Background: Plovers (Charadriidae), within the order of Charadriiformes, a group of modern birds distributed worldwide, are a frequent subject of molecular phylogenetic studies. While research on mitochondrial genome (mitogenome) variation within the family Charadriidae, especially intraspecific variation, is limited. Additionally, the monophyly of Charadrius and the phylogenetic placement of Pluvialis remain contentious. Nevertheless, recent studies utilizing complete mitogenomes from available databases to construct phylogenetic trees for Charadriidae and Charadriiformes remain scarce. Methods: This study aims to explore mitogenome variation within Charadrius dubius and clarify the phylogenetic placement of Pluvialis fulva. We sequenced the complete mitogenome of six C. dubius and one P. fulva, and all additional available mitogenomes were integrated within Charadriiformes. The average complete mitogenome length of C. dubius is 16,889 bp, and P. fulva is 16,859 bp. Results: Our results support the suggestion that the monophyly of Charadrius and P. fulva is nested within Charadriidae. The phylogenetic analysis of Charadriiformes based on mitogenomes strongly supports the recognition of three major shorebird clades: Charadrii, Lari and Scolopaci, with Lari and Scolopaci identified as sister clades. Conclusions: Our study reinforces the credibility of the inferred evolutionary relationships within Charadriidae and Charadriiformes.

Musk deer (Moschidae), a primitive lineage within Ruminantia, are distributed across East Asia and have long been of interest in molecular phylogenetic research. The spotted forest musk deer from Huanglong (HL) Mountain in Shaanxi, China, has long been morphologically classified as Moschus moschiferus (Siberian musk deer). However, its true taxonomic status has remained uncertain due to the lack of comprehensive molecular evidence. Moreover, studies on mitochondrial genome (mitogenome) variation within Moschidae, particularly at the intraspecific level, remain limited. To date, few phylogenetic analyses of Moschidae have incorporated all available complete mitochondrial genomes from public databases. In this study, we sequenced and assembled the complete mitogenomes of two spotted musk deer individuals from Huanglong Mountain, Shaanxi, China, and identified them as M. berezovskii (forest musk deer) by phylogenetic analysis. All available complete mitochondrial genomes of Moschidae were also included in the phylogenetic reconstruction. The average complete mitogenome length of M. berezovskii distributed in HL was 16,355 bp, and comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis and genetic distance indicate that the taxonomic identity of the HL Mountain population as M. berezovskii supports the monophyly of M. berezovskii and provides a robust phylogenetic framework for clarifying evolutionary relationships within the family.

Background: The nasopharyngeal microbiome is crucial for respiratory health in mammals, yet it remains poorly characterized in the endangered forest musk deer (Moschus berezovskii), particularly in the context of disease. Methods: We compared the bacterial (16S rRNA) and fungal (ITS2) communities in the nasopharynx of healthy (n = 6) and clinically diseased (n = 6) individuals. Results: Although alpha diversity did not differ significantly, beta diversity (PCoA) analysis revealed distinct bacterial (PERMANOVA, R² = 0.165, p = 0.014) and fungal (R² = 0.577, p = 0.003) community structures between groups. The diseased group exhibited a significant increase in the bacterial phylum Proteobacteria (70.97% vs. 46.27%), primarily driven by the genera Bibersteinia and Pseudomonas. Fungal communities in the diseased group were dominated by a higher relative abundance of Ascomycota and Basidiomycota, with significant enrichment of Wallemia and Aspergillus. LEfSe analysis identified Pseudomonas and multiple fungal taxa (e.g., Wallemia, Aspergillus) as biomarkers for the diseased group. PICRUSt2 prediction indicated enrichment of pathways related to carotenoid biosynthesis and sphingolipid metabolism in the diseased state, while FUNGuild analysis suggested a higher abundance of animal/plant pathogen-related fungi. Conclusions: Symptomatic respiratory infections in forest musk deer are associated with significant dysbiosis of the nasopharyngeal microbiome, characterized by the marked enrichment of potential bacterial opportunists (e.g., Pseudomonas) and specific fungal taxa (e.g., Wallemia, Aspergillus), alongside distinct functional shifts in the microbiome. These findings provide the first integrated bacterial–fungal profile of the nasopharyngeal microbiome in this endangered species, and highlight potential microbial biomarkers associated with respiratory disease.

The gut microbiota and its metabolic functions are critical for intestinal homeostasis, but their integrated responses to diarrhea remain poorly understood in non-model mammals, such as the complex-toothed flying squirrel (Trogopterus xanthipes). Here, we collected fecal samples from six captive animals with diarrhea and six healthy controls; the diarrheal animals had been provided with moldy corn, but mycotoxin levels were not measured. Fecal microbiota was profiled by full-length 16S rRNA sequencing and untargeted metabolomics with integrative analyses. Diarrheal animals showed significantly decreased fecal microbial alpha-diversity and distinct community separation. LEfSe analysis identified Lawsonia intracellularis and Streptococcus macedonicus as the most enriched taxa in the diarrhea group. Untargeted metabolomics revealed 2216 differential metabolites (1931 downregulated), primarily enriched in steroid hormone biosynthesis, arachidonic acid metabolism, and bile secretion pathways. Procrustes and Mantel tests confirmed significant microbiome–metabolome concordance (M² = 0.422, p < 0.001). Spearman correlation networks showed that L. intracellularis was positively correlated with multiple differential metabolites, while S. macedonicus exhibited predominantly negative correlations. These findings suggest that diarrhea in T. xanthipes may be associated with moldy corn exposure and is accompanied by gut dysbiosis and metabolic disturbances. L. intracellularis and S. macedonicus may be associated with disease progression through pathways linked to lipid and bile acid metabolism and inflammation. This study provides novel microbial–metabolic insights into diarrhea in a medicinal mammal, supporting disease prevention and healthy breeding.

Background: To conserve wild populations and ensure a sustainable supply of musk, China initiated the captive breeding of forest musk deer. The temporal dynamics of gut antibiotic resistance gene (ARG) profiles in captive forest musk deer along a breeding duration gradient remain poorly characterized. Methods: In this study, we employed metagenomic sequencing to systematically characterize the profiles and potential mobility of ARGs. Samples were divided into short-term, medium-term and long-term groups according to breeding durations. Results: A total of 331 ARG subtypes and 71 mobile genetic element (MGE) subtypes were annotated across all samples. ARG Shannon diversity differed overall across groups (Kruskal-Wallis, p = 0.03); Bonferroni-adjusted Dunn’s test showed no significant pairwise differences. PCoA (Bray–Curtis) demonstrated distinct separation of the ST group (p = 0.002), and shared core ARG subtypes gradually increased with extended breeding years. A strong positive correlation between ARG and MGE abundances was identified (r = 0.85, p = 0.0001). In total, 63 contigs carrying co-localized ARG-MGE complexes were recovered. The ST group contained the highest proportion of such contigs. The ST group displayed tight physical ARG-MGE linkage within 1–3 kb genomic intervals. Conclusions: Our results reveal that breeding duration is associated with the gut ARG characteristics of captive forest musk deer. Short-term captivity has higher ARG-MGE co-localization, suggesting a higher possibility of mobilization.

Background: Understanding the nasopharyngeal (NAS) and rectal (INT) microbiomes is critical to maintain host health. However, their functional roles in shaping microbial network structure and niche differentiation remain unexplored in most animal species, especially endangered primates. Here, we compared the NAS and INT microbiomes of golden snub-nosed monkeys (Rhinopithecus roxellana) using full-length 16S rRNA amplicon sequencing and metagenomics, focusing on taxonomic composition, functional profiles (KEGG, CAZy, PHI), and microbial co-occurrence networks. Results: Our results indicate that microbial community structure and diversity (Shannon evenness) differ significantly between the two niches. Taxonomically, both sequencing approaches consistently show that, at the relative-abundance level, NAS is dominated by genera such as Dolosigranulum and Vibrio, whereas the INT is characterized by Campylobacter, Helicobacter, and Aerococcus. Notably, metagenomic analysis indicates a relatively high abundance of potential pathogens, including Helicobacter pylori and Chlamydia psittaci. LEfSe analysis shows Dolosigranulum and Campylobacter are key microbial markers for the NAS and INT niches, respectively. KEGG pathway analysis reveals that the NAS microbiome is enriched in valine/leucine/isoleucine degradation and glutathione metabolism, while the INT microbiome is enriched in amino sugar and nucleotide sugar metabolism and ribosome pathways. At the CAZy level, all 29 differentially abundant families (e.g., GH13_29, GH103, AA3_2) were enriched in the NAS. Distinct pathogen–host interaction profiles further reflect niche-specific adaptations. Exploratory Spearman-based co-occurrence networks (in which no genus–CAZy edge survived Benjamini–Hochberg (FDR) correction) linked core commensals to KEGG pathways and CAZy families (e.g., GT35, GH0). In the INT, Campylobacter and Helicobacter form high-connectivity modules associated with pathways such as those involving the two-component system and ABC transporters. Conclusions: The nasopharyngeal and rectal microbiomes in golden snub-nosed monkeys differ not only taxonomically but also functionally, exhibiting clear spatially specialized functional differentiation. Given the small sample size (n = 8), these findings provide preliminary evidence for niche-specific microbial and functional partitioning and suggest that the nasopharynx may harbor a relatively high abundance of potential zoonotic pathogens. This study provides a basis for further exploration with a larger sample size.