Research has by now established that microbes are a key part of animal evolution. The ‘hologenome’ model considers the host genome and microbiome combined as a unit of evolution which jointly undergoes selection; the involved microbes can include both pathogens and those that live in a mutualistic symbiosis with the host, called ‘symbionts’. A new review by Dr. Michael Shapira from the University of California, Berkeley (USA) explores how scientists are refining their understanding of species evolution in light of increasing data on how symbionts interact with hosts.

A host that is better adapted to its environment, behaviourally and physically, is a key outcome of evolution. The most extensive microbiota of an animal host is located in the gut, and Shapira says this microbiota could contribute to host adaptation in several ways. First, the gut microbiome comprises much more genetic variation than the host genome, and thus it could facilitate evolution at a more rapid pace. Second, the gut microbiome is able to exchange microbes (along with their genes and associated functions) with the environment.

Data suggests symbionts have a prominent role in speciation: “the splitting of a population into two reproducibly incompatible populations”. Shapira says symbionts (or mutualists) facilitate host adaptation to different niches, leading to ecological isolation, and therefore to reproductive isolation and speciation.

When it comes to transmitting symbionts from one generation of host to the next, both vertical and horizontal transmission are probably at play. Vertical (mother-to-child) transmission benefits the host by securing good mutualistic bacterial species for the next generation; horizontal transmission (where each generation acquires symbionts from free-living populations) secures bacteria with higher genetic variation, which could provide more opportunities for adaptation. Shapira cites data from diverse animal species that indicates mixed-mode transmission is probably the norm. Indeed, a combination of vertical and horizontal transmission secures the best of both worlds for the host: a robust collection of mutualistic bacteria, as well as the flexibility to adapt to a changing environment.

Shapira says composition of the gut microbiota is important in the occurrence of evolutionary processes. Within the hologenome model, he posits a multilayered gut microbiota with both a ‘core’ and ‘flexible pools’; these groups of microbes contribute differently to host fitness. The core microbiota of host-adapted microbes may be determined by host genes, while the flexible pool of microbes depend on external conditions and diversity within the host’s environment. The continuum in between the core and flexible pools includes microbes that are associated with the host and also variably affected by the environment.


In the paper, Shapira discusses specific ways in which symbiotic microbes in animal gut microbiota could potentially affect host fitness and evolution. These include:

  • Determining how hosts can use plants as dietary components (i.e. reliance on plant degrading microbes)
  • Influencing adaptation to local niches (e.g. resistance to local pathogens)
  • Affecting life-history traits (resulting from the host’s allocation of resources to different tissues at different life stages)
  • Controlling nutrient inputs that affect host robustness
  • Influencing overall resource allocation to regulate host development and fitness
  • Providing specific signals that facilitate timely and proper development
  • Affecting mate choice
  • Contributing to hybrid incompatibility (i.e. the reproductive barrier between species)

Shapira and other scientists are only beginning to construct a hologenome framework that accounts for data on host-microbe and microbe-microbe interactions. Indeed, the picture of host evolution must also incorporate microbial evolutionary stability and the ways in which certain gut bacterial species have naturally evolved to cooperate with each other. (A recent study, for example, detailed how Bacteroides ovatus digests polysaccharide at a benefit to other bacterial species and at immediate cost to itself; in turn, B. ovatus benefits from the extracellular breakdown of inulin.)

Taken together, these points about host-microbiota coevolution predict the existence of gut microbiotas specific to each species, comprised of beneficial and host-adapted microbes that live together in a complex cooperative system. More data from the wealth of animal species on Earth will gradually allow insights into the intricate events involved in host-microbe coevolution.




Rakoff-Nahoum S, Foster KR, Comstock LE. The evolution of cooperation within the gut microbiota. Nature. 2016; 533: 255–259. doi:10.1038/nature17626

Shapira M. Gut Microbiotas and Host Evolution: Scaling Up Symbiosis. Trends in Ecology & Evolution. 2016. doi: