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Western Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Reveals Signature Microbes

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Western Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Reveals Signature Microbes Western Indian rural gut microbial diversity in extreme Prakriti endo-phenotypes reveals signature microbes Chauhan, Narsingh; Pandey, Rajesh; Mondal, Anupam K.; Gupta, Shashank; Verma, Manoj K.; Jain, Sweta; Ahmed, Vasim; Patil, Rutuja; Agarwal, Dhiraj; Girase, Bhushan Published in: Frontiers in Microbiology DOI: 10.3389/fmicb.2018.00118 Publication date: 2018 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Chauhan, N., Pandey, R., Mondal, A. K., Gupta, S., Verma, M. K., Jain, S., Ahmed, V., Patil, R., Agarwal, D., & Girase, B. (2018). Western Indian rural gut microbial diversity in extreme Prakriti endo-phenotypes reveals signature microbes. Frontiers in Microbiology, 9, [118]. https://doi.org/10.3389/fmicb.2018.00118 Download date: 24. sep.. 2021 ORIGINAL RESEARCH published: 13 February 2018 doi: 10.3389/fmicb.2018.00118 Western Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Reveals Signature Microbes Nar S. Chauhan 1†, Rajesh Pandey 2†, Anupam K. Mondal 3,4†, Shashank Gupta 2, Manoj K. Verma 1, Sweta Jain 2, Vasim Ahmed 1, Rutuja Patil 5, Dhiraj Agarwal 5, Bhushan Girase 5, Ankita Shrivastava 5, Fauzul Mobeen 6, Vikas Sharma 6, Tulika P. Srivastava 6, Sanjay K. Juvekar 5, Bhavana Prasher 2,4,7*, Mitali Mukerji 2,4,7* and Debasis Dash 2,3,4* 1 Department of Biochemistry, Maharshi Dayanand University, Rohtak, India, 2 CSIR Ayurgenomics Unit - TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-Institute of Genomics and Integrative Biology, New Delhi, India, 3 G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India, 4 Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Edited by: Integrative Biology (IGIB), New Delhi, India, 5 Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India, Mike Taylor, 6 School of Basic Sciences, Indian Institute of Technology, Mandi, India, 7 Genomics and Molecular Medicine and University of Auckland, New Zealand CSIR-Institute of Genomics and Integrative Biology, New Delhi, India Reviewed by: Anahit Penesyan, Macquarie University, Australia Heterogeneity amidst healthy individuals at genomic level is being widely acknowledged. Ilana Kolodkin-Gal, This, in turn, is modulated by differential response to environmental cues and treatment Weizmann Institute of Science, Israel regimens, necessitating the need for stratified/personalized therapy. We intend to *Correspondence: Bhavana Prasher understand the molecular determinants of Ayurvedic way (ancient Indian system [email protected] of medicine) of endo-phenotyping individuals into distinct constitution types termed Mitali Mukerji “Prakriti,” which forms the basis of personalized treatment. In this study, we explored and [email protected] Debasis Dash analyzed the healthy human gut microbiome structure within three predominant Prakriti [email protected] groups from a genetically homogenous cohort to discover differentially abundant taxa, †These authors have contributed using 16S rRNA gene based microbial community profiling. We found Bacteroidetes equally to this work. and Firmicutes as major gut microbial components in varying composition, albeit with Specialty section: similar trend across Prakriti. Multiple species of the core microbiome showed differential This article was submitted to abundance within Prakriti types, with gender specific signature taxons. Our study reveals Microbial Symbioses, that despite overall uniform composition of gut microbial community, healthy individuals a section of the journal Frontiers in Microbiology belonging to different Prakriti groups have enrichment of specific bacteria. It highlights the Received: 14 June 2017 importance of Prakriti based endo-phenotypes to explain the variability amongst healthy Accepted: 18 January 2018 individuals in gut microbial flora that have important consequences for an individual’s Published: 13 February 2018 health, disease and treatment. Citation: Chauhan NS, Pandey R, Mondal AK, Keywords: Indian gut microbiome, Prakriti, precision medicine, ayurgenomics, ayurveda, 16S rRNA gene Gupta S, Verma MK, Jain S, Ahmed V, Patil R, Agarwal D, Girase B, Shrivastava A, Mobeen F, Sharma V, INTRODUCTION Srivastava TP, Juvekar SK, Prasher B, Mukerji M and Dash D (2018) Western The human microbiome have been shown to have a functional role in the human physiology. Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Microbial flora and its dynamics are often associated with homeostasis within the body. Systemic Reveals Signature Microbes. characterization of the microbiota for comparison of microbial communities and their contribution Front. Microbiol. 9:118. to health and disease (Dominguez-Bello and Blaser, 2008; Rosenberg and Zilber-Rosenberg, doi: 10.3389/fmicb.2018.00118 2011; Dave et al., 2012) have been carried out by the Human Microbiome Project (HMP) and Frontiers in Microbiology | www.frontiersin.org 1 February 2018 | Volume 9 | Article 118 Chauhan et al. Diversity in Healthy Indian Gut Microbiome Metagenomics of the Human Intestinal Tract (MetaHIT) Pitta- Kapha, and Vata-Pitta-Kapha Prakriti types. Amongst the consortium. These studies have provided insights into the seven constitution types, Vata, Pitta, and Kapha are the three composition of microbial community at various anatomical sites phenotypic extremes with contrasting disease susceptibilities. (Human Microbiome Project Consortium, 2012; Parfrey and Phenotypic assessment of Prakriti is carried out on the basis Knight, 2012). The human microbiota has co-evolved closely of examination of approximately 150 features comprising with its host (Yatsunenko et al., 2012; Moeller et al., 2016) and of anatomical, physiological, activity related attributes, and is modulated by intrinsic and environmental factors. Recent psychological parameters. For example, individuals of Pitta studies have indicated that health and predisposition to various Prakriti would have better digestion and metabolic capacity non-infectious diseases of humans are also determined by the whereas Kapha would have less and Vata with an irregular genes coded by resident microbiome (Albenberg et al., 2012; Cho or unpredictable pattern. Recently, we have also been able and Blaser, 2012; Gordon et al., 2012; Zhang et al., 2015). It is to develop predictive models for Prakriti that recapitulate appreciated now that an understanding of human physiology the Ayurveda constitution types through phenotypic traits of is incomplete without the knowledge of the metagenome. individuals (Prasher et al., 2008, 2016). Contemporary approaches have focused on investigating the Many of the phenotypic attributes that are being associated microbial assemblage of the transient states observed over the with microbiome difference also differ between the constitution course of specific diseases. However, the challenge is to elucidate types. This includes desire and suitability for different diets, whether the association between microbial community changes metabolic and digestive patterns, weight gain tendencies, gut and pathology is causal in nature (Clemente et al., 2012; Haiser motility and excretory patterns (Prasher et al., 2008, 2016). and Turnbaugh, 2012). Integrative analysis of human genome, Besides, certain therapeutic modalities unique to Ayurveda physiology and microbiome will enable better understanding as that are aimed at maintenance of health and homeostasis to whether latter is involved in health and disease. However, lays emphasis on restoration of healthy flora (Prasher et al., there are variables contributed by human host as well as 2016, 2017). Earlier, we and other groups have shown that the microbiome, which could confound the observations. For healthy individuals of extreme Prakriti types, Vata, Pitta, and example, the ethnicity and genetic background, age of the Kapha comprise 8–10% of a population and exhibit genome individual, dietary and lifestyle habits; all of which have been wide differences amongst constitution types, albeit from a known to affect the human physiome and shape the microbiome genetically homogeneous background (Prasher et al., 2008; (Fortenberry, 2013; Chong et al., 2015). Studies to identify Aggarwal et al., 2010; Rotti et al., 2014; Govindaraj et al., association between microbial community structure based on 2015). These sub-types have underlying differences in genes that ethnicity, diet, gender in healthy individuals, have met with modulate pathways for apoptosis, metabolism, hypoxia response, limited success (Chong et al., 2015; Bhute et al., 2016). Absence haemostasis, and development. These differences can contribute of definitive patterns has been ascribed to genetic drift as well to inter-individual variability in adaptation to high altitudes, as population admixture. Therefore, it is a challenge to develop susceptibility to high altitude pulmonary edema or thrombotic a population based catalog of human microbiome markers outcomes in hypoxia (Prasher et al., 2008; Aggarwal et al., 2010, for predicting disease predisposition especially for a diverse 2015). Considering the significance of human microbiome in Indian population. The subcontinent is home to more than one health and diseases, the current study is proposed to analyse gut billion people with thousands of endogamous populations from microbiome in extreme constitution types to explore whether different linguistic lineages
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