The human gut microbiome refers to the microbes found in the human digestive tract and their genomes. It is estimated that the number of microorganisms inhabiting the gastrointestinal tract exceeds 1014 (Bull & Plummer, 2014, pp. 17).
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The human gut microbiota is dominated by bacteria (Clemente et al, 2012, pp. 1259). Over 1000 species of microbes colonize the gut. The most abundant are Firmicutes, Actinobacteria and Bacteroidetes, others include Verrucomicrobia, Cyanobacteria, Proteobacteria and Fusobacteria (D’Argenio & Salvatore, 2015, pp. 98). In the esophagus, duodenum and jejunum Streptococcus dominate while Helicobacter, Veillonella, Prevotella and Streptococcus reside in the stomach. The colon harbors Bacteroides and Firmicutes while luminal microbial genera include Lactobacillus, Ruminococcus, Bifidobacterium, Enterobacteriacae, Clostridium and Streptococcus.
The human gut microbiome presents many benefits to the host like protecting the host against pathogens, regulating host immunity, harvesting energy for the host and strengthening the integrity of the gut (D’Argenio & Salvatore, 2015, pp. 102). It also plays a role in disease due to the presence or overabundance of certain bacteria or metabolites from certain members of the gut microbiota, which may influence the host’s signaling pathways leading to disorders such as obesity or colon cancer (Bull & Plummer, 2014, pp. 17).
The health of the host is determined by how healthy the gut flora is. The normal human gut microbiota is involved in nutrient metabolism and in offering antimicrobial protection.
The interactions of the gut microbiota with each other and with the human host influence nutrition and metabolism (Jandhyala et al, 2015, pp. 8787). The human gut microbiota obtain their nutrients from the dietary carbohydrates from the host. Bacteroides, Enterobacteria, Fecalibacterium, Bifidobacterium and Roseburia found in the colon ferments the undigested carbohydrates and the indigestible oligosaccharides, synthesizing short chain fatty acids (SCFA) (Jandhyala et al, 2015, pp. 8787). Bacteroides thetaiotaomicron metabolizes carbohydrates by expressing glycosyl transferases, polysaccharide lyases and glycoside hydrolases. SCFAs synthesized include butyrate and acetate which are rich energy sources for the host (Flint et al, 2012, pp. 583). It is also involved in protein metabolism by use of microbial proteinases and peptidases which function together with the human proteinases (Jandhyala et al,
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