Modern microbiome was created by bacterial ‘guilds’

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

Biologists at the University of British Columbia (UBC) have found that even the smallest marine invertebrates, some of which are barely bigger than single-celled protists, have their own unique microbial communities, or microbiomes.

The study shows that just like people, many different kinds of animals have microbiomes. But what’s even more surprising is that there isn’t much of a link between how closely related most animals are and how similar their microbiomes are. This is something that most people thought was true based on studies of humans, larger mammals, and insects.

“This tells us a lot about where microbiomes came from and how they change now,” says Dr. Patrick Keeling, an evolutionary microbiologist at UBC and the lead author of a paper that came out today in Nature Microbiology.

“People might think that the goal of a microbiome is to help the host animal and that the microbiome and the host animal evolve together. But the bacteria couldn’t care less about helping the animal host. They have their own plans.”

“Most animals have a community of bacteria that are good at living in animals. It is likely that this “professional guild” of animal specialists gave rise to the more complex microbiomes that humans and insects have and that change together. But as we looked at a wider range of smaller marine animals, it became clear that the microbiomes of bigger animals are probably the exception, not the rule.”

The team found that the microbiomes of the small creatures were different from the microbiomes of the microbes in their surroundings. Sometimes, the microbiomes of closely related invertebrates were also different.

In what may be the largest study of its kind, Dr. Keeling and his colleagues sequenced the microbiomes of 1,037 animals from 21 phyla. This means that most animals were included in the study. Animals from the Annelida (ringed worms), Arthropoda (the largest phylum in the animal kingdom), and Nematoda (parasitic worms) groups were sampled in a more general way (a phylum of unsegmented, cylindrical worms). The researchers also took samples from the surrounding areas in British Columbia, Canada, and Curacao, a Dutch Caribbean island.

“It was important to look at such a wide range of animals,” says Dr. Corey Holt, a postdoctoral fellow at UBC and one of the study’s first authors. “In a smaller study, a number of common bacteria might have been mistaken for host-specific symbionts.”

“We found that most bacteria were only found in some individuals of a species, and most of these bacteria were also found in other host species in the same environment.”

Investigating the time scales of evolution

Dr. Keeling says that the goal of this survey was to look at an incredibly wide range of animals. “The next step is to look more closely at a few of the more interesting groups to see how microbiomes evolved within that group. This will help us figure out how long different kinds of evolution take.”

Further 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

Journal information: Nature Microbiology

Source: University of British Columbia