24 results about "Metagenomics" patented technology

In various aspects and embodiments, the Disclosure provides methods for evaluating subjects for the presence or absence of colorectal neoplasms, such as colorectal cancer (CRC), colorectal adenoma (CRA), and progressive colorectal adenoma (CRAA), by metagenomic and multi-omics analysis of feces or other biological samples. In other aspects, the Disclosure provides methods for generating machine learning models or “signatures” based on metagenomic and multi-omics analysis of feces or other biological samples to evaluate subjects for the presence or absence of colorectal diseases, including but not limited to CRC, CRA, and CRAA.

The invention discloses a high-efficiency PET hydrolase mutant and an application of the high-efficiency PET hydrolase mutant in PET plastic degradation. The PET hydrolase is characterized in that the PET hydrolase is a protein of the following (a) or (b): (a) a protein as shown in SEQ ID NO.1; and (b) a protein which is derived from (a) by substituting, deleting or adding one or more amino acids in the amino acid sequence in (a), has hydrolase activity and is derived from (a). The high-yield PET hydrolase ClbPETase (the expression quantity is 80 mg / L) is excavated from an environmental metagenome through an HMM method, and the high-yield PET hydrolase ClbPETase has great industrial application potential. A plurality of single-point mutants and a series of combined mutants are constructed through a rational design method assisted by machine learning, a mutant UltraPETase with the optimal catalytic performance is obtained through superposition of single-point mutation, complete depolymerization of PET powder can be achieved by reacting for 8 hours at the temperature of 65 DEG C or reacting for 6 hours at the temperature of 60 DEG C. And a novel efficient depolymerization enzyme resource is provided for biological enzyme depolymerization of polyester plastics.

This invention discloses a strain of Aspergillus sp., DLF18, and its applications, belonging to the field of microbial technology, with accession number CGMCC NO.41737. This strain can effectively utilize rice straw and / or sugarcane bagasse to produce humic acid, with a humic acid content of 16.5% per gram of fermentation supernatant after rice straw fermentation. Applying the fermentation product of DLF18 to crops can significantly improve crop growth and increase the humic content in the soil. Simultaneously, metagenomic analysis results show that, compared with the control group, the application of DLF18 to the soil significantly altered species β-diversity, functional gene abundance, and inter-group differences. These findings indicate that DLF18 has broad application prospects in agricultural straw utilization and soil remediation.

The invention relates to the technical field of metagenomics, discloses an automatic analysis method and system for pit mud metagenomic data, and aims at solving the problem that an existing method is poor in efficiency and accuracy, and the scheme mainly comprises the steps that a sequencing data type, a file path and analysis parameters are received; performing quality control on the original offline data; sequence assembly is carried out, and a contigs file is generated; carrying out assembly quality evaluation on the contigs file; carrying out genome binning by using at least two binning tools; integrating output results of the binning tool, and performing optimization based on a preset integrity threshold value and a preset pollution degree threshold value to obtain an optimized binning genome data set; evaluating and optimizing the integrity, the pollution degree and the strain heterogeneity of the binning genome; calculating coverage and relative abundance; performing species classification annotation and function annotation; and integrating the result data of the previous steps to generate an analysis report. According to the method, automatic analysis of metagenome data is realized, and the analysis efficiency and accuracy are improved.

The invention relates to a SrCas13a-3 protein as well as a gene editing system and application thereof. The amino acid sequence of the SrCas13a-3 protein is shown as SEQ ID NO. 1. The invention provides endonuclease SrCas13a-3 identified by utilizing metagenomics in combination with experiments, and the endonuclease SrCas13a-3 is a new member with low CRISPR / Cas13a family homology. The invention also establishes a nucleic acid visual detection technology based on CRISPR / SrCas13a-3 system mediation, and the nucleic acid visual detection technology has a wide application prospect in the field of nucleic acid detection.

This invention discloses a tobacco-derived α-glucan phosphorylase, its mutants, and their applications. Addressing the problems of low catalytic efficiency, poor stability and adaptability, and difficulty in heterologous expression of key enzyme elements in cellulose-to-starch synthesis, this invention utilizes metagenomics and big data analysis of public databases, along with bioinformatics methods, to precisely identify novel key enzyme elements for cellulose degradation and starch synthesis. An α-glucan phosphorylase from tobacco was identified and found to have better enzyme activity and starch synthesis function than the potato-derived PGP. Furthermore, this invention involves a single point mutation of the Cap domain of the α-glucan phosphorylase. The results show that the single point mutant obtained by mutating the tobacco-derived α-glucan phosphorylase with the amino acid sequence shown in SEQ ID No. 1 by the S524H single point mutation has significantly higher enzyme activity and expression level than the wild-type α-glucan phosphorylase.

The present invention is drawn to a novel buffer composition comprising a nuclease quenching agent, a stabilizer, a salt, and a cryoprotectant. The present invention is also drawn to a process of producing the composition of the present invention and its utility. The composition of the present invention supports viability of aerobic and anaerobic microbes for extended periods over significant range of temperatures, without the presence of any significant amount of degradants of the constituents of the samples such as biological macromolecules and DNA. The present invention also relates to an economically viable and wide range applications for storage of biological and environmental samples containing microbes.

The present invention relates to metagenomics methods. The invention also relates to their use in the detection and / or diagnosis of a wide range of infectious diseases, for example, caused by a pathogenic virus, bacterium, fungus or protozoan. The invention also extends to methods for sample preparation and microorganism detection and / or identification, and methods for host cell nucleic acid depletion. The invention further relates to kits and apparatus used in these methods. The invention is especially useful in clinical diagnostic and veterinary medicine.

The application discloses endoglucanases derived from the intestinal flora of Phyllobius oblongus and application thereof. Eight high-activity endoglucanases are obtained from the intestinal flora of Phyllobius oblongus by metagenomics technology, the amino acid sequences of the endoglucanases are respectively shown as SEQ ID NO:1, 3, 5, 7, 9, 11, 13 and 15, and the nucleotide sequences of the encoding genes are respectively shown as SEQ ID NO:2, 4, 6, 8, 10, 12, 14 and 16. The above-mentioned genes are heterologously expressed in Zymomonas mobilis, purified and subjected to enzymatic property determination, and it is confirmed that the endoglucanases have excellent enzymatic activity, and the specific enzyme activity of CSP2705 is as high as 22.1 U / mg. The endoglucanases can be efficiently expressed in Zymomonas mobilis, and provide key enzyme elements for constructing CBP strains with Zymomonas mobilis as a chassis and realizing direct conversion of lignocellulose into fuel ethanol, and have important industrial application value.

The invention discloses a method for identifying a source of soluble inorganic phosphorus in a water body. According to the method for tracing the soluble inorganic phosphorus in the water body by utilizing metagenomics and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) technologies, functional gene information of microbial communities is provided through metagenomics, and the metabolic potential of phosphorus circulation is determined; the FT-ICR-MS reveals a molecular form transformation path of phosphorus and positions a key transformation node, so that'gene-molecule 'two-dimensional analysis is realized, a DIP source is accurately identified, and a scientific basis is provided for water phosphorus pollution prevention and control and ecological system management.

The invention discloses two novel endonuclease Gs12-15 and Gs12-17 of a CRISPR (clustered regularly interspaced short palindromic repeats) / Cas system and an application of the two novel endonuclease Gs12-15 and Specifically, the invention provides two novel guide RNA dependent type endonucleases excavated based on a metagenomics method, and the novel guide RNA dependent type endonucleases have the advantages that the novel guide RNA dependent type endonucleases have the genome editing capability with a wider target site coverage range, the reaction temperature range is wider, and target DNA is cut in a genome in a high-activity and high-specificity manner. Researches find that PAM of Gs12-15 nuclease is preferentially NHHA, and the PAM recognition range of Gs12-17 is NNHV (N is a basic group T / C / G / A, H is a basic group T / C / A, and V is a basic group G / A / C). The invention establishes a nucleic acid visual detection technology based on CRISPR / Gs12-15 and CRISPR / Gs12-17 system mediation, and has a wide application prospect in the fields of genome site-directed modification and nucleic acid detection.

The invention discloses a high-flux real-time fluorescent quantitative PCR (polymerase chain reaction) chip for detecting soil-transmitted pathogenic bacteria and a detection method of the high-flux real-time fluorescent quantitative PCR chip. The chip comprises a primer composition consisting of 64 pairs of primer pairs which are designed for specific genes of 47 species and 7 genera of soil-propagated plant pathogenic fungi, 8 species of soil-propagated plant pathogenic bacteria and two reference genes. On the basis of a high-flux quantitative PCR (HT-qPCR) technology, a novel chip capable of simultaneously detecting 47 species and 7 genera of soil-transmitted plant pathogenic fungi and 8 species of soil-transmitted plant pathogenic bacteria is established, and a powerful tool is provided for evaluating potential risks of soil-transmitted plant pathogens in an environment. The method is applied to pathogenic bacteria spread in soil, the abundance and distribution of the pathogenic bacteria spread in the soil can be detected and analyzed, the defects of low-flux amplification of traditional single-gene qPCR and high cost of metagenomics are overcome, and the method has wide application prospects.

This invention discloses a method for assessing the microbial safety risk of water bodies based on metagenomics and viromics, comprising: metagenomic detection of the relative abundance F of each pathogenic microorganism in the water sample to be assessed. i Where i represents the pathogenic microorganism label; for pathogenic microorganism i, determine its hazard level PM. i Antibiotic resistance gene risk value (ARG) i and virulence factor risk value (VF) i ; Determine the risk coefficient α of increased transmission due to water sample treatment methods, including antibiotic resistance gene risk values ​​and virulence factor risk values; For pathogenic microorganism i, determine the overall hazard level PM i Antibiotic resistance gene risk value (ARG) i Virulence factor risk value (VF) i The risk coefficient α and relative abundance F of increased transmission due to water sample treatment methods i Determine the overall risk value R of pathogenic microorganism i i The comprehensive risk value of all pathogenic microorganisms detected by the metagenomics is used to obtain the microbial safety risk assessment result R of the water sample to be evaluated.

Methods described herein include machine-learning based algorithms identifying and predicting bio-markers associated with microbial-influenced corrosion. Methods may comprise: performing genomic analysis on a genomic material of a collected sample based on metagenomics sequencing to provide sequenced genomic data; clustering the sequenced genomic data to form sequenced genomic clusters; wherein the sequenced genomic clusters represent a predictive function provided by the sequenced genomic data to a trained machine learning (M.L.) predictive algorithm; sorting the sequenced genomic clusters into one or more microbial influenced corrosion-based categories, wherein the one or more microbial influenced corrosion-based categories are based on one or more microbial influenced corrosion-related microorganisms or a compound of the related microorganisms; and characterizing a corrosion biomarker of the one or more microbial influenced corrosion-based categories, wherein the corrosion biomarker is logically linked with an increased likelihood of microbial influenced corrosion based on the predictive function of the sequenced genomic clusters.

The invention provides application of Ackermania muciniphila as a biomarker in preparation of a product for diagnosing and / or treating atherosclerosis, and belongs to the technical field of biological medicines. The invention provides an application of Akkermansia muciniphila (Akkermansia muciniphila) as a biomarker in the preparation of a kit for diagnosing and / or detecting atherosclerosis (AS). The Akkermansia muciniphila can be used for detecting atherosclerosis (AS). A high fat diet induced ApoE gene knockout mouse copies an AS mouse model, metagenomics analysis of a control group and a model group shows that the abundance difference of Ackermania muciniphila is significant, and the AUC value under an ROC curve is 1, which indicates that Ackermania muciniphila is a potential biomarker strain of AS. The Ackermania muciniphila can also significantly reduce the AS plaque area of the aortic sinus of the AS model mouse, and the Ackermania muciniphila can play an anti-AS role through a two-component system, ABC transport and other metabolic pathways.

The invention belongs to the technical field of disease prognosis and molecular biology, and relates to a flora marker for colorectal cancer liver metastasis diagnosis and liver metastasis risk assessment and application of the flora marker. The marker comprises the following three strains: bifidobacterium bifidum, bacteroides fragilis and bacteroides heparinidolyticus. The method comprises the following steps: acquiring information of microorganisms in excrement of a patient through a high-resolution metagenomics detection technology; a random forest algorithm is utilized to construct a colorectal cancer liver metastasis classification model based on the flora markers, the model can distinguish people without colorectal cancer metastasis and people with liver metastasis and accurately predict high-risk patients with colorectal cancer liver metastasis, and the effect of the model is superior to that of a clinical conventional tumor serum marker. The kit has the advantages of noninvasive detection and high accuracy, and can provide a reliable tool for liver metastasis diagnosis and individualized prognosis management of colorectal cancer patients.

The disclosure provides an evaluation of the virome in health and disease of the oral-gut-brain axis, in particular, periodontitis, irritable bowel disease (IBD) and Alzheimer's Disease (AD). For Alzheimer's disease, a striking feature was found via metagenomics of brain autopsy specimens - the presence of parvoviridae (comprised of erythoviruses and erythroparvoviruses) in the brains of individuals diagnosed with Alzheimer's Disease (AD) but not in brains from age-matched healthy individuals without a medical diagnosis of AD. For IBD, For Periodontitis and IBD, an analysis revealed the top 20 most abundant viral and bacterial species in saliva samples from individuals with periodontal disease or with a healthy periodontium and the top viral and bacterial species in stool samples from individuals with irritable bowel syndrome or with gastrointestinal health. Building upon these discoveries, a number of diagnostic methods and materials for AD and IBD are described herein.

The application discloses a Penicillium chrysogenum DLS189 and application thereof, relates to the technical field of microorganisms, and has a preservation number of CGMCC NO.41739. The strain can effectively utilize rice straw and / or sugarcane residue to produce humic acid, and the humic acid content in the fermentation supernatant of the rice straw is 16.84% per gram. The fermentation product of the DLS189 is applied to crops, so that the growth condition of the crops can be significantly improved, and the humic substance content in the soil is improved. Meanwhile, the result of metagenomics analysis shows that, compared with a control group, after the DLS189 is applied to the soil, the species beta diversity is significantly changed, and the functional gene abundance and the difference between groups are significantly changed. The above shows that the DLS189 has a wide application prospect in the utilization of agricultural straw and soil remediation.

This invention discloses a multi-omics joint detection method in the field of microbiology and fermentation technology for Baijiu brewing to analyze regional heterogeneity of high-temperature Daqu (fermentation starter). Taking high-temperature Daqu from different production areas and strata as examples, it integrates physicochemical enzyme activity assays, electronic sensory analysis, volatileomics, microbial amplicon sequencing, metagenomics, and metagenomic assembly technologies to systematically characterize the differences in physicochemical properties, sensory flavors, microbial communities, and metabolic functions of samples. It establishes a correlation model of "phenotype, flavor, microbial community, function, and strain," clarifying the impact of production area and stratum on Daqu quality and elucidating the mechanism of regional heterogeneity formation in high-temperature Daqu. This invention elevates the analytical depth from the genus level to the species and genome level, accurately locating core functional strains. It solves the problems of traditional methods having single detection dimensions, shallow analytical depth, and unclear functional attribution, providing scientific methods and theoretical support for improving the quality of high-temperature Daqu in Maotai-flavor Baijiu and enhancing the flavor of non-core production areas.

The invention relates to the technical field of genomics and metabonomics, in particular to a substance for relieving intestinal injury of crisp tilapia and an application effect analysis method of the substance. According to the invention, the tauroursodeoxycholic acid (TUDCA) is applied to relieving intestinal inflammation damage caused by feed embrittlement of the crisp tilapia for the first time, and intestinal inflammation is relieved. By establishing a three-dimensional evaluation system of'intestinal histomorphology + metabonomics + metagenomics', the relieving effect of TUDCA on intestinal inflammation is systematically quantified. Through combined analysis of intestinal metabolome and metagenome, a'microorganism-host interaction 'health judgment model is constructed, and the maintenance of the quality of fish meat after inflammation is relieved is verified through muscle texture parameters, so that a'repair-evaluation-quality maintenance' closed-loop technical scheme is formed.

The application discloses a method for matching a metagenome queue based on a microbial metabolic background and relates to the technical field of metagenomics.S1: metagenome sequencing data processing; standardizing processing of data from whole metagenomics and manually input meta data;S2: extraction of a main metabolic background of microorganisms;S3: matching of the metabolic background of microorganisms; firstly, a nearest neighbor matching algorithm is used to screen matched samples in a control group without missing any main metabolic components;S4: matching effect checking; balance test is conducted on the mean of covariants of the matched disease group and the control group;S5: difference analysis based on the matched queue; if the data of the matched disease group and the control group meet normal distribution, paired sample t test is conducted for difference analysis, otherwise, group wilcoxon test is used for difference analysis.Through the technical method, a matched queue of case and control samples in microbial research is constructed, and the causal relationship identification capability of metagenomics research is strengthened.

The present application relates to the technical field of metagenomics and data science, and provides a metagenomics binning method and system combined with prior knowledge of a reference library, which comprises: obtaining a target sequence data set, performing feature extraction on each sequence sample in the target sequence data set, and obtaining a binning feature vector set after feature transformation; comparing the target sequence data set with a reference library to obtain a species number estimation value and a confidence degree of each sequence sample belonging to different species, and then obtaining a feasible interval of binning number and a confidence clustering center of each species, and taking the same as prior knowledge; for each feasible binning number of the feasible interval of binning number, a clustering method is used to cluster the binning feature vector set, and the optimal clustering result is selected, and the optimal clustering result is used to realize binning of the target sequence data set. Compared with the prior art, the present application solves the problems of the prior art, such as the inability of existing metagenomic binning to process unknown species sequences or insufficient binning accuracy.

The application belongs to the technical field of nucleic acid editing, and a SrCas12a-2 protein is identified by combining metagenomics with experiments, a specific amino acid sequence is shown as SEQ ID NO. 1, the protein is a new Cas12a enzyme, and the discovery of the new enzyme enlarges the CRISPR / Cas12a system family. The application also establishes a nucleic acid visualization detection technology based on the CRISPR / SrCas12a-2 system mediation, and the nucleic acid visualization detection technology has a wide application prospect in the field of nucleic acid detection.

The invention discloses a standardization method and system for pathogen metagenome background bacterium level identification, and relates to the technical field of clinical pathogenic microorganism detection, the standardization method comprises the following steps: screening core background flora based on metagenome sequencing data; constructing a historical reference library; screening a background bacterium marker; evaluating background bacterium signal intensity; and determining the background bacterium level. According to the standardization method and the judgment system for pathogen metagenome background bacterium level identification, clinical specimen types are not distinguished, a background bacterium judgment method based on the standardized pg amount is introduced, and it is ensured that background bacterium detection amounts of different samples have comparability; and meanwhile, the accuracy of a detection result and the reliability of clinical interpretation can be improved by utilizing a background bacterium identification mechanism with dual-index collaboration, a historical reference library and a dynamic updating mechanism.