Although recent studies have revealed that gut fungi may play an important functional role in animal biology and health, little is known concerning the effects of anthropogenic pressures on the gut mycobiome. Here, we examined differences of the gut mycobiome in wild and captive populations of Tibetan macaques (Macaca thibetana) targeting the fungal internal transcribed spacer (ITS) and using next generation sequencing. Our findings demonstrate that the diversity, composition, and functional guild of the Tibetan macaque gut mycobiome differ across populations living in different habitats. We found that Tibetan macaques translocated from the wild into a captive setting for a period of 1 year, were characterized by a reduction in fungal diversity and an increase in the abundance of potential gut fungal pathogens compared to wild individuals. Furthermore, we found that the relative abundance of two main fungal guilds of plant pathogens and ectomycorrhizal fungi was significantly lower in captive individuals compared to those living in the wild. Our results highlight that, in addition to bacteria, gut fungi vary significantly among individuals living in captive and wild settings. However, given limited data on the functional role that fungi play in the host’s gut, as well as the degree to which a host’s mycobiome is seeded from fungi in the soil or ingested during the consumption of plant and animal foods, controlled studies are needed to better understand the role of the local environment in seeding the mycobiome.

The gut microbiome is expected to adapt to the varying energetic and nutritional pressures in females of different reproductive states. Changes in the gut microbiome may lead to varying nutrient utilizing efficiency in pregnant and lactating female primates. In this study, we examined variation in the gut bacterial community composition of wild female Tibetan macaques (Macaca thibetana) across different reproductive states (cycling, pregnancy and lactation). Fecal samples (n = 25) were collected from ten adult females harvested across different reproductive states. Gut microbial community composition and potential functions were assessed using 16 S rRNA gene sequences. We found significant changes in gut bacterial taxonomic composition, structure and their potential functions in different reproductive states of our study species. In particular, the relative abundance of Proteobacteria increased significantly during pregnancy and lactation. In addition, the relative abundance of Succinivibrionaceae and Succinivibrio (Succinivibrionaceae) were overrepresented in pregnant females, whereas Bifidobacteriaceae and Bifidobacterium (Bifidobacteriaceae) were overrepresented in lactating females. Furthermore, the relative abundance of predicted functional genes of several metabolic pathways related to host’s energy and nutrition, such as metabolism of carbohydrates, cofactors and vitamins, glycans and other amino acids, were enriched in pregnancy and lactation. Our findings suggest that changes in the gut microbiome may play an important role in meeting the energetic needs of pregnant and lactating Tibetan macaques. Future studies of the “microbial reproductive ecology” of primates that incorporate food availability, reproductive seasonality, female reproductive physiology and gut inflammation are warranted.

Documenting the effects of anthropogenic activities on the gut microbiome of wild animals is important to their conservation practices. Captivity and ecotourism are generally considered two common anthropogenic disturbances on the health of nonhuman primates. Here, we examined the divergences of gut microbiome in different environments of Tibetan macaques. Our results showed that there were no significant differences in the alpha diversity, predominant families and genera of gut microbiomes between wild and tourist groups. However, these indexes decreased significantly in the captive individuals. In addition, the significant differences of beta diversity and community compositions between wild and tourism groups also were detected. In particular, higher potential pathogenic and predicted KEGG pathway of drug resistance (antimicrobial) were detected in the gut microbiome of individuals in captive environment. Our results indicated that living in the wild are beneficial to maintaining gut microbial diversity of Tibetan macaques, while captivity environment is harmful to the health of this macaque. Exploring ways to restore the native gut microbiome and its diversity of captive individual should pay more attention to in the future studies.

Soil is a part of the habitat environment of terrestrial or semi‐terrestrial mammals, which contains a wide variety of microbes. Although the soil microbiome of the host habitat is considered to be a potentially important influence factor on the mammalian gut microbiome and health, few data are currently available to explore the relationship between gut and host habitat soil microbiome in wild primates. Here, marked divergence of the bacterial microbiome in composition and structure between Tibetan macaques (Macaca thibetana) guts and its habitat soil were detected. In addition, we found that most of the core genera abundance and ASVs in the Tibetan macaques' gut bacterial microbiome could be detected in the corresponding soil samples, but with low abundance. However, the core abundant genera abundant in soil are almost undetectable in the gut of Tibetan macaques. Although there are some ASVs shared by gut and soil bacterial microbiome, the abundant shared ASVs in the guts of Tibetan macaques were rare bacterial taxa in the corresponding soil samples. Notably, all the ASVs shared by guts and soil were present in the soil at relatively low abundance, whereas they were affiliated with diverse bacterial taxa. By linking the bacterial microbiome between Tibetan macaques’ gut and its habitat soil, our findings suggest that the predominant bacterial groups from the soil were not likely to colonize the Tibetan macaques' gut, whereas the low‐abundance but diverse soil bacteria could be selected by the gut. Whether these rare and low‐abundant bacteria are permanent residents of the soil or a source of fecal contamination remains to be determined in future study.

The distribution and availability of microbes in the environment has an important effect on the composition of the gut microbiome of wild vertebrates. However, our current knowledge of gut-environmental interactions is based principally on data from the host bacterial microbiome, rather than on links that establish how and where hosts acquire their gut mycobiome. This complex interaction needs to be clarified. Here, we explored the relationship between the gut fungal communities of Tibetan macaques (Macaca thibetana) and the presence of environmental (plant and soil) fungi at two study sites using the fungal internal transcribed spacer (ITS) and next generation sequencing. Our findings demonstrate that the gut, plant and soil fungal communities in their natural habitat were distinct. We found that at both study sites, the core abundant taxa and ASVs (Amplicon Sequence Variants) of Tibetan macaques’ gut mycobiome were present in environmental samples (plant, soil or both). However, the majority of these fungi were characterized by a relatively low abundance in the environment. This pattern implies that the ecology of the gut may select for diverse but rare environmental fungi. Moreover, our data indicates that the gut mycobiome of Tibetan macaques was more similar to the mycobiome of their plant diet than that present in the soil. For example, we found three abundant ASVs (Didymella rosea, Cercospora, and Cladosporium) that were present in the gut and on plants, but not in the soil. Our results highlight a relationship between the gut mycobiome of wild primates and environmental fungi, with plants diets possibly contributing more to seeding the macaque’s gut mycobiome than soil fungi.