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Background Captive rearing is often critical for animals that are vulnerable to extinction in the wild. However, few studies have investigated the extent to which captivity impacts hosts and their gut microbiota, despite mounting evidence indicating that host health is affected by gut microbes. We assessed the influence of captivity on the gut microbiome of the Brown Kiwi (Apteryx mantelli), a flightless bird endemic to New Zealand. We collected wild (n = 68) and captive (n = 38) kiwi feces at seven sites on the north island of New Zealand. Results Using bacterial 16 S rRNA and fungal ITS gene profiling, we found that captivity was a significant predictor of the kiwi gut bacterial and fungal communities. Captive samples had lower microbial diversity and different composition when compared to wild samples. History of coccidiosis, a gut parasite primarily affecting captive kiwi, showed a marginally significant effect. Conclusions Our findings demonstrate captivity’s potential to shape the Brown Kiwi gut microbiome, that warrant further investigation to elucidate the effects of these differences on health.

Human modification of the environment, particularly through land-use change, often reduces animal species diversity. However, the effect of land-use change on the gut microbiome of wildlife in human-dominated landscapes is not well understood despite its potential consequences for host health. We sought to quantify the effect of land-use change on wild bird gut microbiomes in a countryside landscape in Costa Rica, comprising a range of habitat types, ranging from primary and secondary forests to diversified and monoculture farms. We collected 280 fresh fecal samples from individuals belonging to six common species of saltator, thrushes, and warblers at 24 sites across this land-use gradient. Through 16S rRNA community profiling, we found that bacterial species composition responded to host species identity more strongly than to habitat type. In addition, we found evidence that habitat type affected microbial composition only for two of the six bird species. Our findings indicate that some host species and their microbiota may be more vulnerable to human disturbances than others.

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Microbial communities in the honey bee gut have emerged as a model system to understand the effects of host-associated microbes on animals and plants. The specific distribution patterns of bacterial associates among honey bee gut regions remains a key finding within the field. The mid- and hindgut of foraging bees house a deterministic set of core species that affect host health. In contrast, the crop, or honey stomach, contains a more diverse set of bacteria that is highly variable in composition among individual bees. Whether this contrast between the two gut regions also applies to fungi, another major group of gut-associated microbes, remains unclear despite their potential influence on host health. In honey bees caught foraging at four sites across the San Francisco Peninsula, we found that fungi were much less distinct in species composition between the crop and the mid- and hindgut than bacteria. Unlike bacteria, fungi were highly variable in composition throughout the gut, and much of this variation was attributable to bee collection site. These patterns suggest that the fungi may be passengers rather than functionally significant gut symbionts. However, many of the fungi we found in the bees have been recognized as plant pathogens. Assuming that some fungi remain viable after passage through the gut, the distribution patterns we report here point to the potential importance of honey bees as vectors of fungal pathogens and suggest a more prominent role of honey bees in plant pathogen transmission than generally thought.