Robust variation in infant gut microbiome assembly across a spectrum of lifestyles

Establishing early diversity
Humans living an urbanized lifestyle in industrialized countries tend to have less diverse microbiota than people living more rural existences. Using fecal 16S ribosomal RNA sequencing, Olm et al. found that after the first 6 months of life, the microbiome of infants living in contrasting environments diverged from Bifidobacteria-dominated assemblages. Deep metagenomic sequencing revealed that a large proportion of the bacterial species detected in samples from hunter-gatherer infants were new and were undetectable in samples from urbanized children. Gut microbiota diversity appears early in the lives of hunter-gatherer infants and is traceable to maternal transmission, with some influence from the local environment. The main driver for differences among gut microbiota originates in lifestyle rather than geography. It is suspected, but still enigmatic, that such differences in microbiota have functional implications for the health of developing children

Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species. Industrialized infants—even those who are breastfed—have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.