The Human Gut Microbiome

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). 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.

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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, 2015, pp. 8787). The gut microbiota is also deconjugates and dehydrates primary bile acids into secondary bile acids in the colon. This is done by Escherichia coli, Bacteroides fragilis and Bacteroides intestinalis.

The human gut microbiome has the capability to confer protection to the host against infections through non- immune- and immune- mediated mechanisms (Ubeda et al, 2017, pp. 128). Non- immune- derived mechanisms of protection include the consumption and depletion of simple sugars that could be utilized by pathogenic organisms such as Escherichia coli preventing them from causing infection (Jandhyala et al, 2015, pp. 8787). Gut microbiota also confers resistance to pathogens directly by producing and releasing molecules that have bacteriostatic or bactericidal properties (Ubeda et al, 2017, pp. 128). Innate immune- derived mechanisms of protection include the use of the mucus layer whose quantity and quality is determined by the intestinal microbiota (Jandhyala et al, 2015, pp. 8787).

The human gut microbiome present detrimental effects in case of an imbalance. Consequences of microbial imbalance in the gut include an increased risk of systemic metabolic diseases and chronic gastrointestinal diseases.

The gut microbiota has been implicated in systemic metabolic diseases such as type 2 diabetes mellitus and obesity due to the key role they play in the process of digestion. Dysbiosis in the gut, that is gut microbial imbalance, has been shown by research to have a direct association with the pathophysiology of type 2 diabetes and obesity (Bull & Plummer, 2014, pp. 17). Gut microbiota such as Firmicutes and Bacteroides that are implicated in nutrient acquisition and harvesting energy are implicated in obesity and diabetes type 2.

The human gut microbiome has been implicated in chronic gastrointestinal diseases such as irritable bowel syndrome and inflammatory bowel disease. In dysbiosis, microbial imbalance, the gut facilitates the adhesion of enteric pathogens which are responsible for the symptoms associated with irritable bowel syndrome such as abdominal discomfort and change in bowel habits (Bull & Plummer, 2014, pp. 17). An imbalance in gut microbiota leads to reduced bactericidal properties, thus allowing the adherence of enteric pathogens. A reduction in numbers of Firmicutes, Bacteroidetes and Proteobacteria is associated with inflammatory bowel disease. Firmicutes are responsible for the synthesis of short chain fatty acids like butyrate and acetate, which have anti- inflammatory properties, thus a reduction in their numbers increases the risk of inflammatory bowel disease (Flint et al, 2012, pp. 586).

The human gut has the largest number of microbes compared to any other part of the human body. There exists a symbiotic relationship between the gut microbiota and the host. The gut microbiota functions in nutrition, metabolism and antimicrobial protection. However, when an imbalance occurs in the gut microbiota, harmful consequences such as the onset of chronic gastrointestinal diseases and an increased risk of systemic diseases occurs. It therefore becomes crucial that the balance of gut microbiota remains at healthy levels.


Bull, M.J. and Plummer, N.T., 2014. Part 1: The human gut microbiome in health and disease.? Integrative Medicine: A Clinician’s Journal, 13(6), p.17.

Clemente, J.C., Ursell, L.K., Parfrey, L.W. and Knight, R., 2012. The impact of the gut microbiota on human health: an integrative view. Cell, 148(6), pp.1258-1270.

D’Argenio, V. and Salvatore, F., 2015. The role of the gut microbiome in the healthy adult status. Clinica Chimica Acta, 451, pp.97-102.

Flint, H.J., Scott, K.P., Louis, P. and Duncan, S.H., 2012. The role of the gut microbiota in nutrition and health. Nature Reviews Gastroenterology and Hepatology, 9(10), pp.577-589.

Jandhyala, S.M., Talukdar, R., Subramanyam, C., Vuyyuru, H., Sasikala, M. and Reddy, D.N., 2015. Role of the normal gut microbiota. World journal of gastroenterology: WJG, 21(29), p.8787.

Thursby, E. and Juge, N., 2017. Introduction to the human gut microbiota.? Biochemical Journal, 474(11), pp.1823-1836.

Ubeda, C., Djukovic, A. and Isaac, S., 2017. Roles of the intestinal microbiota in pathogen protection. Clinical & translational immunology, 6(2), p.e128.

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The Human Gut Microbiome. (2018, Dec 29). Retrieved May 24, 2022 , from

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