new zealand critically endangered The world’s heaviest parrot, the kākāpō, is a flightless, nocturnal parrot with fragrant moss-green plumage, an oddly bearded face, and a lifespan of up to 90 years—with a gut microbiome made up almost entirely of bacteria Escherichia coli. Like humans, other animals harbor trillions of bacteria, viruses, archaea and fungi in their guts, skin and elsewhere: internal ecosystem Help them extract nutrients from food, fight pathogens and boost immunity. Now, as genetic sequencing becomes cheaper and more advanced, scientists are studying the unique microbiomes of endangered animals, providing insights that may help avert extinction.
Studies like this show that kākāpō are weird inside and out, says Annie West, a microbial ecologist at the University of Auckland: “Their microbiomes are very weird—like everything else about them.” About 250 kakapos remain on five remote, predator-free islands that are centrally managed by New Zealand wildlife officials. In 2019, government workers and volunteers collected fresh brown-green feces and nest material from 67 growing chicks and sent samples to West for DNA analysis.
Escherichia coli It’s ubiquitous in the human digestive system, yet it makes up only a small fraction of the bacteria that live there.Previous Research This microbe has been shown to control the guts of adult kākāpō; the proportion varies widely between individuals, and in some cases it makes up 99 percent of the entire microbiome. The new study by West and her colleagues is reported in animal microbiomeNot long after the kakapo were found to hatch, Escherichia coli A microbial host has formed in its gut. And that dominance will only increase as the chicks get older.
“It’s unusual. If you saw it in humans, you’d be worried,” West said. It’s unclear whether this is detrimental to kākāpō, but such a homogeneous microbiome may be of concern because it might not be able to perform all the functions a species needs. “If you lose diversity, you may lose some function of the microbiome,” West added. The researchers also found that when they supplemented kākāpō chicks with baby parrot feed, another bacteria took over their microbiomes instead.
The kākāpō’s simplified microbiome may be due in part to the bird’s extreme rarity. Other studies have shown that when animal populations decrease or become fragmented, some of their host’s microbes are also lost, says Lifeng Zhu, an ecologist at Nanjing Normal University in China, who was not involved in the new work. “In addition to ecosystem and species diversity, we also need to protect microbiome diversity in animals,” Zhu said. He explains that climate change, habitat degradation, contact with humans and time in captivity can all drastically alter an animal’s microbiome — and when humans start intervening to save endangered species, we may have unintended effects on the miniature worlds inside animals .
Zhu’s own research has show The microbes in giant pandas raised in captive facilities are completely different from those in the wild, mainly because they eat different foods. When captive pandas are released, their microbiomes must undergo a year-long transformation, during which time they become more susceptible to illness. “We realized that giant pandas need wildness in their gut microbiomes,” Zhu said, “not just wildness in their behavior.”
Elizabeth Dinsdale, a marine biologist at Flinders University who dives with sharks and collects samples of their skin microbes, says biologists are still learning which microbes live on and in most endangered species classification, and how these microbial communities have changed over time. About 90 percent of the microbes she found were new to science, and her team identified distinct populations of whale sharks by their typical skin microbiomes.
The next big question is what all these microbes are actually doing for their hosts. Whole-genome sequencing can provide clues by revealing genes that make proteins for tasks such as digesting fiber, tolerating salinity and handling heavy metals. Growing colonies in the lab helps confirm the role of microbes, but is currently slow, expensive and difficult for many microbes. But emerging robotics promise to speed up the process, allowing scientists to watch how each microbe works with other microbes.
Some researchers are already experimenting with microbiome engineering. For example, the slime microbiome of corals is sensitive to temperature and pollution; excessively warm oceans can prompt corals to expel the symbiotic microalgae they depend on, leading to bleaching. In Australia, scientists are testing whether they can withstand climate change by treating corals with “a sort of microbial elixir” from bacteria more accustomed to temperature fluctuations, Dinsdale said. Other ecologists in Australia have shown that it is possible to alter a koala’s microbiome through fecal transplants so that the iconic marsupial can digest a different species of eucalyptus.
In the US, the lab of Valerie J. McKenzie at the University of Colorado Boulder is using probiotics to try to protect northern toads from chytridiomycosis.Amphibians’ slime-covered skin harbors rich microbiome, home to devastating fungus BAD attack. McKenzie’s team identified a strong antifungal bacterium that occurs naturally in the endangered toad’s Rocky Mountain habitat and in small amounts on their skin.group Demonstrated in the lab Dousing toads in this probiotic boosted their ability to survive fungal infections by 40%.
Next, McKenzie and her colleagues captured young wild toads and placed them in a spa-like “water hotel,” bathing them in probiotics for 24 hours before releasing them. “You have to hit them in the perfect developmental time window” for the treatment to work, McKenzie said. When the treated toads were recaptured, they had less disease than the control group.
West hopes her microbiome research will one day lead to similar treatments for kākāpō. At the very least, she says, regular analysis of kākāpō poop could provide conservation managers with early warnings of disease now that the typical gut makeup of birds is known. “The idea is that instead of taking an invasive sample, you can use microbiome analysis to identify when an animal might be sick, even if you haven’t seen any obvious symptoms,” West said. “That’s starting to have a big impact on conservation planning.”
