Professional 'guilds' of bacteria gave rise to the modern microbiome

University of British Columbia evolutionary microbiologists collecting marine invertebrate samples off Calvert Island, British Columbia, Canada. Credit: University of British Columbia.

Even the smallest marine invertebrates some barely larger than single-celled protists are home to distinct and diverse microbial communities, or microbiomes, according to new research from the University of British Columbia (UBC) biologists. The study underscores that a vast diversity of animals have microbiomes, just as humans do. But more surprisingly, there's little correlation between how closely related most animals are and how similar their microbiomes are something widely assumed to be true based on the study of humans, larger mammals, and insects.

UBC evolutionary microbiologist Dr. Patrick Keeling, senior author of the paper published today in Nature Microbiology said, this says a lot about how microbiomes originated and how they evolve today. 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. 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 team found the microbiomes of the tiny creatures differ from the microbes living in the surrounding environment, and often differed from the microbiome of even closely related invertebrates.

In what might be the broadest study of its kind, 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.

Dr. Corey Holt, a postdoctoral fellow at UBC and one of the study's first authors said, 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. We found most bacteria were only present in some individuals of a species, and most of these were also present in other host species in the same environment.

Dr. Keeling said, this survey was designed to look at an incredibly broad diversity of animals. 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.

Journal Information: Vittorio Boscaro, Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis, Nature Microbiology (2022). DOI: 10.1038/s41564-022-01125-9. www.nature.com/articles/s41564-022-01125-9