In humans, the gut microbiome is an extensively researched area, with hundreds of hypotheses concerning the microbiome’s role in everything from simple digestion to complex disease. The gut microbiome of fish is not as popular a research topic and has been poorly understood through the years. Now, a new study published in Proceedings of the Royal Society B suggests the microbial communities within fish are as diverse as coral reefs and may actually be an important functional trait.
Douglas Rasher, senior research scientist at Bigelow Laboratory for Ocean Sciences, and his colleagues studied the feeding behaviors of five common Caribbean fish species and found that they markedly differ in what they eat and where they feed on the reef. Using genetic sequencing and computing techniques, the researchers identified the microbes collected from within each fish's gut—and discovered that each herbivore species harbors a unique gut microbiome.
“The microbiome appears to be a defining feature of each herbivorous fish species, as unique as its size or feeding behavior," said Rasher, senior author of the paper.
While some gut microbes live broadly throughout the ocean, the study reveals that other resident microbes appear to have a symbiotic relationship with fish. Furthermore, those “symbionts” are loyal to just one type of fish.
For example, Lachnospiraceae ASV microbes were only found in the intestines of A. coeruleus and A. tractus. The Lachnospiraceae class of microbiomes belong to a family of giant enteric microbes that are known to help Indo-Pacific surgeonfishes digest and assimilate brown algal polysaccharides. A. coeruleus and A. tractus also selectively consume brown macroalgae and must digest and assimilate the algae's carbohydrate-rich content. Rasher’s study suggests these Lachnospiraceae microbes benefit the Caribbean fish in much the same way their “relatives” benefit their Indo-Pacific counterparts.
Microbiome and fish relatedness may play an even bigger role in the reef than expected. While the symbionts the scientists discovered had not been identified previously, genetic testing revealed that their closest known relatives are actually microbes living in the intestines of other reef fish. The researchers mapped the genetic relationships among these microbes, offering a new perspective on the relatedness of fish and their ecology around the globe.
“Our symbionts were remarkably similar to microbes found within the guts of related fishes in other, distant oceans,” said Jarrod Scott, a postdoctoral researcher at the Smithsonian Tropical Research Institute and lead author of the paper. “Such a finding indicates that herbivorous fishes that are separated by millions of years of evolution and thousands of kilometers nonetheless harbor similar microbes.”
Scott, Rasher and their collaborators want to continue their work by revealing the functions of symbionts in the gut, and how specific microbes aid their fish hosts.
“Our study is an exciting advance that sets the stage for future research in this area,” Rasher said. “Treating microbiomes as a fundamental characteristic of fish can help us understand how the ocean functions and the hidden roles of microbes in nature.”
Photo: An herbivorous fish grazes on a Caribbean coral reef. Credit: José Alejandro Alvarez/Bigelow Laboratory for Ocean Sciences