Metagenomic Study of the Large Intestinal Bacterial Flora in South India

The human gastrointestinal tract comprises different and connected organs which are involved in the supply of nutrients and energy sources to the human body by conversion and absorption of food. In adult human, the GI tract measures approximately 7 m in length and has a surface area of approximately 300 m2. The human GI tract is a natural habitat for a diverse community of microorganisms which are complex and have coevolved with humans. This large community of microorganisms includes representatives of the bacteria, archaea, eukaryotes (fungi) protozoa and viruses. These microorganisms are collectively known as microbiota. The intestinal microbiota plays a significant role in determining the overall health status of the host. They influence the human physiology and nutrition. The host immune responses are shaped by the intestinal microbiota. These microorganisms have an important role in the digestion of host’s food, vitamin production, metabolism of endogenous and exogenous compounds, and in preventing the colonization by pathogens. A closer vision is needed to understand the interactions of these microbes with the human host. Both resident and transient microbes are present in the intestine forming about 60% of total faecal mass reaching a cell density of 1011 to 1012 cells per gram of the luminal contents. Studies have shown that a number of important factors are controlled directly or indirectly by the resident or transient microbiota that reside in the human gut. The following were concluded from this study: 1. In South Indian healthy rural adult population, 6 phyla, 25 families and 58 genera were detected using culture-independent cloning-sanger sequencing approach. The abundant phyla were Firmicutes followed by Proteobacteria. The Firmicutes: Bacteroidetes ration in adult population was 4.0. The abundant genera in South Indian rural adults were Escherichia/Shigella, Faecalibacterium, Oscillibacter and Klebsiella. 2. The number of phyla increased with age in childhood through adolescents (i.e., from post-weaning, pre-school to school going). Firmicutes and Bacteroidetes were equally distributed in the post-weaning children. Phylum Firmicutes followed by Proteobacteria were abundant in preschool and school going groups. Less variability of genera was observed in post-weaning group compared to preschool and school going groups. Firmicutes: Bacteroidetes ratio increased with age with 1.0, 2.4 and 5.1 in post-weaning, preschool and school going groups respectively. The abundant genera in post-weaning group were Prevotella and Bacteroides. Genera Gemmiger, Bacteroides, Dialister and Escherichia/Shigella were abundant in preschool children and Genera Escherichia/Shigella, Prevotella, Acetivibrio, Allobaculum and Klebsiella were more prevalent in school going adolescents. 3. In the South Indian rural elderly population over 65 years of age, 6 phyla, 25 families and 61 genera were detected. The phylum Bacteroidetes was dominant followed by Firmicutes. The Firmicutes: Bacteroidetes ratio in elderly population was 0.6. Prevotella formed the most abundant genus in elderly group. 4. Archaea belonging to 2 phyla and 5 genera were detected in different age groups. Euryarchaeota and Crenarchaeota were the two genera detected. Euryarchaeota formed the most abundant phylum. Methanobrevibacter was the most prevalent genus among all the age groups accounting for 98% in neonates, 96% in post-weaning, 100% each in preschool, school going and adult population. In the elderly, Methanobrevibacter accounted for 96% and in tribal adult, 99% of the clones belonged to Methanobrevibacter genus. Other genera detected in very minor proportions belonged to Caldisphaera (Phylum Crenarchaeota), Halobaculum (Phylum Euryarchaeota), Methanosphaera (Phylum Euryarchaeota), and Thermogymnomonas (Phylum Euryarchaeota). Thus, Genus Methanobrevibacter formed the most common archaea in all the age groups in the present study. 5. Interindividual and intergroup variability was observed between rural and tribal adults. Phylogenetic analysis suggested evolution of these two groups from a common ancestor