A highly specialized diet combined with rampant sexually transmitted infections are threatening Australia's cuddly emblematic marsupial. Habitat destruction and human encroachment have lowered numbers in the past few decades but "chlamydial disease is rapidly becoming the major threat to many koala populations," says Peter Timms, an adjunct professor at Queensland University of Technology and koala genetics expert. This bacterial overgrowth can cause infertility, blindness and even death. The disease currently infects as many as half the estimated 80,000 wild koalas in Australia, the only place where they live in the wild.

To combat this scourge animal caretakers have deployed antibiotics on a large scale—and with relative success. Sick animals are brought into a rehabilitation facility, treated with a full course of broad-spectrum antibiotics (such as chloramphenicol or enrofloxacin) and then released back into the wild.

But some researchers are now worried that these powerful drugs are wrecking koalas' gut microbiotas—in particular the microbes that digest otherwise toxic eucalyptus leaves, koalas' only food source. "Koalas represent a fascinating case study of a rare extreme in mammals—where we know specific functions of the microbiome that are required for survival," says Jonathan Eisen, an evolutionary biologist at the University of California, Davis.

Now Katie Dahlhausen, a doctoral student in Eisen's lab, is launching a study to assess just how antibiotics are altering these iconic animals' microbes. She plans to embark later this year on a crowdfunded expedition to sample koala poop in Australia. Genetic signatures from microbes in the feces should reveal which microbes remain after antibiotic treatments—and how continued treatments might affect future generations.

Lasting legacy
In humans antibiotics can cause mild side effects, such as diarrhea and opportunistic infections, as the drugs wipe out native flora. But most people typically rebound quickly and eventually reestablish a functioning gut microbial ecosystem—even if it is not identical to the one they had prior to treatment.

For koalas, however, losing a particular microbe species could hamper their ability to process their sole food source. Eucalyptus leaves are not very nutritious and contain high levels of tannins, which are toxic to most mammals. Koalas have an especially long and slow digestive process that gives them more time to absorb precious fuel and nutrients from this inauspicious food source. But part of the digestive power likely derives from tannin-protein-complex-degrading enterobacteria—microbes that can break down tannins. If these bacteria are as key as researchers suspect, "their removal will impede the koalas' ability to get nutrients from an already quite poor source of energy," says Alex Greenwood, head of wildlife diseases at the Leibniz Institute for Zoo and Wildlife Research in Berlin, who co-authored an analysis of koala microbiotas earlier this month. Even with a healthy digestive system koalas spend most of the day sleeping to conserve what energy they do receive from their diets—and nearly all their precious waking hours eating, he notes.

An altered microbiota might also put future generations at risk by slashing the traditional microbial inheritance passed from mother to offspring. As joeys wean, they eat a substance from the mother known as pap. An excretion similar to feces, pap is rich in microbes from the mother's digestive tract, including a particularly high number of the live tannin-protein-complex-degrading enterobacteria. "Pap is so critical to the koala's biology, foster providers still use milk and pap from a donor mother when caring for joeys," Dahlhausen says. She suspects antibiotic treatment of koala females might decrease or wipe out their loads of critical bacteria that they can pass along to their young.

Despite these suspected microbial assaults, halting chlamydia treatment is not currently an option, with the infection continuing to spread. So researchers are looking for alternatives to standard antibiotics. In 2013 Timms and collaborators discovered a gene (the koala interferon gamma gene) that appears to help regulate the immune system and fend off infections, including chlamydia. The group is now using this genetic information to create a vaccine to protect against this sexually transmitted infection, and it has shown promising results from its first field trial, Timms says. He is also at work on more targeted drugs that will "kill only the chlamydia and not the koala's friendly and essential gut bacteria," he says.

Dahlhausen's work and others are also broadening our view of the animal kingdom. "We tend to think of an animal as a unique single individual but all animals—including humans—represent an immense community of microbes," Greenwood notes. "The more we learn, the more we realize how important these microbes are in making each one the individual they are. A koala is a koala in part because of the bacteria that lives in it and on it." And perhaps the new research will help show a microbial path forward to keep them that way.