Role of the normal gut microbiota

Abstract

Relation between the gut microbiota and human health is being increasingly recognised. It is now well established that a healthy gut flora is largely responsible for overall health of the host. The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes. Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. Nevertheless, there exist temporal and spatial variations in the microbial distribution from esophagus to the rectum all along the individual's life span. Developments in genome sequencing technologies and bioinformatics have now enabled scientists to study these microorganisms and their function and microbe-host interactions in an elaborate manner both in health and disease. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Several factors play a role in shaping the normal gut microbiota. They include (1) the mode of delivery (vaginal or caesarean); (2) diet during infancy (breast milk or formula feeds) and adulthood (vegan based or meat based); and (3) use of antibiotics or antibiotic like molecules that are derived from the environment or the gut commensal community. A major concern of antibiotic use is the long-term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in reservoir of organisms with a multidrug resistant gene pool.

Keywords: Bioinformatics; Health; Immunomodulation; Metabolic function; Normal gut microbiota.

Figure 1

Bioinformatics work flow. This figure explains the various steps involved in the bioinformatics analysis, starting from collection of samples, extraction, sequencing and statistical analysis. The interaction between host and microbes along with the functional capacity of the microbiota can be studied. MG-RAST: Metagenomics rapid annotation using subsystem technology; CAZy: Carbohydrate active-enzymes; MetaPhlAn: Metagenomic phylogenetic analysis; KEGG: Kyoto encyclopaedia for genes and genomics; COG: Clusters of orthologous group; PICRUst: Phylogenetic investigation of communities by reconstruction of unobserved states; MEGAN: Meta genome analyzer; MEDUSA: Metagenomic data utilization and analysis; FANTOM: Functional annotation and taxonomic analysis of metagenomes; HUMAan: Human microbiome project unified metabolic analysis network; BLAST: Basic local alignment search tool; TIGRFAM: Protein sequence classification; PFAM: Protein families; SOAP: Short oligonucleotide analysis package; QIIME: Quantitative insights into microbial ecology.

Figure 2

Distribution of the normal human gut flora.

Figure 3

Broad schematic representation of cell types and mediators involved in immunomodulation in the gut. Black arrow indicate either physiological secretion or activation; Red arrow indicates pathological event; Blue arrows with rounded ends indicates pathogen inhibition; ? indicates unknown mechanisms; SFB indicates short filamentous bacteria.