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Hominids Underwent Co-Speciation With Some of Their Gut Microbes

NEW YORK (GenomeWeb) – Hominids and some of their gut microbes co-speciated, according to a new study appearing today in Science.

Researchers from the University of Texas and elsewhere collected fecal samples from humans, chimpanzees, bonobos, and gorillas to analyze their gut microbiomes. The phylogenetic trees for strains of Bacteroidaceae and Bifidobacteriaceae largely reflect those of their hosts, as did their divergence times, the researchers reported.

"It's surprising that our gut microbes, which we could get from many sources in the environment, have actually been co-evolving inside us for such a long time," senior author Howard Ochman said in a statement.

He and his colleagues collected fecal samples from 16 people from the US, 47 chimpanzees from Tanzania, 24 bonobos from the Democratic Republic of the Congo, and 24 gorillas from Cameroon. They amplified a variable region of the DNA gyrase B gene from the bacteria present in those samples and use multiple sets of primers targeting three main gut microbiome bacterial families: the Bacteroidaceae, the Bifidobacteriaceae, and the Lachnospiraceae. The researchers sequenced the resulting amplicons on the Illumina MiSeq platform to generate more than 4.5 million reads or about 41,000 reads per sample.

The team constructed separate phylogenetic trees for each bacterial family using a maximum-likelihood approach, and estimated relative node ages using the BEAST software package.

The phylogenetic relationships among the Bacteroidaceae mirror that of their hosts, Ochman and his colleagues reported. They uncovered three bacterial clades that contain strains isolated from two or more species. Within each clade, the researchers noted that strains from bonobos and strains from chimpanzees form sister groups that, together, form their own clade that is a sister group to either strains from gorillas or strains from humans. This, they noted, indicates that ancient co-speciation occurred between Bacteroidaceae and Hominidae.

But while the researchers found Bacteroidaceae lineages diversified with their host lineages, they also uncovered some deviations from that pattern. For instance, they noticed two Bacteroidaceae lineages on the chimpanzee branch that arose from a single lineage without a corresponding host split — each Bacteroidaceae lineage then continued to co-diversify with the host. In addition, the researchers also reported the loss of bacterial lineages in humans, which they said is in line with previous reports of people having depleted microbiomes.

Similarly, the phylogenies for Bifidobacteriaceae are largely analogous to the Bacteroidaceae and their host species, again with a few exceptions.

The Lachnospiraceae phylogenetic tree, meanwhile, differed. According to Ochman and his colleagues, that phylogeny reflected at least four transfer events between host species since the common ancestor of the Hominidae. Since Lachnospiraceae can form spores while Bifidobacteriaceae and Bacteroidaceae cannot, the researchers suggested that Lachnospiraceae could better survive outside the gut, thus improving their ability to disperse and be transferred among host species.

As the Lachnospiraceae pattern differed, the researchers said that the human and ape gut microbiomes likely include a jumble of co-speciating and independently diversifying bacterial lineages.

Ochman and his colleagues also used the Bifidobacteriaceae and Bacteroidaceae phylogenies to estimate divergence times, and traced the human-chimpanzee split to approximately 5.3 million years ago. While they noted that this is later than some previous nuclear genome-based estimates, it is similar to mitochondrial genome-based estimates. They likewise estimated the human-gorilla split to have occurred 15.6 million years ago, which older than what mitochondrial genome-based approaches estimated, but closer to what nuclear genome-based estimates revealed.

In a related commentary in Science, the National Human Genome Research Institute's Julie Segre and Nick Salafsky from Foundations of Success wrote that this work sets "the stage for exploring the evolutionary processes that underlie the symbiotic relationship between hominids and their gut-dwelling microbes."