Probiotic for use in the therapeutic treatment of diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction

Abstract

A new probiotic for use in the therapeutic treatment of diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction, including type 2 diabetes mellitus, obesity, or metabolic syndrome.

Description

[0001] “PROBIOTIC FOR USE IN THE THERAPEUTIC TREATMENT OF DISEASES ASSOCIATED WITH CARBOHYDRATE METABOLISM OR CARBOHYDRATE TRANSPORT DYSFUNCTION”

[0002] FIELD OF THE INVENTION

[0003] Some embodiments described here concern a probiotic for use in the therapeutic treatment of diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction, including type 2 diabetes mellitus, obesity, or metabolic syndrome.

[0004] BACKGROUND OF THE INVENTION

[0005] Metabolism diseases, and in particular diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction, including type 2 diabetes mellitus, obesity and metabolic syndrome, are known to be severe conditions which in turn predispose a subject suffering from them to heart and artery diseases.

[0006] Type 2 diabetes mellitus is a chronic disease characterized by increased blood glucose levels, that is, hyperglycemia, caused by an alteration in the amount or functioning of insulin. Excess circulating glucose can cause various long-term damage to various organs and systems, in particular blood vessels and the nervous system, typically to the eyes, heart, and kidneys. This condition is multifactorial, usually caused by the interaction of incorrect nutrition, sedentary lifestyle, obesity or being overweight, and genetic predisposition.

[0007] Obesity is a real chronic disease in which there is an abnormal and excessive accumulation of adipose tissue, generally due to an imbalance in the supply of energy, as well as genetic predisposition, with serious repercussions on quality of life, linked to the consequent disabilities. This disease is often correlated to others, such as cardiovascular diseases, type 2 diabetes mellitus, diseases of the osteo- articular system, sleep apnea syndrome and certain types of cancer.

[0008] Metabolic syndrome is a set of factors that predispose to the development of cardiovascular diseases and type 2 diabetes mellitus, where some diagnostic criteria include abdominal circumference, blood pressure, triglycerides, HDL- cholesterol, fasting blood glucose.

[0009] The carbohydrate metabolism or carbohydrate transport diseases or dysfunctions mentioned above are generally associated with an incorrect lifestyle. Conversely, following a correct diet and undertaking constant physical activity leads not only to the reduction of body weight but also to the modification of the level of circulating lipids, reduction of blood pressure, prevention of type 2 diabetes mellitus, lower risk of developing cardiovascular diseases and ultimately improvement in the quality of life and increased survival.

[0010] In this context, there is the need to provide a new probiotic that is useful to treat diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction, including type 2 diabetes mellitus, obesity, or metabolic syndrome.

[0011] The Applicant has devised, tested and embodied the present invention to overcome the shortcomings of the state of the art and to obtain this and other purposes and advantages.

[0012] DESCRIPTION OF THE INVENTION

[0013] The present invention is set forth and characterized in the independent claim, while the dependent claims describe other characteristics of the present invention or variants to the main inventive idea.

[0014] In accordance with the above purposes, some embodiments described here concern Fusicatenibacter saccharivorans for use in the therapeutic treatment of a disease associated with carbohydrate metabolism or carbohydrate transport dysfunction. F. saccharivorans is a probiotic.

[0015] Other embodiments described here also concern a composition for oral administration and suitable for human consumption comprising F. saccharivorans for use in the therapeutic treatment of a disease associated with carbohydrate metabolism or carbohydrate transport dysfunction.

[0016] In possible embodiments, the disease is type 2 diabetes mellitus, obesity or metabolic syndrome.

[0017] In one embodiment, F. saccharivorans is for use in the treatment of type 2 diabetes mellitus.

[0018] In another embodiment, F. saccharivorans is for use in the treatment of obesity.

[0019] In yet another embodiment, F. saccharivorans is for use in the treatment of metabolic syndrome.

[0020] In some embodiments, the composition as above can comprise additional probiotics and / or fibers or prebiotics and / or vitamins and / or adjuvants for the health of the bacterial flora. As used here, “probiotic” refers to a substantially pure microbe (that is, a single isolate) or a mixture of microbes, and may also include any additional component that can be administered to a subject (for example, a human) to restore or alter the microbiota or microbiome in the subject. In some embodiments, a probiotic composition can be administered with an agent to allow the microbe(s) to survive in the environment of the gastrointestinal tract, that is, to resist a low pH and / or to grow in the gastrointestinal environment.

[0021] In some possible embodiments, one or more probiotics used in the embodiments described here, which may also include F. saccharivorans, can be tyndallized probiotics.

[0022] In some embodiments, the composition as above can comprise prebiotics, in particular dietary fibers, wherein the dietary fibers comprise insoluble fibers and / or soluble fibers.

[0023] As used in the present document, “prebiotic” refers to an agent that increases the number and / or activity of one or more microbes. Such microbes can include microbes to restore or alter a subject’s microbiota or microbiome. Non-limiting examples of a prebiotic include fibers, fructooligosaccharides (FOS, for example oligofructose, inulin, or an inulin-type fructane), galactooligosaccharides (GOS), an amino acid, or an alcohol.

[0024] In some embodiments, the composition as above can comprise medium chain fatty acids (MCTs).

[0025] In some embodiments, the composition as above can comprise fortifying food ingredients and / or micronutrients, in particular including one or more omega 3s, minerals, trace elements, vitamins or a combination thereof.

[0026] In some embodiments, the composition as above can be in liquid, solid, semisolid, lyophilized or powder form.

[0027] In some embodiments, the composition as above is formulated for oral administration and can be in the form of, or prepared in the form of, a tablet, capsule or lozenge, possibly of the gastro-resistant type, powder or liquid.

[0028] In some embodiments, one or more compositions described here can be supplied as nutritional supplements (also referred to as dietary supplements, food supplements and / or nutraceuticals) and / or medication for treating the above mentioned diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction.

[0029] Fusicatenibacter saccharivorans (Bacteria; Terrabacteria group; Bacillota; Clostridia; Eubacteriales ; Lachnospiraceae; Fusicatenibacter) was first isolated from human faeces in 2013 (Takada, T., Kurakawa, T., Tsuji, H., and Nomoto, K. “Fusicatenibacter saccharivorans gen. nov., sp. nov., isolated from human faeces.” Int. J. Syst. Evol. Microbiol. (2013) 63:3691-3696). The strain of F. saccharivorans referred to conforms to the deposited strain identified as AM67- 22ACA.

[0030] To date, its mediation (increase) of the probiotic activity of other bacterial taxa when administered under IBS conditions has been reported (Shin SY, Park S, Moon JM, Kim K, Kim JW, Chun J, Lee TH, Choi CH; Microbiome Research Group of the Korean Society for Neurogastroenterology and Motility. Compositional Changes in the Gut Microbiota of Responders and Non -responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial. J Neurogastroenterol Motil. 2022 Oct 30;28(4):642-654. doi: 10.5056 / jnm21202. PMID: 36250371; PMCID: PMC9577570).

[0031] The genome of F. saccharivorans has a size of 3,782,803 bases, with a GC content of 46.8%. The annotation, obtained through the use of the RAST Server (https: / / rast.nmpdr.org / ) showed the presence of 3,720 coding sequences. The metabolic detail for the main functions is reported in the following table, in which F. saccharivorans is compared with two probiotic strains (Bifidobacterium animalis subsp. lactis BB-12 and Lactobacillus acidophilus LA-14) with literature associated with the condition of type 2 diabetes mellitus (Tonucci LB, Olbrich Dos Santos KM, Licursi de Oliveira L, Rocha Ribeiro SM, Duarte Martino HS. Clinical application of probiotics in type 2 diabetes mellitus: A randomized, double-blind, placebo-controlled study. Clin Nutr. 2017 Feb;36(l):85-92. doi:

[0032] As it is possible to observe, F. saccharivorans has a very broad gene repertoire with regards to carbohydrate metabolism and, going into more detail, has the ability to metabolize monosaccharides such as fructose, mannose and xylose. Although the last two sugars are also potentially metabolized by the other two bacterial species listed in the table, the ability to metabolize fructose is a peculiar characteristic of F. saccharivorans .

[0033] Also with regard to the oligosaccharides metabolism potential, it is possible to observe how F. saccharivorans has a greater gene variety, being able to metabolize sucrose, maltose and lactose. In detail, the ability to degrade sucrose is present only in the genome of L. acidophilus LA-14, while it is missing in the genome of B. animalis BB-12, showing how individually F. saccharivorans can carry out the potential metabolic action toward different substrates of interest for the control of type 2 diabetes mellitus.

[0034] Comparing F. saccharivorans with the other bacterial strains with proven probiotic activity, it can be observed that the metabolic potential of the former is more varied and focused on the metabolism of monosaccharides and oligosaccharides of interest, for example, for the condition of type 2 diabetes mellitus.

[0035] Additionally, no virulence factor is present within its genome.

[0036] In addition, it shows hypothetical resistance to tetracycline and fluoroquinolones, also shared with the other two bacterial species being compared (and already used as probiotics and with a consolidated history of safety in their use). The aforementioned antibiotic resistances are limited and perfectly comparable to those present in the other probiotic strains analyzed.

[0037] The Applicant used its own bio bank of actual fecal samples from subjects who consented to their use for research purposes (N ~ 26,000).

[0038] Within this collection of samples sequenced using method 16S, F. saccharivorans was detected as a discriminating marker between the conditions “type 2 diabetes mellitus” and “non-diabetes”. In more detail, this indication was obtained by implementing an algorithm based on decision trees (RandomF orest). Following this analysis, it was possible to classify the various bacterial taxa according to their relevance for the discrimination between the “type 2 diabetes mellitus” and the “non-diabetes” phenotypes. The classification categorized F. saccharivorans as one of the most relevant variables in the entire dataset for the classification of the samples, with an average depth of the decision tree significantly smaller than the next block of variables. Once its relevance was identified through the aforementioned approach, the correlation between the relative abundance of F. saccharivorans was verified using classical methods, revealing that the latter is significantly higher in “non-diabetes” subjects (Wilcoxon test P value 2.81 le-7 - fig. 1) and therefore the bacterial species F. saccharivorans is depleted in the samples of “type 2 diabetes mellitus” subjects, also showing a protective association against “type 2 diabetes mellitus” if verified by linear regression (OR 0.92, P value 7.56 e-6).

[0039] This first analysis carried out on our 16S collection highlighted the relevance of F. saccharivorans for the discrimination between the “type 2 diabetes mellitus” and “non-diabetes” phenotypes, highlighting the protective action exerted by the taxon in question.

[0040] The same samples mentioned above were subsequently re-sequenced by the Applicant with shotgun metagenomic methodology. Following taxonomic assignment using the MetaPhlan tool (Blanco-Miguez, A., Beghini, F., Cumbo, F. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 41, 1633-1644 (2023). https: / / doi.org / 10.1038 / s41587-023-01688-w), the same algorithm as previously applied was applied. At the end of the process, F. saccharivorans was again among the main variables identified by the selection process, showing a significantly higher relative abundance in the “non-diabetes” group (Wilcoxon test P value 3.841 e-5) and, therefore, a depletion of F. saccharivorans in the “type 2 diabetes mellitus” samples, confirming the above.

[0041] Some embodiments thus concern methods and uses for the therapeutic treatment of diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction, including type 2 diabetes mellitus, obesity, or metabolic syndrome, which include the administration of F. saccharivorans or a composition comprising F. saccharivorans to a subject.

[0042] Some embodiments described here also concern methods and uses for the therapeutic treatment of diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction, including type 2 diabetes mellitus, obesity, or metabolic syndrome in a subject, which comprise (a) detecting a dysbiosis associated with carbohydrate metabolism or carbohydrate transport dysfunction in a sample from the subject; and (b) administering F. saccharivorans or a composition comprising F. saccharivorans to the subject.

[0043] Any one of the methods and uses described here may also include detecting a dysbiosis associated with carbohydrate metabolism or carbohydrate transport dysfunction in a sample from the subject. In some embodiments, the sample is a fecal sample.

[0044] In some embodiments, detecting the dysbiosis associated with carbohydrate metabolism or carbohydrate transport dysfunction includes determining the potential for bacterial gene expression in the subject’s sample. In some embodiments, detecting the dysbiosis includes determining the bacterial composition in the subject’s sample.

[0045] In some embodiments, detecting the dysbiosis associated with carbohydrate metabolism or carbohydrate transport dysfunction comprises determining that the bacterial species F. saccharivorans is depleted in the subject’s sample.

[0046] The term “dysbiosis” refers to a state of the microbiota or microbiome of the gut or other area of the body (for example, mucosal or skin surfaces or any other niche populated by microorganisms) of a subject (that is, the host) in which the diversity and / or function of the ecological network is disrupted, for example, relative to the state of the microbiota or microbiome of the gut or other areas of the body in a control population. Any alteration whatsoever of the microbiota or microbiome of a subject (that is, the host) relative to the microbiota or microbiome of a control population may be considered a dysbiosis, even if such dysbiosis does not result in a detectable decrease in the subject’s health.

[0047] The term “microbiome” refers to the collection of microorganisms and viruses and / or their genes from a given environment. For example, “microbiome” can refer to the collection of microorganisms and viruses and / or their genes from the gastrointestinal tract of humans. “Microbiota” refers to the microorganisms in a specific environment.

[0048] In some embodiments, it can be provided to administer F. saccharivorans or the composition to the subject one, two, or three times, or even more, per day.

[0049] Any one of the methods and uses described here can also include administering another treatment to the subject, for example, one or more drugs, for the aforementioned diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction.

[0050] In some embodiments, the subject has previously been identified as suffering from one of the aforementioned diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction.

[0051] The Applicant believes that F. saccharivorans and / or metabolic pathways associated therewith could be a potential target for therapeutic treatment of the aforementioned diseases associated with carbohydrate metabolism or carbohydrate transport dysfunction, and / or for purposes of prediction, diagnosis or prognosis of such diseases. Some examples of how F. saccharivorans could be used as a specific therapeutic target for the aforementioned diseases could include:

[0052] - modulation of the microbiome: targeting F. saccharivorans to modulate the composition of the intestinal microbiota in patients with one of the aforementioned diseases could help restore microbial balance and potentially alleviate the symptoms of the disease;

[0053] - probiotic interventions: incorporating probiotics containing strains such as F. saccharivorans into the treatment regimen for patients with one of the aforementioned diseases could offer a targeted approach to disease management;

[0054] - disease modifying effects: by targeting F. saccharivorans it may be possible to modify the progression of the disease. Manipulating the gut microbiota in order to improve the presence of beneficial bacteria such as F. saccharivorans could potentially lead to better outcomes for patients.

[0055] - combination therapies: considering F. saccharivorans as a therapeutic target may open up possibilities for combination therapies involving modulation of the microbiome alongside traditional treatments. This integrated approach could offer a comprehensive management of the disease that includes the related bowel dysbiosis.

[0056] It is clear that modifications and / or additions may be made to the present invention, without thereby departing from the field and scope of protection, as defined by the claims. It is also clear that, although the present invention has been described with reference to some specific examples, a person of skill in the art will be able to achieve other equivalent forms, having the characteristics as set forth in the claims and hence all coming within the field of protection defined thereby.

Claims

CLAIMS1. Fusicatenibacter saccharivorans for use in the therapeutic treatment of a disease associated with carbohydrate metabolism or carbohydrate transport dysfunction, wherein such disease is type 2 diabetes mellitus, obesity, or metabolic syndrome.

2. Fusicatenibacter saccharivorans as in claim 1 for use in the therapeutic treatment of type 2 diabetes mellitus.

3. Composition for oral administration and suitable for human consumption comprising Fusicatenibacter saccharivorans for use in the therapeutic treatment of a disease associated with carbohydrate metabolism or carbohydrate transport dysfunction, wherein said disease is type 2 diabetes mellitus, obesity or metabolic syndrome.

4. Composition as in claim 3 for use in the therapeutic treatment of type 2 diabetes mellitus.

5. Composition for use as in claim 3 or 4, wherein said composition comprises additional probiotics and / or fibers or prebiotics and / or vitamins and / or adjuvants for the health of the bacterial flora.

6. Composition for use as in claim 3, 4 or 5, wherein said composition comprises prebiotics, in particular dietary fibers, wherein said dietary fibers comprise insoluble fibers and / or soluble fibers.

7. Composition for use as in claim 3, 4 or 5, wherein said composition comprises medium chain fatty acids.

8. Composition for use as in any claim from 3 to 7, wherein said composition comprises fortifying and / or micronutrient food ingredients, in particular including one or more omega 3, minerals, trace elements, vitamins or a combination thereof.

9. Composition for use as in any claim from 3 to 8, in liquid, solid, semi-solid, lyophilized or powder form.

10. Composition for use as in any claim from 3 to 9, in the form of, or prepared in the form of, a tablet, capsule or lozenge, possibly of a gastro-resistant type.

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