Development of infant microbiome varies across a spectrum of lifestyles

A metagenomic comparison of the infant gut microbiota assembly from industrialized and nonindustrialized populations reveals robust and systematic lifestyle-dependent divergences, researchers report. According to the authors, the population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.

Beginning immediately after birth, the human gut microbiome undergoes a complex assembly process, and it’s thought that the final adult microbiome composition may be contingent upon the species acquired early in life. For infants living in industrialized nations, this process is well characterized and tends to follow a series of steps that ultimately lead to the low-diversity gut microbiome characterized by adults living industrialized lifestyles.

However, adults living nonindustrialized lifestyles often have characteristically diverse microbiome assemblies. While the infant microbiome assembly has been intensely studied in infants from industrialized nations, very little is known about this process in infants from nonindustrial populations and how it contributes to the marked differences in adult microbiome composition. To better understand how lifestyle impacts microbiome assembly in nonindustrial infants, Matthew Olm and colleagues performed deep metagenomic sequencing on infant stool samples from the Hadza, a group of modern hunter-gatherers living in Tanzania.

Comparing these data with a global dataset of rRNA sequences of healthy infant fecal samples from 18 populations, Olm et al. found that after the first 6 months of life, the microbiome of infants living in contrasting environments diverge from similar Bifidobacteria dominated assemblages. After this divergence, the authors found that a large proportion of the bacterial species detected in samples from the Hadza – more than 20% – were novel, and many of these were undetectable in samples from children living industrial lifestyles.

According to the findings, the notable diversity of gut microbiota diversity appears early in the lives of nonindustrial populations and is traceable to maternal transmission with some influence from the local environment. However, the main driver for differences in gut microbiota globally appears to originate in lifestyle rather than geography. “Our results also highlight the question of whether lifestyle-specific differences in the gut microbiome’s developmental trajectory predispose populations to diseases common in the industrialized world, such as those driven by chronic inflammation,” write Olm et al.