Hakai Magazine

Coastal science and societies

Rainbow parrotfish (Scarus guacamaia) swimming above coral reef
The microorganisms living in the guts of fish, such as this rainbow parrotfish swimming in a Florida reef, may dictate their dietary choices. Photo by Danita Delimont/Alamy Stock Photo

Do Fish Tummy Bugs Dictate Their Diets?

A preliminary study of Florida fish microbes hints at how and why each fish fills a unique ecological role.

Authored by

by Nancy Averett

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Like a detective tailing a suspect, marine ecologist Tom Adam lurked in the turquoise waters of the Florida Keys National Marine Sanctuary a few years ago trying to spot parrotfish, rabbitfish, and surgeonfish, feeding on algae that grow on the reef. When Adam spotted one, he followed it, but not too close. He didn’t want to scare the fish away, yet needed to be near enough to see precisely where it nibbled.

“We watched very carefully to see exactly where [each] fish was taking a bite,” says Adam, who along with a colleague from the University of California, Santa Barbara, logged more than 1,000 bites. They then identified the exact types of algae living in those spots.

Their work is part of a recent study that shows each fish species eats different types of algae on different parts of the reef, and that each species has a unique set of microorganisms—or microbiome—in its gut.

The team used DNA sequencing and computational analysis to identify and sort the millions of gut microbes taken from fish harvested in the same waters, zeroing in on the 59 that were most dominant. Each species harbored a unique subset of that 59. The bacteria Lachnospiraceae, which is known to ferment diverse plant carbohydrates, was only found in the surgeonfish, for example, and the bacteria Erysipelotrichaceae, which has been linked to protein digestion, was only found in the parrotfish.

The researchers hope to use the data in future studies that examine the microbes’ genetic interactions to see if a fish’s unique gut microbiome may drive it to select different algae. “That’s sort of the big burning question,” says Douglas Rasher, a marine ecologist at the Bigelow Laboratory for Ocean Sciences in Maine and coauthor of the paper. “To what degree are these microbes playing a role in shaping the feeding behavior of the fish, versus responding to the feeding activities of the fish?”

Rasher has previously published research showing reefs need a diversity of fish species that forage on different types of algae to stay healthy.

Microbes are essential for every living creature, allowing plants and animals to take energy from food and to fight against pathogens. As DNA sequencing gets ever cheaper and more accurate, research on human microbiomes has exploded. Researchers have found that human bodies host 100 trillion microbes, which could affect everything from autism to obesity. Ecologists are increasingly recognizing that these colonies could shed new light on why different organisms behave the way they do.

Marine biologists have evidence, for example, that a microbe living in the bobtail squid allows it to camouflage with a bioluminescent glow that looks like moonlight on the water. “It’s an extremely specific, coevolved symbiotic association between the squid and a particular microbe,” says Jarrod Scott, a postdoctoral researcher at the Smithsonian Tropical Research Institute and lead author on the new microbiome paper.

This work by Rasher, Scott, and colleagues is the first look at microbes in Caribbean fish. Surprisingly, when they compared their species’ unique microbial pools against publicly available global databases, they found similar microbiomes in reef fish living thousands of kilometers away in the Indo-Pacific Ocean. “That was one of our most unexpected and interesting findings,” Rasher says. “These Caribbean and Indo-Pacific fish species have been separated by millions of years of evolution and live thousands of miles apart, yet they share similar microbes.”

Although the researchers can’t yet say if a symbiotic relationship between these reef fish and their microbiomes dictates their diets, the study is an important first step, says Jonathan Lefcheck, a marine ecologist at the Smithsonian Institution, who was not involved in the research. It narrows down which microbes investigators should pay attention to, he says, if they want to link microbes to feeding behavior. That might help, he notes, to understand just how critical each species is within an ecosystem, adding heft to arguments for their conservation.