-lapse progression associated with the microbiome of the user of the apparatus.

54. The non-transitory, processor-readable medium of claim 53, wherein the representation of the time-lapse progression includes an animation sequence.

55. The non-transitory, processor-readable medium of claim 54, wherein the representation of the time-lapse progression is associated with an overnight period.

56. The non-transitory, processor-readable medium of claim 51, further storing instructions to cause the processor to:cause display, via the GUI, of a third graphic feature that includes an animation sequence associated with the microbiome of the user of the apparatus, andcause display, via the GUI, of an interactive object that, when interacted with by the user of the apparatus, causes the animation sequence to advance between a start point thereof and an end point thereof.

57. The non-transitory, processor-readable medium of claim 51, further storing instructions to cause the processor to transmit a signal to cause illumination of at least one indicator light of the apparatus to indicate at least one of: powering on the apparatus, powering off the apparatus, connecting the apparatus to Bluetooth®, a beginning of a sample processing procedure, a completion of a sample processing procedure, and a reminder to the user of the apparatus to provide a sample.

58. The non-transitory, processor-readable medium of claim 51, further storing instructions to cause the processor to transmit a signal to cause a modification to at least one incubation setting of the apparatus.

59. The non-transitory, processor-readable medium of claim 51, further storing instructions to cause the processor to initiate a cartridge reorder in response to at least one of (i) a userinteraction with the GUI, and (ii) receiving a signal from the apparatus indicating that the cartridge requires replacement.

60. The non-transitory, processor-readable medium of claim 51, further storing instructions to cause the processor to generate a recommendation for the user based on at least one of the first microbiome data, the second microbiome data, and data received via an application programming interface (API) of a wearable fitness tracker.

61. The non-transitory, processor-readable medium of any of claim 51, wherein at least one of the first microbiome data or the second microbiome data includes at least one of image data, data generated by analyzing a biological sample received by the apparatus, and data generated by analyzing the image data.

62. The non-transitory, processor-readable medium of claim 51, wherein the first graphic feature also includes an arc-shaped health score indicator and an array of representations of developmental stages from a plurality of developmental stages.

63. An apparatus, device or method according to any of the disclosed embodiments.

Images