Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls
Bodkhe, Rahul ; Shetty, Sudarshan A. ; Dhotre, Dhiraj P. ; Verma, Anil K. ; Bhatia, Khushbo ; Mishra, Asha ; Kaur, Gurvinder ; Pande, Pranav ; Bangarusamy, Dhinoth K. ; Santosh, Beena P. ; Perumal, Rajadurai C. ; Ahuja, Vineet ; Shouche, Yogesh S. ; Makharia, Govind K. - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.
Molecular characterization and meta-analysis of gut microbial communities illustrate enrichment of prevotella and megasphaera in Indian subjects
Bhute, Shrikant ; Pande, Pranav ; Shetty, Sudarshan A. ; Shelar, Rahul ; Mane, Sachin ; Kumbhare, Shreyas V. ; Gawali, Ashwini ; Makhani, Hemal ; Navandar, Mohit ; Dhotre, Dhiraj ; Lubree, Himangi ; Agarwal, Dhiraj ; Patil, Rutuja ; Ozarkar, Shantanu ; Ghaskadbi, Saroj ; Yajnik, Chittaranjan ; Juvekar, Sanjay ; Makharia, Govind K. ; Shouche, Yogesh S. - \ 2016
Frontiers in Microbiology 7 (2016)MAY. - ISSN 1664-302X
16S rRNA amplicon - Indian subjects - Prevotella and Megasphaera - QPCR
The gut microbiome has varied impact on the wellbeing of humans. It is influenced by different factors such as age, dietary habits, socio-economic status, geographic location, and genetic makeup of individuals. For devising microbiome-based therapies, it is crucial to identify population specific features of the gut microbiome. Indian population is one of the most ethnically, culturally, and geographically diverse, but the gut microbiome features remain largely unknown. The present study describes gut microbial communities of healthy Indian subjects and compares it with the microbiota from other populations. Based on large differences in alpha diversity indices, abundance of 11 bacterial phyla and individual specific OTUs, we report inter-individual variations in gut microbial communities of these subjects. While the gut microbiome of Indians is different from that of Americans, it shared high similarity to individuals from the Indian subcontinent i.e., Bangladeshi. Distinctive feature of Indian gut microbiota is the predominance of genus Prevotella and Megasphaera. Further, when compared with other non-human primates, it appears that Indians share more OTUs with omnivorous mammals. Our metagenomic imputation indicates higher potential for glycan biosynthesis and xenobiotic metabolism in these subjects. Our study indicates urgent need of identification of population specific microbiome biomarkers of Indian subpopulations to have more holistic view of the Indian gut microbiome and its health implications.