Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome

Metagenomic and culture-dependent analysis of Rhinopithecius bieti gut microbiota and characterization of a novel genus of Sphingobacteriaceae

Culture-dependent and metagenomic binning techniques were employed to gain an insight into the diversification of gut bacteria in Rhinopithecius bieti, a highly endangered primate endemic to China. Our analyses revealed that Bacillota_A and Bacteroidota were the dominant phyla. These two phyla species are rich in carbohydrate active enzymes, which could provide nutrients and energy for their own or hosts' survival under different circumstances. Among the culturable bacteria, one novel bacterium, designated as WQ 2009T, formed a distinct branch that had a low similarity to the known species in the family Sphingobacteriaceae, based on the phylogenetic analysis of its 16S rRNA gene sequence or phylogenomic analysis. The ANI, dDDH and AAI values between WQ 2009T and its most closely related strains S. kitahiroshimense 10CT, S. pakistanense NCCP-246T and S. faecium DSM 11690T were significantly lower than the accepted cut-off values for microbial species delineation. All results demonstrated that WQ 2009T represent a novel genus, for which names Rhinopithecimicrobium gen. nov. and Rhinopithecimicrobium faecis sp. nov. (Type strain WQ 2009T = CCTCC AA 2021153T = KCTC 82941T) are proposed.

The gut microbiota facilitate their host tolerance to extreme temperatures

BACKGROUND

Exposure to extreme cold or heat temperature is one leading cause of weather-associated mortality and morbidity in animals. Emerging studies demonstrate that the microbiota residing in guts act as an integral factor required to modulate host tolerance to cold or heat exposure, but common and unique patterns of animal-temperature associations between cold and heat have not been simultaneously examined. Therefore, we attempted to investigate the roles of gut microbiota in modulating tolerance to cold or heat exposure in mice.

RESULTS

The results showed that both cold and heat acutely change the body temperature of mice, but mice efficiently maintain their body temperature at conditions of chronic extreme temperatures. Mice adapt to extreme temperatures by adjusting body weight gain, food intake and energy harvest. Fascinatingly, 16 S rRNA sequencing shows that extreme temperatures result in a differential shift in the gut microbiota. Moreover, transplantation of the extreme-temperature microbiota is sufficient to enhance host tolerance to cold and heat, respectively. Metagenomic sequencing shows that the microbiota assists their hosts in resisting extreme temperatures through regulating the host insulin pathway.

CONCLUSIONS

Our findings highlight that the microbiota is a key factor orchestrating the overall energy homeostasis under extreme temperatures, providing an insight into the interaction and coevolution of hosts and gut microbiota.

Surviving at the highest and coldest: Nutritional and chemical components of fallback foods for Yunnan snub-nosed monkeys

Fallback foods (FBF), categorized into staple and filler types, are suboptimal food sources chosen by animals in response to a scarcity of preferred food items during specific periods. Using lichens as FBF by Yunnan snub-nosed monkeys (Rhinopithecus bieti) represents a distinctive ecological adaptation and evolutionary development within nonhuman primates. This study delves into the annual dietary choices of the species to address issues, elucidate the nutritional value, and understand the ecological significance of lichens for this primate species, which resides at the highest altitudes and experiences the coldest weather among global primates. The findings reveal that the lichens consumed by the monkeys serve as the staple FBF, with Bryoria spp. and Usnea longissima being the primary dietary species. The former is the preferred choice, providing higher digestible fiber (neutral detergent fiber) levels but lower tannin, fat, ADF, and energy levels. During the dry season, lichens dominate as the monkeys' primary food and nutritional resources. In the wet season, they act as a fundamental food selection rather than an ideal dietary choice, substituting nutrients from fruits, seeds, and leaves. Compared to other Asian colobine counterparts, this species exhibits the highest lichen consumption but the lowest proportions of leaves, flowers, and seeds. This study provides valuable evidence and information for developing or amending conservation strategies and guidelines for the dietary management of captive breeding of monkeys, one of the world's critically endangered primate species.

The effects of food provisioning on the gut microbiota community and antibiotic resistance genes of Yunnan snub-nosed monkey

Yunnan snub-nosed monkeys (Rhinopithecus bieti) are the highest elevation lived non-human primate, and their survival has been threatened for decades. To promote their population growth, a reserve provides a typical monkey population with supplemental food. However, the influences of this food provisioning on their gut microbiota and antibiotic resistance genes (ARGs) were unknown. Therefore, we investigated the gut microbiota and ARGs of the food-provisioned monkey population compared with another wild foraging population. We found that food provisioning significantly increased the gut microbiota diversity and changed the community composition, particularly increased both the Firmicutes abundance and Firmicutes/Bacteroidetes ratio. Meanwhile, the food provisioning decreased the complex and stable gut microbiota network. KEGG functions were also influenced by food provisioning, with wild foraging monkeys showing higher functions of metabolism and genetic information processing, especially the carbohydrate metabolism, while food-provisioned monkeys exhibited increased environmental information processing, cellular processes, and organismal systems, including valine, leucine, and isoleucine degradation. In addition, food provisioning increased the abundance of ARGs in the gut microbiota, with most increasing the abundance of bacA gene and changing the correlations between specific ARGs and bacterial phyla in each population. Our study highlights that even food provisioning could promote wildlife nutrient intake, and it is necessary to pay attention to the increased ARGs and potential effects on gut microbiota stability and functions for this human conservation measure.

Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors

BACKGROUND

Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision.

RESULTS

Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota.

CONCLUSIONS

Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.

Analysis of winter diet in Guizhou golden monkey (Rhinopithecus brelichi) using DNA metabarcoding data

The Guizhou golden monkey (Rhinopithecus brelichi) is a critically endangered wildlife species, and understanding its diet composition may be useful for assessing its feeding strategies. DNA metabarcoding was used to determine the dietary diversity of R. brelichi. DNA was extracted from 31 faecal samples and amplified chloroplast rbcL and mitochondrial COI DNA was sequenced using the Illumina NovaSeq platform. A comparative analysis of the sequences revealed that the five most abundant plant genera were Magnolia, Morinda, Viburnum, Tetradium and Eurya. In winter, R. brelichi mostly consumed shrubs, herbs and shrubs/trees according to the habit of plant genera with higher abundances comparatively. The five most abundant families in animal diet were Psychodidae, Trichinellidae, Staphylinidae, Scarabaeidae and Trichoceridae. This study is the first to show the composition of the winter animal diets of R. brelichi based on DNA metabarcoding. These results provide an important basis for understanding the diet of wild R. brelichi, which inhabits only the Fanjingshan National Nature Reserve, China.

Human Disturbance Increases Health Risks to Golden Snub-Nosed Monkeys and the Transfer Risk of Pathogenic Antibiotic-Resistant Bacteria from Golden Snub-Nosed Monkeys to Humans

From the perspective of interactions in the human-animal-ecosystem, the study and control of pathogenic bacteria that can cause disease in animals and humans is the core content of "One Health". In order to test the effect of human disturbance (HD) on the health risk of pathogenic antibiotic-resistant bacteria (PARBs) to wild animals and transfer risk of the PARBs from wild animals to humans, golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel animals. Metagenomic analysis was used to analyze the characteristics of PARBs in the gut microbiota of golden snub-nosed monkeys. Then, the total contribution of antibiotic resistance genes (ARGs) and virulence factors (VFs) of the PARBs were used to assess the health risk of PARBs to golden snub-nosed monkeys, and the antimicrobial drug resistance and bacterial infectious disease of PARBs were determined to assess the transfer risk of PARBs from golden snub-nosed monkeys to humans. There were 18 and 5 kinds of PARBs in the gut microbiota of golden snub-nosed monkeys under HD (HD group) and wild habitat environments (W group), respectively. The total health risks of PARBs to the W group and the HD group were -28.5 × 10-3 and 125.8 × 10-3, respectively. There were 12 and 16 kinds of KEGG pathways of human diseases in the PARBs of the W group and the HD group, respectively, and the gene numbers of KEGG pathways in the HD group were higher than those in the W group. HD increased the pathogenicity of PARBs to golden snub-nosed monkeys, and the PARBs in golden snub-nosed monkeys exhibited resistance to lincosamide, aminoglycoside, and streptogramin antibiotics. If these PARBs transfer from golden snub-nosed monkeys to humans, then humans may acquire symptoms of pathogens including Tubercle bacillus, Staphylococcus, Streptococcus, Yersinia, Pertussis, and Vibrio cholera.

The putatively high-altitude adaptation of macaque monkeys: Evidence from the fecal metabolome and gut microbiome

Animals living in high-altitude environments, such as the Tibetan Plateau, must face harsh environmental conditions (e.g., hypoxia, cold, and strong UV radiation). These animals' physiological adaptations (e.g., increased red cell production and turnover rate) might also be associated with the gut microbial response. Bilirubin is a component of red blood cell turnover or destruction and is excreted into the intestine and reduced to urobilinoids and/or urobilinogen by gut bacteria. Here, we found that the feces of macaques living in high-altitude regions look significantly browner (with a high concentration of stercobilin, a component from urobilinoids) than those living in low-altitude regions. We also found that gut microbes involved in urobilinogen reduction (e.g., beta-glucuronidase) were enriched in the high-altitude mammal population compared to the low-altitude population. Moreover, the spatial-temporal change in gut microbial function was more profound in the low-altitude macaques than in the high-altitude population, which might be attributed to profound changes in food resources in the low-altitude regions. Therefore, we conclude that a high-altitude environment's stress influences living animals and their symbiotic microbiota.

Species variations in the gut microbiota of captive snub-nosed monkeys

Introduction

Snub-nosed monkeys are species in danger of extinction due to habitat fragmentation and human activities. Captivity has been suggested as an Auxiliary Conservation Area (ASA) strategy. However, little is known about the adaptation of different species of snub-nosed monkeys to captive environments.

Methods

This study compared the gut microbiota between Rhinopithecus bieti, R. brelichi, and R. roxellana under identical captive conditions to provide insights for improving captive conservation strategies.

Results

The results showed that these three Rhinopithecus species shared 80.94% of their Operational Taxonomic Unit (OTU), indicating high similarity in gut microbiota composition. The predominant phyla were Firmicutes and Bacteroidetes for all three Rhinopithecus species, but differences were observed in diversity, characteristic bacterial communities, and predicted function. Significant enrichment of cellulolytic families, including Ruminococcaceae, Clostridiales vadinBB60 group, Christensenellaceae, and Erysipelotrichaceae, and pathways involved in propionate and butyrate metabolism in the gut of R. bieti suggested that it may have a superior dietary fiber utilization capacity. In contrast, Bacteroidetes, Ruminoccaceae, and Trichospiraceae were more abundant in R. brelichi and R. roxellana, and were associated with saccharide and glycan metabolic pathways. Moreover, R. brelichi and R. roxellana also had higher similarity in microbiota composition and predicted function.

Discussion

In conclusion, the results demonstrate that host species are associated with the composition and function of the gut microbiota in snub-nosed monkeys. Thus, host species should be considered when formulating nutritional strategies and disease surveillance in captive snub-nosed monkeys.

Comparative study of the gut microbiota in three captive Rhinopithecus species

BACKGROUND

Snub-nosed monkeys are highly endangered primates and their population continues to decline with the habitat fragmentation. Artificial feeding and breeding is an important auxiliary conservation strategy. Studies have shown that changes and imbalances in the gut microbiota often cause gastrointestinal problems in captive snub-nosed monkeys. Here, we compare the gut microbiota composition, diversity, and predicted metabolic function of three endangered species of snub-nosed monkeys (Rhinopithecus bieti, R. brelichi, and R. roxellana) under the same captive conditions to further our understanding of the microbiota of these endangered primates and inform captive conservation strategies. 16 S rRNA gene sequencing was performed on fecal samples from 15 individuals (R. bieti N = 5, R. brelichi N = 5, R. roxellana N = 5).

RESULTS

The results showed that the three Rhinopithecus species shared 24.70% of their amplicon sequence variants (ASVs), indicating that the composition of the gut microbiota varied among the three Rhinopithecus species. The phyla Firmicutes and Bacteroidetes represented 69.74% and 18.45% of the core microbiota. In particular, analysis of microbiota diversity and predicted metabolic function revealed a profound impact of host species on the gut microbiota. At the genus level, significant enrichment of cellulolytic genera including Rikenellaceae RC9 gut group, Ruminococcus, Christensenellaceae R7 group, UCG 004 from Erysipelatoclostridiaceae, and UCG 002 and UCG 005 from Oscillospiraceae, and carbohydrate metabolism including propionate and butyrate metabolic pathways in the gut of R. bieti indicated that R. bieti potentially has a stronger ability to use plant fibers as energy substances. Bacteroides, unclassified Muribaculaceae, Treponema, and unclassified Eubacterium coprostanoligenes group were significantly enriched in R. brelichi. Prevotella 9, unclassified Lachnospiraceae, and unclassified UCG 010 from Oscillospirales UCG 010 were significantly enriched in R. roxellana. Among the predicted secondary metabolic pathways, the glycan biosynthesis and metabolism had significantly higher relative abundance in the gut of R. brelichi and R. roxellana than in the gut of R. bieti. The above results suggest that different Rhinopithecus species may have different strategies for carbohydrate metabolism. The Principal coordinate analysis (PCoA) and Unweighted pair-group method with arithmetic mean (UPGMA) clustering tree revealed fewer differences between the gut microbiota of R. brelichi and R. roxellana. Correspondingly, no differences were detected in the relative abundances of functional genes between the two Rhinopithecus species.

CONCLUSION

Taken together, the study highlights that host species have an effect on the composition and function of the gut microbiota of snub-nosed monkeys. Therefore, the host species should be considered when developing nutritional strategies and investigating the effects of niche on the gut microbiota of snub-nosed monkeys.

Beyond bacteria: Reconstructing microorganism connections and deciphering the predicted mutualisms in mammalian gut metagenomes

Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of Neocallimastigomycetes). The Methanobacteriaceae and Plasmodiidae families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas Onchocercidae and Trichuridae were the two most common nematodes, and Siphoviridae and Myoviridae the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.

Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome

The consumption of similar diets has led to the convergence of gut microbial compositions and functions across phylogenetically distinct animals. However, given the functional redundancy in gut microbiomes, it remains unclear whether synchrony occurs in their functions only and not in their composition, even within phylogenetically close animals consuming a similar diet. In this study, we collected fresh fecal samples from a Rhinopithecus roxellana population in April 2021 (before food provisioning) and June and December 2021 (after food provisioning) and used high-throughput sequencing methods (full-length 16S rRNA gene sequencing and metagenomes) to investigate changes in the gut microbiome due to food provisioning. Combining the results from our previous studies on a wild Rhinopithecus bieti population, we found that the artificial food provisions (e.g., apples, carrots, and peanuts) affected the gut microbiome, and synchrony occurred only in its functions and antibiotic resistance gene community in both Rhinopithecus species, reflecting its ecological functional redundancy. Given the current findings (e.g., depletion in probiotic microbes, dysbiosis in the gut microbial community, and changes in the antibiotic resistance gene profile), anthropogenic disturbances (e.g., food provisioning) would have potential negative effects on host health. Therefore, human activity in animal conservation should be rethought from the standpoint of gut microbial diversity.

Characterizing the Gut Microbiota of Eurasian Otter (Lutra lutra chinensis) and Snub-Nosed Monkey (Rhinopithecus roxellana) to Enhance Conservation Practices in the Foping National Nature Reserve of China

Understanding the interaction between the microbial composition in the habitat and the gut of wildlife will contribute to conservation efforts since changes in the gut microbiome have been proven to influence the healthy and nutritional status of the host. This study analyzed the relationship between soil microbes and the microbial diversity and structure of the distal gut of the terrestrial golden snub-nosed monkey and Eurasian otter in the Foping National Nature Reserve (FNNR). A total of 15 otter fecal samples and 18 monkey fecal samples were collected from which 5 and 6 samples, respectively, were randomly selected for microbiome analysis. The remaining samples were used for fecal short-chain fatty acids (SCFAs) analysis. Soil samples from the otter and monkey habitats at each sampling point (eight in total) were also collected for microbiome analysis. The microbial phyla with the greatest relative abundance in soil or animal samples were Proteobacteria (41.2, 32.7, and 73.3% for soil, otters, and monkeys, respectively), Firmicutes (0.4% soil, 30.1% otters, and 14.4% monkeys), Bacteroidota (5.6% soil, 17.0% otters, and 8.3% monkeys), and Acidobacteriota (24.6% soil, 1.7% otters, and 0.1% monkeys). The estimation of alpha diversity indices revealed that the feature, Chao1, and Shannon indices of the soil microbiome were the greatest (p < 0.01) among the three groups, followed by those of the otter microbiome and those of the monkey microbiome (p < 0.01). Beta diversity analyses confirmed differences in the microbiota of the three types of samples. The determination of SCFA concentration in feces revealed that total volatile fatty acids, acetic acid, and isovaleric acid were greater (p < 0.05) in otters than in monkeys, while propionic acid followed the opposite pattern (p < 0.05). Correlation analysis of the microbiome and SCFA contents showed that propionic acid was positively correlated with significantly different bacterial groups, while acetic and butyric acid and total volatile acids were negatively correlated. This study confirmed that the fecal microbes of Eurasian otters and golden snub-nosed monkeys in the reserve are related to the soil microbial communities of their habitats, but they have different bacterial community structures and compositions, and there are different SCFA metabolic patterns in the gut of the two animals. The present study will help to improve wildlife protection in the FNNR.