NEW YORK (GenomeWeb) – A team led by Stanford University researchers used data from populations in the foothills of the Himalayas to document the gut microbiome profiles that coincide with recent or more long-term shifts away from traditional foraging lifestyles and toward agriculture.
"This study indicates that human microbiomes may have changed gradually as human lifestyle changed, and those changes can happen within a human's lifetime," first author Aashish Jha — a post-doctoral researcher in co-senior author Carlos Bustamante's biomedical data science and computational, evolutionary, and human genetics lab at Stanford — said in a statement.
As they reported online today in PLOS Biology, the researchers used 16S ribosomal RNA sequencing to identify gut microbial community members in fecal samples from dozens of members of the Tharu, Raute, Raji, and Chepang populations. While the groups have comparable ancestry, language patterns, and cultural practices, the investigators noted, their dietary habits range from hunting and gathering to long-standing or recent agricultural practices, which corresponded to gut microbiome differences between them.
The team noted that the Chepang population continues to practice foraging and other elements of the hunter-gatherer lifestyle, while the Raute and Raji populations from the same region have turned to more agricultural lifestyles over the last three or four decades. In contrast, the Tharu have reportedly had agricultural practices for some 250 to 300 years.
"We show that the divergence of gut microbiome from the foraging population is strongly correlated with agricultural dependence in these populations," Jha and his colleagues wrote.
The researchers used the Illumina MiSeq instrument to do paired-end, multiplexed sequencing on 16S rRNA amplicons generated by PCR primers targeting the V4 region of the gene in fecal samples from 54 individuals from the four target populations and from 10 control individuals of European descent from North America.
Along with general gut microbe community clustering by lifestyle, they detected declining levels of certain microbes such as those in the Ruminobacter, Campylobacter, Treponema, and Prevotella genera in groups with agriculture-based diets compared to those in the foraging Chepang group.
At the same time, the team's results suggest that individuals from more agricultural or industrial populations tended to have higher levels of microbes from the Actinobacteria, Verrucomicrobia, and Firmicutes phyla. Those microbes were particularly pronounced in the North Americans, found at intermediate levels in the Himalayan farming populations, but turned up very infrequently in hunter-gatherers.
Results from the new analyses — and from a study of seasonal gut microbes in the Hadza population that members of the same team published in in Science in 2017 — hinted that not only food types, but also water sources, can influence gut bugs.
The extent to which drinking water, cooking fuel types, and other environmental factors contribute to the gut microbiome remain to be explored further, the researchers noted. And, they explained, the current findings will likely be refined and expanded in the future through using more extensive gut microbial sequencing approaches such as metagenomics.
"Incorporating metagenomics to characterize the gut microbial variation at finer scales, metabolomics and strain culturing to assess functional differences, and immune and metabolic profiling of these populations may reveal the functional consequence of these changes, both in terms of the intrinsic microbial ecology of the gut and the impact on human biology," the authors concluded.