Human gut microbiome viewed across age and geography

Abstract

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ between human populations when viewed from the perspective of component microbial lineages, encoded metabolic functions, stage of postnatal development, and environmental exposures, we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes. This cohort encompassed infants, children, teenagers and adults, parents and offspring, and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the representation of genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial species assemblages and functional gene repertoires were noted between individuals residing in the USA compared to the other two countries. These distinctive features are evident in early infancy as well as adulthood. In addition, the similarity of fecal microbiomes among family members extends across cultures. These findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations, and the impact of Westernization.

The gut microbiota and inflammatory noncommunicable diseases: Associations and potentials for gut microbiota therapies

“…functional changes over the first years of life 28 , eventuating in a relatively stable microbial community 4,28 . This is influenced by interactions between the environment, diet, microbeassociated and host-related factors 29,30 .…”

“…In contrast, infants delivered by caesarean section (CS) initially acquire microbial communities typically found on maternal skin followed by the gradual acquisition of a more complex microbiota -typically more slowly than in VD infants. However there is high individual variability in the patterns of bacterial species, and the timing of acquisition 4,28 . Even so, across individuals and populations, infant microbiomes generally have a higher proportion of bifidobacteria and lower species richness than adults 28 and share common functional characteristics -for example, infants typically show metagenomes enriched in genes for simple sugar breakdown and folate synthesis 4,28 .…”

“…However there is high individual variability in the patterns of bacterial species, and the timing of acquisition 4,28 . Even so, across individuals and populations, infant microbiomes generally have a higher proportion of bifidobacteria and lower species richness than adults 28 and share common functional characteristics -for example, infants typically show metagenomes enriched in genes for simple sugar breakdown and folate synthesis 4,28 . Microorganisms colonizing the gastrointestinal tract are involved in a number of vital processes 5,6,8,29 .…”

“…introduction of solid foods 28 influence establishment of the gut microbiota. Infants born by CS have a higher incidence of respiratory distress 38 and appear to be at higher risk for developing asthma and atopy 39 , obesity 40 and type 1 diabetes 41 .…”

The regulation of host defences to infection by the microbiota

“…Colonization begins in earnest after birth, with the mother normally providing the bacterial inoculum that seeds the microbiota of her offspring 4, 5. Initially, the bacterial communities of each surface have a similar taxonomic composition, but through the course of infancy each surface develops a microbiota with a unique composition that stabilizes during adulthood 2, 6, 7. In the adult gastrointestinal tract, the microbiota is dominated by bacteria from two phyla: the Bacteroidetes and Firmicutes 3.…”