Cospeciation of gut microbiota with hominids | Science

Cospeciation of gut microbiota with hominids | Science

Gut bacteria co-evolved with animal hosts, offers human evolution clues

Based on the DNA sequence of a moderately conserved gene in all bacteria, researchers have found that bacterial strains diverged and began to evolve separately in the guts of humans and chimpanzees 5 million years ago, and in humans and gorillas 15 million years ago. These dates are similar to when humans and apes evolved into a new species. It may now be possible to determine if this mutually beneficial relationship between gut bacteria and their animal hosts contributed to the formation of a new species. A perspective on the research from NHGRI Senior Investigator Julie Segre, Ph.D., appeared in the July 22 issue of Science.
Read the perspective | Read the study

REPORT

Cospeciation of gut microbiota with hominids

1. Andrew H. Moeller¹,², 
2. Alejandro Caro-Quintero³, 
3. Deus Mjungu⁴, 
4. Alexander V. Georgiev⁵,⁶, 
5. Elizabeth V. Lonsdorf⁷, 
6. Martin N. Muller⁸, 
7. Anne E. Pusey⁹, 
8. Martine Peeters¹⁰, 
9. Beatrice H. Hahn¹¹, 
10. Howard Ochman¹,*

+ Author Affiliations

1. ↵*Corresponding author. Email: howard.ochman@austin.utexas.edu

Science  22 Jul 2016:
Vol. 353, Issue 6297, pp. 380-382
DOI: 10.1126/science.aaf3951

Human-microbiota coevolution

The bacteria that make their home in the intestines of modern apes and humans arose from ancient bacteria that colonized the guts of our common ancestors. Moeller et al. have developed a method to compare rapidly evolving gyrB gene sequences in fecal samples from humans and wild chimpanzees, bonobos, and gorillas (see the Perspective by Segre and Salafsky). Comparison of the gyrB phylogenies of major bacterial lineages reveals that they mostly match the apehominid phylogeny, except for some rare symbiont transfers between primate species. Gut bacteria therefore are not simply acquired from the environment, but have coevolved for millions of years with hominids to help shape our immune systems and development.

Science, this issue p. 380; see also p. 350

Abstract

The evolutionary origins of the bacterial lineages that populate the human gut are unknown. Here we show that multiple lineages of the predominant bacterial taxa in the gut arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over the past 15 million years. Analyses of strain-level bacterial diversity within hominid gut microbiomes revealed that clades of Bacteroidaceae and Bifidobacteriaceae have been maintained exclusively within host lineages across hundreds of thousands of host generations. Divergence times of these cospeciating gut bacteria are congruent with those of hominids, indicating that nuclear, mitochondrial, and gut bacterial genomes diversified in concert during hominid evolution. This study identifies human gut bacteria descended from ancient symbionts that speciated simultaneously with humans and the African apes.