As gut bacteria garner more attention every day, scientists are starting to make forays into uncharted waters: the microbes of marine mammals.
The collection of benign bacteria living within our bodies, our “microbiota,” helps us digest food, ward off infection, and has even been linked to mood and behavior. Research on microbial communities has branched out from humans to include terrestrial animals, plants and soil bacteria, and even homes and office spaces. Marine mammals are tough to study, though, as they are far-flung and elusive. Sample collection usually involves following dolphins or whales until they defecate, then rushing to scoop the poop before it sinks.
A recent study, published in Nature Communications (February 2016), took a more in-depth approach, directly sampling captive marine mammals to investigate their internal microbial world. The researchers found that dolphins harbor a unique suite of bacteria, unlike that of any other mammal. Moreover, this unique community can be found within dolphins across the world.
“It’s not eating fish or living in the water that is driving this strange microbiota composition,” says lead author Elisabeth Bik, a microbiologist formerly at Stanford University. “It is something that is very specific for the dolphin and whale lineage.”
In addition to discovering some previously uncharacterized bacteria in dolphin samples, Bik and her colleagues at Stanford found that bacterial communities in dolphins were distinct from those in both the surrounding waters and in sea lions that lived in the same location and ate the same food.
Investigating marine mammal microbes allows scientists to begin filling in gaps in our understanding of marine mammal health and evolution. In land animals, for example, the gut microbes of carnivores are often distinct from those of herbivores. Researchers have also been able to trace how closely animals are related to one another based on similarities in their suites of gut bacteria.
How might diet, environment, and evolutionary ancestry play a role in microbial composition within marine mammals? This project provided an opportunity to look at this question in a very different physical environment compared to terrestrial animal studies, says senior author David Relman, of Stanford.
Relman’s lab collaborated with the US Navy’s Marine Mammal Program to characterize the bacteria living within captive dolphins and sea lions. Marine Mammal Program scientists sampled the mouths, stomachs, and rectums of 38 dolphins and 18 sea lions living in San Diego Harbor. Relman’s group identified the kinds of bacteria within each sample type by analyzing a piece of genetic code found in all bacteria with slightly different versions. These different versions help classify the bacteria into different groups, or phyla.
To detect any overlap between the marine mammals and their environment, the researchers tested the animals’ food—the same fish and squid are on the Navy’s menu for both sea lions and dolphins—and scooped up the seawater immediately adjacent to the animals’ mouths. They thought that marine mammals, in constant contact with a rich environmental soup of bacteria, could harbor bacteria similar to the surrounding waters. Or, that dolphins and sea lions might share some bacteria found in their food, akin to lactobacilis-infused yogurt boosting that bacteria’s presence in human intestines.
What the scientists found, instead, was very little similarity in the animals’ bacteria and the bacteria in seawater. Additionally, sea lion and dolphin bacterial communities were very different, despite originating from animals living in the same water and eating the same diet.
To probe further into that enigma, the scientists compared the bacterial communities of captive dolphin to those of 10 wild dolphins in Sarasota, Florida. Dolphin bacterial suites were a closer match to one another, regardless of location, than to those of sea lions.
Bik was intrigued by the strange bacterial communities of dolphins, and how unique they were compared to other mammals. In particular, dolphin stomachs contained a high number of Tenericutes, a group of bacteria not typically seen in mammals. Bik speculated that perhaps the bacteria could help digest fish, as dolphins swallow their food whole, though she called it “a very wild hypothesis.”
Fecal samples of wild dolphins, and even the freshwater Yangtze finless porpoise, also contain unusually high levels of Tenericutes and bacterial communities very similar to those of the captive dolphins in San Diego Harbor.
How might that be possible? A recent Science paper described how our gut microbes evolved with us, splitting off from the microbes inside chimpanzees, bonobos, and gorillas millions of years ago. It is possible that something similar happened with dolphins, sea lions, and other marine mammals. As animals evolve and diverge from one another to form new species, the bacteria living within them are also cut off from one another.
Andrew Moeller, lead author of the Science paper and an evolutionary biologist at University of California, Berkeley, said in an email that studying marine mammals is a great way to measure the interplay of environment and the animal’s biology and bacterial community composition.
To shed more light on the source of bacterial diversity, Alix Switzer, a veterinarian and graduate student in Relman’s lab, is conducting a broader survey of marine mammals and their internal bacteria. She has amassed a collection of oral and rectal samples from 11 kinds of marine mammals—ranging from manatees to orcas to sea otters—and their closest evolutionary relatives.
But she isn’t stopping there. To further step back into evolutionary history, she is also testing bacteria from terrestrial animals more distantly related to marine mammals. One example: sampling bacteria from a manatee, an elephant, an aardvark and an elephant shrew.
Switzer hopes her bacterial analyses will uncover a larger pattern that fits the mammalian tree of life. It may ultimately help us determine when and how gut bacteria hitched a ride into the ocean with different kinds of marine mammals.