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Gut Microbiome Strains Evolved Along With Humans

NEW YORK — Some human gut microbial strains have evolved side by side with humans as the latter spread out of Africa and across the world, a new study has found.

Humans in different parts of the world share many of the same species of gut microbes, but what strains of those species are present differs, raising the possibility that the microbial strains diversified alongside humans. To answer this question, a team led by researchers at the Max Planck Institute for Biology has analyzed the gut metagenomes and paired human genomes of more than 1,200 individuals living in Africa, Asia, and Europe, including mother-child pairs, to look for signs of co-diversification.

As they reported in Science on Thursday, they found that dozens of gut microbes diversified in parallel with humans. Some strains that co-diversified with humans further appear to be evolving dependency on their hosts and have smaller genomes, as well as oxygen and temperature sensitivities. Accounting for these population-specific strains could further be important when trying to treat microbiome-related diseases.

"These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes," senior author Ruth Ley from Max Planck and colleagues wrote in their paper.

The researchers collected paired host-gut microbiome data from individuals in Gabon, Germany, and Vietnam, which they combined with existing data from individuals from Cameroon, South Korea, and the UK. The Gabon, Germany, and Vietnam datasets included samples from mothers and their children. In all, they amassed 1,225 paired samples.

Based on more than 20,000 SNPs, the researchers constructed a maximum likelihood phylogeny, which clustered the humans into three groups based on their geographic origins. They likewise generated phylogenies for 59 well-represented archaeal and bacterial gut microbes and compared these phylogenies to those of the human hosts.

Three dozen of these gut microbes exhibited signs of co-diversification with humans, including Collinsella aerofaciens, Catenibacterium mitsuokai, Eubacterium rectale, and Prevotella copri. P. copri further exhibited signs of within-country diversification.

Within the samples from children, nine of the 20 most prevalent child gut microbiome taxa also appeared to have undergone co-diversification. Further, co-diversifying strains tended to be shared by mothers and children, consistent with familial transmission.

The strains that co-diversified with humans also appear to have become more dependent on their hosts. Co-diversified species had decreased antibiotic resistance, were more likely to die upon exposure to atmospheric oxygen, and grew poorly at temperatures below those of the hosts. They also had smaller genomes — likely reflecting the loss of nonessential functions — and increased AT content.

"Their results highlight that gut bacterial communities are not haphazard collections of bacteria but reflections of the distinct ancestries of human populations," wrote Cornell University's Andrew Moeller in an accompanying commentary in Science.

These findings additionally suggested that the role of population-specific microbial strains in microbiome-linked diseases may need to be better understood as researchers develop treatments for them.

"The microbiome is a therapeutic target for personalized medicine, and our results underscore the importance of a population-specific approach to microbiome-based therapies," Ley and colleagues added.