The Survival Secrets of Wearing Rare Animal Microbiomes

New Zealand’s critically endangered kākāpō, the world’s heaviest parrot, is flightless and nocturnal, with scented moss green feathers, odd face and mustache, up to 90 lifespan years and a gut microbiome composed almost entirely of bacteria Escherichia coli. Like humans, other animals carry billions of bacteria, viruses, archaea and fungi in their digestive tracts, on their skin and elsewhere: internal ecosystems that help them extract nutrients from food, fight pathogens and develop their immunity. Today, as genetic sequencing becomes cheaper and more advanced, scientists are examining the distinctive microbiomes of endangered animals, providing information that could help avert extinctions.

Such research has revealed that kākāpō are weird inside and out, says University of Auckland microbial ecologist Annie West: “Their microbiome is pretty weird, like everything else about them. About 250 kākāpō remain on five remote, predator-free islands, where they are intensively managed by New Zealand wildlife officials. In 2019, government staff and volunteers collected fresh, brownish-green feces and nesting material from 67 growing chicks and sent the samples to West for DNA analysis.

E.coli is ubiquitous in the human digestive system, but it only makes up a small percentage of the bacteria that live there. Previous research had shown that this microbe dominates the guts of adult kākāpō; the proportion varies considerably from individual to individual and in some cases it represents 99% of the entire microbiome. The new study by West and colleagues, reported in animal microbiomefound that shortly after hatching a kākāpō, E.coli already forms the microbial majority in its gut. And this dominance only increases as the chick grows.

“It’s very unusual. If you had seen it in a human, you would be worried,” West says. It is not yet known if this is bad for the kākāpō, but such a homogenous microbiome can be of concern because it may not perform all the functions that a species needs. “If you’ve lost diversity, you’ve potentially lost some microbiome functionality,” adds West. The researchers also found that when they fed kākāpō chicks additional parrot baby food, a different bacteria took over their microbiome instead.

The simplified kākāpō microbiome can be partially explained by the bird’s extreme rarity. Other studies have shown that when animal populations dwindle or fragment, some of the microbes they harbor are also lost, says Lifeng Zhu, an ecologist at Nanjing Normal University in China, who was not involved in the new works. “In addition to the diversity of ecosystems and species, we also need to conserve the diversity of the microbiome inside the body of animals,” Zhu says. Climate change, degraded habitats, contact with humans and time spent in captivity can all drastically alter an animal’s microbiome, he explains. And when humans start stepping in to save endangered species, we can have unintended effects on the miniature worlds within.

Zhu’s own research has shown that giant pandas kept in breeding facilities harbor completely different microbes than wild pandas, mainly because they eat different foods. When captive pandas are released, their microbiome must undergo a year-long transformation, during which they are more likely to get sick. “We realized that pandas needed the wildness of their gut microbiota,” Zhu says, “and not just the wildness of their behavior.”

Biologists are still cataloging what microbes live on and inside the most endangered species, and how those communities change over time, says Elizabeth Dinsdale, a marine biologist at Flinders University who dives with sharks. to collect samples of their skin microbes. About 90% of the microorganisms she found are new to science, and her team identified different populations of whale sharks by their typical skin microbiomes.

The next big question is exactly what all of these microorganisms do for their hosts. Whole genome sequencing can provide clues by revealing the genes that make proteins for tasks such as fiber digestion, salt tolerance and heavy metal handling. The culture of colonies in the laboratory, which makes it possible to confirm the role of a microorganism, is currently slow, expensive and difficult for many microbes. But emerging robotic technology promises to speed up the process, allowing scientists to observe how each microbe acts in concert with others.

A few researchers are already experimenting with microbiome engineering. For example, the mucus microbiomes of corals are sensitive to temperature and pollution; seas that are too warm can encourage corals to eject the symbiotic microalgae they depend on, causing bleaching. In Australia, Dinsdale says, scientists are testing whether they can protect corals from the climate by treating them with “a kind of microbial elixir” of bacteria more accustomed to temperature fluctuations. Other Australian ecologists have shown that it is possible to alter koala microbiomes with faecal transplants so that the iconic marsupials can digest different species of eucalyptus.

In the United States, the laboratory of Valerie J. McKenzie at the University of Colorado at Boulder is using probiotics to try to save boreal toads from the fungal disease chytrid. Amphibians have a rich microbiome on their mucus-covered skin, where the devastating fungus Batrachochytrium dendrobatidis attacks. McKenzie’s team identified a potent antifungal bacterium that is found naturally in the Rocky Mountain habitat of endangered toads and in small amounts on their skin. The group showed in the lab that dousing toads with this probiotic microbe increased their ability to survive a fungal infection by 40%.

Next, McKenzie and her colleagues captured young wild toads and set them up in spa-like “aqua hotels” to bathe in the probiotic for 24 hours before release. “You have to hit them in the perfect development time window” for the treatment to work, McKenzie says. When the treated toads were recaptured, they showed less disease than the controls.

West hopes his microbiome research will one day lead to similar treatments for kākāpō. At the very least, she says, now that the typical gut makeup of birds is known, systematic analysis of kākāpō poop could give conservation managers early warning signs of disease. “The idea is that instead of taking invasive samples, you could use microbiome profiling to identify when an animal might be sick, even if you don’t see visible symptoms yet,” West says. “And that’s starting to have big implications for conservation programs.”

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