Metagenomic microbiota composition of anaerobically enriched fecal samples from diabetic and healthy volunteers

Title : Metagenomic microbiota composition of anaerobically enriched fecal samples from diabetic and healthy volunteers

Abstract:

With a pool of more than 100 trillion cells and diversity of thousands of different bacterial genera and millions of functional genes, the gut microbiome works almost like an organ in the human body. Not surprisingly, the dysfunction of this essential entity termed as “gut dysbiosis” is linked with almost every human disease or disorder including diabetes. In turn, Gut dysbiosis relates to an imbalance in composition of microbial communities wherein abundance of signature microbes invariably differs from that in normal healthy condition. Over 99% of gut bacteria are reported to be anaerobic thus it is very important to process fecal samples before studying its microbiota composition. Therefore, in this study fecal samples were collected from healthy and diabetic (fasting sugar > 150 mg/dl) volunteers, followed by anaerobic incubation in ANOXOMAT machine having an environment of (N₂, H₂ and CO₂). The samples were enriched anaerobically for over a month with weekly additions of anaerobic growth media. This time series studies has been planned wherein, samples from the same volunteers will be taken for a one year period to develop a baseline data. After enrichment, full-length 16S rRNA amplicon sequencing was performed using MinION sequencer (ONT) to study complete microbial diversity of fecal samples. Parallelly, anaerobic cultivable microbial isolates from fecal samples were identified by MALDI-TOF Mass Spectrometer.

Metagenomic study involving 16S rRNA amplicon data revealed prominent differences between healthy and diabetic fecal samples with respect to anaerobic microbiome composition. As compared to healthy condition the gut microbiome composition varies significantly in diabetic condition as indicated by differential taxa abundance at every level of taxonomic hierarchy viz. Phylum, Class, Order, Family, Genus and Species. Remarkably, Anaerostipes genus was statistically most dominant in normal healthy samples. Anaerostipes along with other SCFA producing bacteria were found to be under-represented in diabetic conditions suggesting dysbiosis with respect to beneficial bacteria.

In contrast to 16S rRNA amplicon data, we found very less diversity in cultivable anaerobic bacteria when identified using MALDI-TOF. This implies that the majority of anaerobic gut microbes remains to be cultivated and characterized. This study aims to create a baseline of gut microbiota composition corresponding to different health conditions in humans including diabetes. The presentation will cover the comparative results for anaerobically enriched fecal samples from healthy and diabetic volunteers. Furthermore, the importance of anaerobic gut microbiota composition will be presented in view of its role in maintaining gut eubiosis.

Biography:

Dr. Rajesh Pal studied Biochemistry from University of Pune and graduated as M.Sc in 2009. He then joined CSIR-National Environmental Engineering Research Institute for his PhD in Environmental Microbiology & Genomics and graduated in 2015. With about 9 years of industrial experience, he has worked in different domains such as development of agri-products, Viz. biofertilizers, biopesticides and biostimulants. In his previous industrial collaboration, he also led the development of human gut microbiome test based on fecal sample microbiota leading to personalised food & diet recommendations. He has published his research work in national and international journals. Currently, as Lab Manager with HiMedia Laboratories, his research is focused on the study of gut microbiomes from humans and animals. Understanding of human gut microbiota and its relationship with overall host physiology and different clinical conditions, are some of his current R&D projects at HiMedia Microbiome Research Center.