The Gut Microbiome: Current Understanding and Future Perspectives

Abstract

This chapter complements recent reviews by providing an overview of how the human gut microbiome develops, with a specific emphasis on the colon; some insights into life cycle assessment of gut microbiome structure-function relationships; and description of specific roles that foods might play in modulating these responses. The gastrointestinal (GI) microbiome in many carnivores is, in effect, in competition with the digestive and absorptive processes of the host animal, though the commensal microflora does serve to protect the host from pathogens, principally by colonization resistance. The chapter focuses on distal regions of the human GI tract. The greater abundance of staphylococci in the feces of breast-fed than in those of formula-fed infants may reflect a continuous inoculation of the GI tract of breast-fed infants. Phylogenetic studies employing cloning and sequencing of 16S rRNA genes amplified by PCR have greatly expanded one's knowledge of the diversity and composition of the adult gut microbiome. As noted by Peterson et al., advances in one's abilities to examine gut microbiomes at the RNA, protein, and metabolite levels of investigation will further the mechanistic understanding of microbiome function. In a human trial, Abell et al. noted that the inclusion of resistant starch in the diet significantly increased butyrate and acetate concentrations. The recent advances in genomics and metagenomics provide the opportunity to develop a better understanding of human gut microbiome structure-function relationships and their role in human health and disease, including modulating effects.