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Background  Differences between individuals in their gastrointestinal microbiomes can lead to variation in their ability to persist on particular diets. Koalas are dietary specialists, feeding almost exclusively on  Eucalyptus  foliage but many individuals will not feed on particular  Eucalyptus  species that are adequate food for other individuals, even when facing starvation. We undertook a faecal inoculation experiment to test whether a koala’s gastrointestinal (GI) microbiome influences their diet. Wild-caught koalas that initially fed on the preferred manna gum ( Eucalyptus viminalis)  were brought into captivity and orally inoculated with encapsulated material derived from faeces from koalas feeding on either the less preferred messmate ( E. obliqua ; treatment) or manna gum (control).    Results  The gastrointestinal microbiomes of wild koalas feeding primarily on manna gum were distinct from those feeding primarily on messmate. We found that the gastrointestinal microbiomes of koalas were unresponsive to dietary changes because the control koalas’ GI microbiomes did not change even when the nocturnal koalas were fed exclusively on messmate overnight. We showed that faecal inoculations can assist the GI microbiomes of koalas to change as the treatment koalas’ GI microbiomes became more similar to those of wild koalas feeding on messmate. There was no overall difference between the control and treatment koalas in the quantity of messmate they consumed. However, the greater the change in the koalas’ GI microbiomes, the more messmate they consumed after the inoculations had established.    Conclusions  The results suggest that dietary changes can only lead to changes in the GI microbiomes of koalas if the appropriate microbial species are present, and/or that the koala gastrointestinal microbiome influences diet selection.    Electronic supplementary material  The online version of this article (10.1186/s42523-019-0008-0) contains supplementary material, which is available to authorized users.

Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala