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Study Follows Infant Gut Microbiome Development in Nonindustrialized Hunter-Gatherer Population

NEW YORK – The development of microbial communities in infant guts varies between human populations and in accordance with lifestyle patterns found in those populations, according to new research by a team from Stanford University, the Chan Zuckerberg Biohub, the University of California at Berkeley, and New York University Abu Dhabi.

"The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations," senior and corresponding author Justin Sonnenburg, a microbiology and immunology researcher affiliated with Stanford and the Chan Zuckerberg Biohub, and his co-authors wrote in Science on Thursday.

Using metagenomic sequencing and 16S ribosomal RNA sequencing, the researchers assessed microbial community members and gene repertoires in fecal samples from dozens of infants in a Hadza hunter-gatherer group in Tanzania, along with maternal fecal samples from 23 of the infants.

The team analyzed the findings as part of a 16S rRNA sequence set that included some 1,900 samples in all, representing healthy infants spanning 18 global populations. It also looked at some 745 metagenome-assembled genomes (MAGs) within a broader context of MAGs described in the human gut in the past. Together, the analyses uncovered microbial species and strains that were distinct or found in altered proportions in the guts of infants in the hunter-gatherer population.

The researchers highlighted previously unappreciated microbes in the Hadza infant gut microbiomes, for example. More than one in five microbial genome sequences found with metagenomic sequencing on the infant stool samples had not been described in the past, for example, along with a robust representation of Bifidobacterium infantis microbes linked to the ability to use human milk oligosaccharides.

While B. infantis was the predominant microbe in gut communities found in more than two dozen Hadza infants during their first six months, the researchers saw signs that that microbe was found at reduced levels in the guts of 151 infants under six months old who grew up in industrialized locations. Instead, gut microbiomes from industrialized sites had enhanced levels of a bacteria called B. breve that is known for more modest human milk oligosaccharide breakdown.

Moreover, the authors noted that "B. infantis is anti-associated with B. breve in infants across all lifestyles … suggesting it may be driven by competitive exclusion rather than lifestyle-specific factors."

Along with more detailed analyses on co-occurring microbe clusters and lifestyle-related microbial species, strains, and genes, the team went on to retrace gut microbiome inheritance, using deep fecal sequencing data representing 23 Hadza mother and their infants, along with similar strain tracking in mothers and infants from Sweden.

"The Hadza-specific discoveries reported in this work … exemplify the importance of studying people outside of industrialized nations and highlights the need for additional studies to provide equity in understanding microbiomes across global societies," the authors concluded. "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."