The gut microbiome, as defined by molecular biologist Joshua Lederberg, is the totality of microorganisms, bacteria, viruses, protozoa, and fungi, and their collective genetic material present in the gastrointestinal tract (GIT). The gut microbiota is comprised of all the bacteria, commensal, and pathogenic, residing in the GIT. In the past decade the gut microbiota has been explored for potential gut microbe–host interactions including effects on metabolism, immune, and neuroendocrine responses. The gut microbiota plays an important role in nutrient and mineral absorption, synthesis of enzymes, vitamins and amino acids, and production of short-chain fatty acids (SCFAs). The fermentation byproducts acetate, propionate, and butyrate are important for gut health and provide energy for epithelial cells, enhance epithelial barrier integrity, and provide immunomodulation and protection against pathogens. Current investigations are exploring resident bacterial gene function and the potential corresponding role in human health and metabolism. Additionally, study of whether nonpathogenic bacterial strains can stimulate recovery of the immune responses to pathogenic causing diseases is ongoing (Cresci and Bawden, 2015).
The human gut microbiota is divided into many groups called phyla. The gut microbiota is comprised primarily of four main phyla which include Firmicutes, Bacteriodetes, Actinobacteria, and Proteobacteria (Belizario and Napolitano, 2015). While bacteria colonizes the human body, including oral cavity, placenta, vagina, skin, and GIT, the majority of bacteria reside within the GIT, with the majority of predominantly anaerobic bacteria housed in the colon (Fig. 4.1). To gain perspective of the magnitude of bacterial presence and potential effects on the host, the human body expresses 20,000 eukaryotic genes while the gut microbiome expresses 3.3 million prokaryotic genes (NIH, 2012).
The development and alteration of the gut microbiome are affected by a variety of factors including birthing and infant feeding method, exposure to stress, environment, diet, medications, stage of lifecycle, and comorbid diseases (Fig. 4.2). Dysbiosis is described as the alteration in microbial community that results in decreased diversity and numbers of commensal bacteria. Studies suggest relationships between gut dysbiosis and chronic health conditions such as inflammatory bowel disease, metabolic syndrome, cardiovascular disease, obesity, and cancer (Carding et al., 2015).
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