Abstract: This is a method and a system for designing a personalized therapeutic intervention for an individual. Each individual has a unique composition of microbiome in the gut, one probiotic or dietary regimen may not have same efficacy in different individuals. The disclosure recommends a personalized therapeutic intervention for improving gut health of an individual by designing personalized therapeutics and diet based on functions of microbiome. The personalized therapeutic intervention is recommended based on several steps including generating a set of knowledge bases, identifying a change in the gut health of an individual by monitoring the gut samples and recommending a personalized therapeutic intervention. The personalized therapeutic intervention comprises at least one of a prebiotic, a probiotic and an optimized diet, wherein the optimized diet is estimated based on optimizing a gut food score, where the gut food score is computed based on the change in the gut health of an individual.

Abstract: This disclosure relates generally to the field of taxonomic profiling of microbial organisms such as bacteria, and, more particularly, to system and method for simultaneous interpretation of taxonomic distribution and replication rates of microbes constituting microbial communities. The present disclosure extracts bacterial genomic DNA from a plurality of bacterial organisms comprised in collected microbiome sample. Maps the plurality of the DNA sequence fragment reads to a precomputed reference sequence database of a plurality of all available completely sequenced bacterial genomes. Based on the mapping, the read coverage is measured at the genomic locations of the phylogenetic marker genes, wherein measured read coverage is used for interpretation of taxonomic distribution of the plurality of bacterial organisms. A plurality of slopes is obtained by fitting a linear function.

Abstract: Analysis of the flow of fluxes through the metabolic network of a cell type is useful in gaining knowledge about cellular physiology. Such knowledge can be used in understanding host's interactions with pathogens, drug response etc. However there is dearth of techniques that can incorporate metabolomics data into genome scale metabolic model (GEM) for FBA. A method and system for analyzing metabolic state of a cell at a genome scale by measuring concentrations of a one or more metabolites has been disclosed. The method is utilizing intracellular and/or extracellular metabolite concentrations for constraining reaction fluxes in FBA by incorporating it as part of stoichiometric constraint to metabolic model. The method is used to predict the change in flux flow through all reactions in an organism/cell type under different experimental conditions. The method enables constraining the flow of fluxes through reactions while performing FBA of GEMs using measured metabolite concentrations.

Abstract: Mosquito species cause severe and debilitating illnesses. Despite significant advances in clinical medicine, no specific drugs or vaccines are available for diagnosis, treatment, and management of majority of mosquito-borne illnesses. A method and system for evaluating and reducing the degree of mosquito attractiveness of an individual is provided. The methodology involves computation of a metric based on analysis of the host’s skin microbial profile and is thus expected to estimate individualized attractiveness profiles. A specific set of bacterial species contributing to skin attractiveness for mosquitoes have been identified and relative abundances of the bacterial species in the identified set have been custom engineered to generate novel features. These features have been utilized for computing an index referred to as a ‘Mosquito Attractiveness Quotient (MAQ)’ that quantifies or measures the degree of mosquito-attractiveness of individual.

Abstract: Skin-associated autoimmune diseases are common these days. A method and composition for microbiome based amelioration of skin associated autoimmune inflammatory diseases has been provided. The composition is made of at least one or more of microbiome-associated compounds such as proteins, metabolites, antibiotics, probiotics, etc. The method provides a composition for an affected individual through application of these compositions aimed at improving the bioavailability of lipoic acid. It acts through modulation of the lipoic acid metabolic pathway to do the same. The suggested microbes and compounds can either be used as an effective probiotic supplement in increasing the microbial population involved in lipoic acid biosynthesis (only), or increasing the number of competitors of the microbes involved in escalation of lipoic acid salvage system, or through direct antibiotic or physical action against the latter.

Abstract: A system and method for predicting gut health of an individual using non-invasive technique has been provided. The system is making use of two types of pathways i.e. one which are beneficial to gut health and the second which are harmful to gut health. These two types of pathways are annotated in the genomes of gut bacteria. Best combinations of subsets of these pathways capable of distinguishing between gut commensals and pathogens are assigned as pathway biomarkers. The identified pathway biomarkers are then used to develop scheme for prediction of gut health status.

Abstract: This disclosure relates generally to methods and systems for designing a personalized composition that can counteract or reduce skin malodor. Conventional techniques that prepare compositions to treat specific malodorants are limited and such compositions cannot be personalized to an individual according to the type of malodorant produced on skin of the individual. The present disclosure provides a method for designing a personalized composition for degrading the malodorant present in skin of the subject. First, a biological sample from the subject is collected, and metabolite composition of the sample is determined. next, one or more malodorant in the sample are identified based on the metabolite composition. Further, a combination of bacteria capable of degrading the identified malodorant are identified using the microbe-malodorant microbial knowledge base and lastly the personalized composition of the identified bacteria is designed using the combination of bacteria.

Abstract: A system and method for identification of key driver responsible for bringing changes in a microbial population is provided. The method involves construction of microbial association networks with each microbial taxa as nodes and their associations as edges and subsequent identification of crucial ‘driver’ nodes involved in the studied disease progression. While comparing a particular node between two networks, this method takes individual nodes and their associations into account as well as the identity of their interacting partners. A taxon in the diseased state with an altered set of associations while still being increasingly important for the whole network necessarily holds a key significance in microbial interplay. Using this rationale, this methodology computes a score to quantify this change for each node and calculates its statistical significance.

Abstract: A method and system for annotation and classification of biomedical text having bacterial associations have been provided. The method is microbiome specific method for extraction of information from biomedical text which provides an improvement in accuracy of the reported bacterial associations. The present disclosure uses a unique set of domain features to accurately identify bacterial associations from the biomedical text. The disclosure further provides a method to use the set of domain features to improve a microbiome crowd sourcing setup and create a refined microbial association network. The refined bacterial association network can also be made corresponding to a disease or healthy state, which can be used for an improved understanding of the bacterial community structure and design therapeutic interventions. This refined bacterial association networks for a disease can then be used for clinical, therapeutic and diagnostic applications for treatment of the disease.

Abstract: The need for an accurate, early, and precise estimation of expected delivery date (EDD) for the pregnant subject is vital. A system and method for predicting a day/date of delivery for a pregnant subject using one or more microbiome samples collected from the pregnant subject is provided. The disclosure relates to applying machine learning techniques on the microbiome characterization data corresponding to the biological sample(s) collected from the pregnant subject. The method further comprises using the predicted EDD to suitably plan and take required medical treatment or precautions or medical advice for the pregnant subject to prevent any pregnancy and/or delivery related complications and to manage the delivery appropriately. The disclosure also provides compositions of the microbiome data which can potentially influence the delivery date, or the method provides exemplary compositions of the microbiome data which plays vital role in estimating the EDD of the pregnant subject.

Abstract: Many microbes are capable of synthesizing anti-cancer products, however existing state of art is limited by focus on industrial production of the said products. A method and system for preparing a knowledgebase of microbes and microbial functions to identify good and bad microbes have been provided. The present disclosure therefore further describes methods and compositions for the risk assessment, prevention and management of various forms of cancer by using microbes, microbial products utilizing the knowledgebase of microbes and microbial function. The method is configured to priming the microbes inside the host for boosting the immune response against cancer initiation, progression, recurrence and associated side effects. The use of microbes and microbial products can be provided in the form of probiotics, supplements, and prebiotics etc. along with creation of right sets of nutrition conditions in the host for the proper functioning of the microbes and microbial products.

Abstract: Many of the known infectious pathogens that pose a challenge to available treatment methods because of their antibiotic resistant properties, belong to the phylum Proteobacteria. A method and system for combating infections due to pathogens belonging to phylum Proteobacteria is provided. The system is configured to provide strategies to combat pathogenic infections caused by multi-drug resistant (MDR) and extensively drug resistant (XDR) strains of pathogens belonging to phylum Proteobacteria. It is possible to target multiple pathogens simultaneously using a single target site as these pathogens belong to the same phylum and share similarities in their genetic signature. The strategy involves identifying potential target sites in the pathogen, which can be utilized to compromise its multiple virulence or essential functions at the same time.

Abstract: Mycobacterium tuberculosis is the most common pathogenic agent responsible for tuberculosis (TB) infection. Over a period of time, the methods used for combating TB have become more challenging by the prevalence of multi-drug resistant and extensively drug resistant strains. The disclosure relates generally to method and system for combating infections due to Mycobacterium tuberculosis. The system provides strategies to combat pathogenic infections caused by multi-drug resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis. The strategy involves identifying potential target sites in a pathogen, which can be utilized to compromise its multiple virulence or essential functions at the same time.

Abstract: Bacterial plant pathogens such as Xanthomonas sp. and Pseudomonas syringae are developing resistance to various classes of antibiotics. A method and system for combating plant pathogenic bacterial infections have been provided. The system is configured to provide strategies to combat infections in plants caused by multi-drug resistant (MDR) plant pathogens. The strategy involves identifying potential target sites in the plant pathogen, which can be utilized to compromise its multiple virulence or essential functions at the same time. The idea used in this disclosure utilizes the fact that a conserved stretch of nucleotide sequence occurring multiple times on a pathogen genome in genomic neighborhood of genes encoding virulence factors or in vicinity of genes essential for pathogen survival encoded within the genome of the candidate pathogen can be targeted to disrupt the overall genetic machinery of the plant pathogen.

Abstract: A system and method for estimation of functional potential of pathways in genomes/meta-genomes is provided. Initially seed modules are identified and a multi-dimensional tag map is created. Further, pathway annotation is done using a novel 6Q annotation step. Hidden Markov Model (HMM) based search augmented with an analysis of gene context is used to refine the modules using a graph theory based approach. The method uses the multidimensional module tag map to build a backend knowledge base and use the same for an iterative literature search to verify the clustered organization of genes within a pathway. Finally, a score is assigned to compute the contribution of each pathway within the genome/meta-genome.

Abstract: Schizophrenia is a chronic and severe psychiatric disorder that affects how a person thinks, feels, and behaves. If Schizophrenia is diagnosed early, most symptoms of Schizophrenia can be managed with appropriate medical interventions. A system and method for assessing the risk of Schizophrenia in a person has been provided. The system is configured to assess individuals to check the presence or absence of Schizophrenia, by quantifying the abundance of sensory proteins in their microbiome. The disclosure relates to a defined methodology that involves assessment and categorization of the person into healthy and schizophrenic based on the abundance of sensory proteins in the microbiome. The systems and methods further describe microbiota based therapeutics for management of Schizophrenia through generating a therapeutic model and administering a consortium of healthy microbes which could modulate the disease microbiome composition towards a healthy equilibrium.

Abstract: Prediabetes is an intermediary physiological condition (in between healthy and diabetic states) which may be reversed through timely intervention. A system and method for assessing the risk of prediabetes in a person has been provided. The system 100 is configured to assess individuals to check the absence or presence of prediabetic symptoms, by quantifying the abundance of sensory proteins in their microbiome. The invention relates to a defined methodology that involves assessment and categorization of the person into healthy and prediabetic based on the abundance of sensory proteins in the sample collected from the faeces of the person. The systems and methods further describe microbiota based therapeutics for treatment/management of prediabetes through generating a therapeutic model and administering a consortium of healthy microbes which could modulate the disease microbiome composition towards a healthy equilibrium.

Abstract: Co-infection of Pseudomonas aeruginosa and Staphylococcus aureus, exacerbates the virulence gene expression as well as shows higher antibacterial resistance than when they cause infections individually thereby making the infection extremely difficult to combat. A method and system for combating infections due to Pseudomonas aeruginosa and Staphylococcus aureus has been provided. The system provides strategies to combat pathogenic infections caused by multi-drug resistant (MDR) and extensively drug resistant (XDR) strains of Pseudomonas aeruginosa and Staphylococcus aureus. The strategy involves identifying potential target sites, which can be utilized to compromise its multiple virulence or essential functions at the same time.

Abstract: A system and method for identification of target sites in a pathogenic genome and combating a pathogenic infection have been provided. The present disclosure utilizes the fact that a conserved stretch of nucleotide sequence in genomic neighborhood of genes important for bacteria can be targeted to disrupt the overall functioning of the pathogen. The method involves identification of nucleotide repeat sequences in the DNA. The method and system also involve administration of a cocktail comprising antimicrobial drugs, biofilm inhibitors and a construct. The genomic neighborhood or vicinity or ‘flanking genes’ refers to regions lying within a predefined number of genes to the identified conserved stretch of nucleotide repeat sequence (or its reverse complement) on the candidate pathogen genome or within a distance of predefined number of bases with respect to the conserved stretch of nucleotide repeat sequence (or its reverse complement) on the candidate pathogen genome.

Abstract: Colorectal cancer is a severe disease, if not assessed properly, it may lead to the death of an individual. A system and method for assessing the risk of colorectal cancer has been provided. The system is configured to assess individuals to check the risk of presence of colorectal cancer (CRC) and/or adenomatous (colonic/rectal) polyps, by quantifying the abundance of sensory proteins in their gut microbiome. The system further categorizes the person into one of healthy, adenoma and cancerous categories based on the nature and abundance of sensory proteins in the gut microbiome. The system further describes microbiota based therapeutics for treatment of the person with colorectal adenoma and/or cancer through administration of at least one of a consortium of healthy microbes, antibiotic drugs and pre-/pro-/syn-/post-biotic compounds or fecal microbiome transplant which could modulate the disease microbiome composition towards a healthy equilibrium.