Researchers in Canada have determined that the smallest marine invertebrates are home to distinct microbial communities—so distinct, in fact, that there is little correlation between how closely related animals are and similarities in their microbiomes.
“This says a lot about how microbiomes originated and how they evolve today,” says University of British Columbia (UBC) evolutionary microbiologist Dr. Patrick Keeling. "People might intuitively think the purpose of a microbiome is to be of benefit to the host animal, and that they co-evolve together. But the bacteria could care less about helping the animal host—they have their own agenda.”
Most animals harbor a community of bacteria that are simply good at living in animals, Dr. Keeling says. “From this ‘professional guild’ of animal specialists likely evolved the more elaborate, co-evolving microbiomes that are well studied in humans and insects. But as we looked at a broader set of smaller marine animals, it became clear that the microbiomes of bigger creatures are likely exceptions, not the rule.”
The study found that distantly related but coexisting invertebrates tend to share many of the same bacteria, suggesting that guilds of microorganisms preferentially associated with animals, but not tied to any specific host lineage, are the main drivers of the ecological relationship.
Dr. Keeling and colleagues sequenced the microbiomes from 1,037 animals from 21 phyla, covering most animals. Some of the lineages of animals sampled more broadly included Annelida (ringed worms), Arthropoda (the largest phylum in the animal kingdom) and Nematoda (a phylum of unsegmented, cylindrical worms). The researchers also collected samples from the surrounding habitats in British Columbia, Canada and Curaçao, a Dutch Caribbean island.
“Studying such a broad range of animals was crucial—in a smaller study a number of prevalent bacteria may have been mistaken for host-specific symbionts,” says Dr. Corey Holt, a postdoctoral fellow at UBC and one of the study’s first authors. “We found most bacteria were only present in some individuals of a species, and most of these were also present other host species in the same environment.”
Dr. Keeling says the next step is to take a few of the more interesting groups and dig deeper to see how microbiomes evolved within that group to clarify the time scales at which different evolutionary processes are operating.
The findings were published recently in the journal Nature Microbiology.