The koala is an iconic Australian species. Unfortunately, some wild populations are at risk of extinction. Captive breeding programs aiming to manage endangered populations face high mortality rates of pouch-dwelling koala young. Recently, researchers investigated infant koala mortality rates associated with bacterial infection by analyzing the microbiome of koala pouches. Gene sequencing showed that the pouch microbiomes of successfully bred female koalas were dominated by Muribaculaceae bacteria early in lactation, while mother koalas who lost their young had Enterobacteriaceae-dominated pouch microbiomes. The bacterial species associated with poor reproductive outcomes were shown to be resistant to antibiotics commonly administered to captive koalas. This work could help reduce mortality rates of infant koalas in captive breeding programs, assess medication regimens used to treat captive koalas, and support general studies of at-risk wild koala populations.