The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau. The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production. These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.

Wild ungulates play crucial roles in maintaining the structure and function of local ecosystems. The alpine musk deer (Moschus chrysogaste), white-lipped deer (Przewalskium albirostris), and red serow (Capricornis rubidus) are widely distributed throughout the Nyenchen Tanglha Mountains of Tibet. However, research on the mechanisms underlying their coexistence in the same habitat remains lacking. This study aimed to investigate the mechanisms underlying the coexistence of these species based on their dietary preferences through DNA barcoding using the fecal samples of these animals collected from the study area. These species consume a wide variety of food types. Alpine musk deer, white-lipped deer, and red serow consume plants belonging to 74 families and 114 genera, 62 families and 122 genera, and 63 families and 113 genera, respectively. Furthermore, significant differences were observed in the nutritional ecological niche among these species, primarily manifested in the differentiation of food types and selection of food at the genus level. Owing to differences in social behavior, body size, and habitat selection, these three species further expand their differentiation in resource selection, thereby making more efficient use of environmental resources. Our findings indicate these factors are the primary reasons for the stable coexistence of these species.

The effects of mother-infant separation (i.e., weaning) on the physiology, psychology and nutrition of mammalian infants have attracted much attention. Forest musk deer (FMD) is a first-class protected species in China and listed endangered in the IUCN Red List. The captive breeding population is not only an important source for restocking of wild resources, but also a necessary way to supply the market with legal musk. So far, there is no scientific basis for the appropriate separation time of FMD females and their infants. Therefore, we used metagenome sequencing and enzyme-linked immunosorbent assays to study changes in the fecal cortisol concentration, as well as the intestinal microbiome composition and function of females and fawns at three different separation times, i.e., after 80 days, 90 days and 100 days. The results showed that the increment of the cortisol concentration in female FMD increased with increasing lactation time. The increment of cortisol concentration in infant FMD was highest in the 80 days weaning group, but there was no significant difference between the 90 days and the 100 days separation time. Based on the annotation results of COG, KEGG and CAZy databases, the abundance of different functions annotated by the intestinal microbiome of mothers and fawns of the 90 days weaning group changed slightly after separation. Based on the above results, the separation of mother and infant FMD is recommended after 90 days, i.e., the separation time that triggered the lowest rate of weaning stress and that supported a relatively stable gastro-intestinal physiology.

The breeding of large animals in the family Cervidae in China contributes to achieving two tasks: restoring the provenance of wild populations and providing raw materials for traditional Chinese medicine. Currently, red deer (Cervus elaphus), sika deer (C. nippon), and white-lipped deer (C. albirostris) maintain a large number of breeding populations. Some studies on the relationship between the intestinal microbiota and the feed of these deer have been conducted; however, owing to differences in feeding conditions between studies, it has been impossible to compare the intestinal microecology and related adaptability between species. Therefore, the present study is aiming to investigate whether the differences in intestinal microbiota of the three deer species are related to the distance of phylogenetic relationships under the same feeding environment. On this basis, we discuss whether there are differences in the adaptability of the intestinal microbiota of the three deer species to feed nutrients, deepen the understanding of the relationship between the three deer intestinal microbiota and feed nutrition, and provide basic data for improving the scientific feeding of the three deer species. In this study, 16S rRNA high-throughput sequencing technology was utilized to analyze the intestinal microbiota in feces of the abovementioned healthy deer species. The results of this study indicated that the intestinal microbiota diversity and relative abundance in female white-lipped deer (FWLD) were significantly lower than those in female sika deer (FSD) and female red deer (FRD; p < 0.05); however, there was no significant difference between the latter two groups (p > 0.05). The community compositions of the intestinal microbiota in FSD and FRD were more similar, whereas that of FWLD was significantly different from those of the first two groups. Firmicutes and Bacteroidetes were the most abundant phyla in the intestinal microbiota of all three deer species, and Ruminococcceae_UCG-005 was the most abundant genus. No known obligatory pathogenic bacteria were observed in any sample. The relative abundance of the operational taxonomic units Christensenellaceae_R-7_group, Treponema_2, and Akkermansia exhibited significant differences among FSD, FRD, and FWLD, respectively. Therefore, the phylogenetic relatedness of the three deer species appears to play a major role in their intestinal microecology under the same feeding conditions—the greater the phylogenetic relatedness between hosts, the more similar is their intestinal microbiota. In addition, the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) function prediction results indicated that FSD were less capable than FRD and FWLD in the functional category of nutrient metabolism, and FWLD were less capable than FSD and FRD in the functional category of intestinal absorption. These results indicated that there may be differences in the nutritional adaptation abilities of the three deer species under different feeding conditions. In summary, these results revealed the differences in intestinal microbiota among the three deer species under the same food conditions, indicating that the intestinal microbiota of the three deer species had significant differences in food adaptation. Based on this, the nutritional supply of feed for the three deer should consider the species differences.

Wild Forest musk deer (FMD) has been declining due to continuing poaching and habitat loss. Although captive breeding has increased population numbers, maintaining genetic diversity in these farmed populations has become increasingly urgent and challenging due to depleted wild stocks and loss of genetic diversity from inbreeding in captive populations. Using samples from 683 individuals, we assessed mitochondrial genetic diversity (ATP8-6, Cytb, control region [CR]), structure, and maternal lineage patterns in a newly established ex-situ population (BB; founded 2019 with 44 breeders) and its three founding source populations (PZH, TZL, GL) in western China. Our results demonstrate that the ex-situ population maintains higher nucleotide diversity (π) in ATP8-6 and Cytb than its source populations, while exhibiting comparable haplotype diversity (Hd). Phylogenetic and haplotype network analyses identified three maternal lineages across populations, with the ex-situ population containing representatives of all lineages and showing significant genetic differentiation from at least some founder groups, indicating the mixed-source introduction strategy successfully created a genetically distinct population. Neutrality tests and mismatch distributions suggested historical bottlenecks in baseline populations, whereas the ex-situ population showed signatures of recent admixture and expansion. These findings highlight the potential benefits of mixed-source introductions in enhancing genetic diversity during ex-situ conservation. We recommend long-term genetic monitoring and in-depth analysis of population history to refine translocation strategies and support the long-term viability of FMD under managed care.

The gut microbial ecosystem is structured by the gut microbiota residing in animal hosts. It plays a critical role in modulating core host physiological functions, covering food digestion, nutrient absorption, energy metabolism and immune regulation. In this study, we performed 16S rDNA high-throughput sequencing to characterize the gut microbiota of wild alpine musk deer (Moschus chrysogaster, AMD) and ex situ conserved forest musk deer (Moschus berezovskii, FMD). We then inferred the putative functional profiles based on known taxon–function relationships. Our analyses revealed no significant difference in gut microbiota alpha diversity between wild AMD and ex situ conserved FMD. However, significant divergence in gut microbiota beta diversity was detected between the two species. The family Muribaculaceae and its unclassified affiliated genus as well as the genus Monoglobus and Pseudomonas were significantly more abundant in wild AMD than in ex situ conserved FMD. By contrast, the genera Prevotellaceae_UCG_004, Alistipes, Christensenellaceae_R-7_group, Akkermansia and the family Oscillospiraceae were significantly more abundant in ex situ conserved FMD than in wild AMD. Furthermore, the Firmicutes/Bacteroidetes ratio was numerically higher in FMD than in AMD. Together, these results indicate that the gut microbiota differences between the two musk deer species are consistent with the dietary factors differences. These findings further suggest that the formulated concentrate diet fed to FMD was lower in fiber and higher in digestible energy than the natural diet of AMD. These dietary factors may partly underlie the observed microbiota differences. Accordingly, we recommend adjusting the feeding regime and husbandry practices for FMD to better match the native food plants consumed by AMD. Such adjustment represents an evidence-based strategy for improving the health of FMD populations.