Abstract

Disorder of gut-brain interactions also known as gastrointestinal diseases(IBD) impacts 40% of world population & 18% of Indian population according to a study from the Longitudinal Aging Study in India. Around 7 out of every 10 Indians have digestive discomfort with gastrointestinal diseases facing functional challenges in detection & treatment protocols. The current set of diagnostics are restricted to clinical evaluations, laboratory tests, imaging & endoscopic biopsies which fail to detect the early onset of irritable bowel disease while endoscopic biopsies are painful. 

The blood & stool tests, the standard of care approach before the gastroenterologist goes for advanced stage endoscopy, check for macro level few biomarkers to identify inflammation or infection. However these tests lack a precision approach for accurate & confirmed diagnosis at an early stage & could also exhibit disparities in diagnosis

The interventions & treatment strategies including drugs, biologics, steroids, therapies, stress management strategies & standard diets are generic, far away from addressing precise biological markers & just focuses on managing symptoms 

Here we present an approach to elucidate the role of gut + oral microbiome in onset of irritable bowel diseases. We use gut + oral microbial pathways, to decipher dysregulation & disruption in 48,000 plus biochemical functions in order to detect onset of IBS at stage 0-1. Our clinical approach uses our current repository of 25 billion molecular data & 60 million phenotype data as well as learning from existing scientific literature to develop a machine learnt model( 2X2 matrix method) that curates & combines expression level of 21 microbial functional pathways relevant to known gut & oral microbial activities to detect the onset of IBS. Each of the pathways represents activity of interacting microbial functions based on KEGG Orthology. We use a normative approach within a sub-population (n=75) to define “ maintain”, “needs improvement” & “needs urgent attention”. We hypothesise that “needs urgent attention” pathways are associated with onset of Irritable bowel syndrome & its sub-types within an independent validation cohort (n=200) using Rome IV Diagnostic questionnaire, IBS-SSS clinically validated questionnaire & self reported phenotype.

Instead of waiting for diagnosis of symptoms related to IBS, these functional scores can provide precision health insights into molecular pathways that lead to onset of IBS. These molecular scores combined mathematically is used to detect IBS at stage 0-1, serve as basis & monitoring mechanism for constructing & reviewing the efficacy of disease modifiable therapeutics & can be integrated with clinical practice of healthcare practitioners for treatment of IBS 

Gastrointestinal disorder menace

Over 70% of the Indian adult population suffer from some form of digestive discomfort with symptoms ranging from bloating, constipation, abdominal pain, altered stool quality, gut transit time, stool color, stool frequency,  altered motility & more. Disorder of gut brain interactions are affected by biological, physiological  & environmental factors which include dietary factors. While we generally relate gastrointestinal disorders with issues in our gut, research & empirical evidence has found that our oral health & neurological health are deeply connected with our digestive issues. As such, people having digestive trouble also report bouts of gum issues as well as suffer from stress, anxiety, anger, depression & cognitive issues. 

IBS affects around 11% of the global population & subtypes of IBS including IBS-C(Constipation), IBS-D(Diarrhoea) & IBS-M(Mix). IBS patients also experience bloating, slower gut transit time with increased motility & associated bowel movement with increased or decreased firmness, gum issues & depression situations. These overlap of symptoms among different subtypes of gut-brain disorders including IBS ( & its subtypes) provide healthcare practitioners with diagnostic challenges. This makes IBS a classic case of disparities in diagnosis & theory of exclusion, making patients pursue multiple & different medical procedures in order to exclude irrelevant diagnosis which means increased cost, suffering, pain, confusion & lost time. Since IBS is associated with harmful & inflammatory gut & oral microbiome functions, it becomes important to identify & measure specific IBS related microbiome functions to drive early accurate diagnosis of IBS & deliver disease modifiable therapeutics & treatment strategies. Current efforts focus on profiling metabolites & species of gut microbiome as part of clinical research to identify underlying signals of IBS while there has been no focus on oral microbiome & its interaction with gut microbiome. The current diagnostics are reactive in nature & involves huge healthcare costs while there are few options that focus on preventative approach. 

Genefitletics is filling in the early detection gap

While the current Indian healthcare ecosystem is waiting for precision diagnostics, detection model & preventative treatments, they are far away from elucidating the role of gut & oral microbiome in development of IBS. Still the companies operating in microbiome science have adopted restrictive diagnostic approaches with focus on only taxonomic presentations ( only gut microbiome). Research has found that active biochemical functions of gut & oral microbiome are far more relevant that taxonomy of gut microbiome. We at Genefitletics based on our years of research have elucidated the role of microbial functions in IBS. 

Over last 6 years, microbiome research & commercial application of our system biology + ML platform has enabled us to deeply understand the molecular underpinning of chronic & metabolic diseases & develop:

1.Machine Learning led algorithm that analyzes India-specific microbiome and phenotypic data

2.High-throughput sequencing workflows and bioinformatics pipelines for molecular data processing

3.Clinically validated disease models for Type 2 diabetes, cardiovascular disease, and CKD & their correlation with cancer

4.A molecular data repository of over 25 billion data points, derived from our existing metabolic health program

We have now developed a disease model to detect IBS at an early stage leveraging the molecular functions performed by gut & oral microbiome. The test is backed by a machine learning model we have built using a clinical study we have conducted on 25 billion molecular data points. The test measures  gut & oral microbiome functions & harnesses 21 molecular pathways to identify subtle yet clinically significant biochemical changes in saliva samples. We quantify these pathways using functions defined by KEGG orthology during next generation sequencing of gut & oral microbiome. Molecular insights related to gut & oral microbiome functions are delivered through 105 microbial pathways scores. Given our extensive research on microbiome- IBS connection & correlation models around gum diseases & IBS, we have curated, constructed, quantified & combined 21 relevant molecular pathways to elucidate early signals & detected IBS at stage 0-1.

The insights from the pathways are applied downstream & our recommendation engine maps them with our therapeutics ontology to deliver precision therapeutics interventions to modulate the pathways. The interventions can be integrated with clinical practice of gastroenterologists. 

Our approach

We demonstrate a scalable approach to quantify & combine the gut & oral microbial functions from gut & oral molecular data collected using next generation sequencing with self reported phenotype(+ Rome IV questionnaire + IBS-SSS clinically validated questionnaire).

We have combined 21 pathway scores which are designed to reflect insights for gastrointestinal, oral & systemic health. Each score was developed by populating & combining biochemical functions performed by different microbes using a proprietary patent pending computational method. 

The specific purpose is to validate the ability of these pathways to assess the impact of altered microbiome in onset of IBS. For the current validation, we demonstrate the relationship of these 21 pathway scores among individuals with IBS & symptomatic classifications-Digestive dysfunction, metabolic dysfunction, neuroinflammation & oral inflammation as defined by self reported phenotype. Each score is used to identify abnormalities in specific oral & gut microbial activities which provides data driven insights to modulate microbiome using precision therapeutics approach blended with standard of care.

The key analysis

We have applied a 2X2 vector matrix & single value decomposition method to assign relevant weights to each of microbes, phenotype & respective pathways that have been combined mathematically to determine a range of scores which defines absence or presence of IBS.

The following process was involved to develop & validate the IBS early detection model

 1.Scientifically classifying these huge mammoth molecular datasets from subjects into model development(+healthy controls) & validation groups

2.Constructing & validating the model( as described above) on the model development group(+healthy controls) using multivariate statistical & regression models to detect onset of IBS for each sample subject

We also run statistical analyzes on the pathways scores & activity level differences between discovery & validation groups with respect to different symptomatic conditions- Oral Inflammation, metabolic dysfunction, neuroinflammation & digestion dysfunction to further verify the efficacy of our model. All 21 pathways had adjusted P value <0.05

Conclusion

Using statistical tools & application of our detection model, we could establish a specificity of 71% & sensitivity of 75% as against self-reported phenotype. The adjusted P value was less than 0.05

Disease modifiable therapeutics

Based on activity level of each of these 21 pathways, our recommendation engine maps these pathways with our proprietary therapeutics ontology database that aims at feeding our microbiome with right food substrates that suppress pro-inflammatory functions & promotes beneficial metabolites production to regulate & optimise our digestive health

Commercial application

The detection model is incorporated with our full body biochemistry test- ORAHYG Pro & is available for all patients who sign up for the test. You can find more about ORAHYG PRO.

In case any researcher, scientists or gastroenterologist is interested to deep dive into the research & validation study, please email us at support@genefitletics.com with your profile & objective to access the research.