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The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

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Human activities create novel food resources that can alter wildlife–pathogen interactions. If resources amplify or dampen, pathogen transmission probably depends on both host ecology and pathogen biology, but studies that measure responses to provisioning across both scales are rare. We tested these relationships with a 4-year study of 369 common vampire bats across 10 sites in Peru and Belize that differ in the abundance of livestock, an important anthropogenic food source. We quantified innate and adaptive immunity from bats and assessed infection with two common bacteria. We predicted that abundant livestock could reduce starvation and foraging effort, allowing for greater investments in immunity. Bats from high-livestock sites had higher microbicidal activity and proportions of neutrophils but lower immunoglobulin G and proportions of lymphocytes, suggesting more investment in innate relative to adaptive immunity and either greater chronic stress or pathogen exposure. This relationship was most pronounced in reproductive bats, which were also more common in high-livestock sites, suggesting feedbacks between demographic correlates of provisioning and immunity. Infection with both Bartonella and haemoplasmas were correlated with similar immune profiles, and both pathogens tended to be less prevalent in high-livestock sites, although effects were weaker for haemoplasmas. These differing responses to provisioning might therefore reflect distinct transmission processes. Predicting how provisioning alters host–pathogen interactions requires considering how both within-host processes and transmission modes respond to resource shifts.This article is part of the theme issue ‘Anthropogenic resource subsidies and host–parasite dynamics in wildlife’.

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The ecological mechanisms that sustain high species richness in Neotropical bat communities have attracted research attention for several decades. Although many ecologists have studied the feeding behavior and diets of Neotropical bats on the assumption that food is a limiting resource, other resource axes that might be important for species coexistence are often ignored. Diurnal refugia, in particular, are a crucial resource for bats, many of which exhibit conspicuous morphological or behavioral adaptations to the roost environment. Here we report and analyze information about roost occupancy based on >500 field observations of Amazonian bats. Statistical analyses of these data suggest the existence of distinct groups of species roosting (1) in foliage, (2) exposed on the trunks of standing trees, (3) in cavities in standing trees, (4) in or under fallen trees, (5) beneath undercut earth banks, and (6) in arboreal insect nests; additionally, we recognize other groups that roost (7) in animal burrows, and (8) in rocks or caves. Roosting-guild membership is hypothesized to have a filtering effect on Amazonian bat community composition because some types of roosts are absent or uncommon in certain habitats. Among other applications of our results, cross-classifying bat species by trophic and roosting guilds suggests that the often-reported deficit of gleaning animalivores in secondary vegetation by comparison with primary forest might reflect habitat differences in roost availability rather than food resources. In general, ecological and evolutionary studies of Neotropical bats would be enhanced by considering both trophic-and roosting-guild membership in future analyses, but additional fieldwork will be required to determine the roosting behavior of many data-deficient species.