Biochemical features of beneficial microbes: Foundations for therapeutic microbiology

The gastrointestinal tract (GIT) is a diverse and complex ecosystem shaped by continual interactions between host cells, nutrients, and the gut microbiota. The gut microbiome is estimated to contain approximately 1013 bacterial cells and is dominated by the major phyla Firmicutes, Bacteriodetes, Actinobacteria, Proteobacteria, and Verrucomicrobia (1, 2). Early colonizers of the GIT include bifidobacteria from the phylum Actinobacteria. These commensal microbes colonize immediately after birth and are speculated to prime the GIT and influence the gut-brain axis (3 - 5). The infant microbiota is considered to be relatively unstable. Despite dramatic changes in the microbiome structure during early life, the gut microbiota increases in diversity and stability over the first 3 years of life (6). Following this initial establishment, the microbiomes of children are generally enriched in Bifidobacterium spp., Faecalibacterium spp., and Lachnospiraceae compared to adults (7 - 9). During adulthood, the gut microbiome is considered to be stable and is dominated by the phyla Firmicutes and Bacteriodetes. While bacterial populations vary between individuals, the fecal microbiota of adults is highly stable through time (6). This stability is maintained until older age (>65), when the microbiome stability and function begin to decline (10, 11).