Toxoplasmosis is a widespread zoonotic disease causing severe outcomes in immunocompromised individuals and during pregnancy. Current therapeutic options target actively replicating stages of the parasite and show limited efficacy against chronic infection, underscoring the need for complementary therapeutic strategies. While efforts have largely focused on on eliminating the parasite, host-directed strategies aimed at enhancing disease tolerance and preserving tissue integrity remain comparatively underexplored. In this study, we used untargeted serum metabolomics to characterize host metabolic responses to acute and chronic Toxoplasma gondii (T. gondii) infection in a murine model. Our analysis revealed extensive metabolic remodeling during infection, with prominent perturbations in lipid metabolism and amino acid pathways. Among the metabolites most significantly depleted during infection was the essential amino acid L-lysine. We evaluated the impact of L-lysine supplementation on disease outcomes in vivo. L-lysine supplementation was associated with improved survival and reduced tissue pathology during acute and chronic infection. Supplemented mice exhibited reduced inflammatory cytokine dysregulation and lower tissue parasite burdens, effects that are consistent with enhanced host resilience rather than direct antiparasitic activity. These findings identify L-lysine depletion as a metabolic feature of T. gondii infection and demonstrate that its supplementation confers protective benefits in the host. Our study highlights the value of metabolomics-guided approaches for uncovering host metabolic vulnerabilities and supports the concept of L-lysine supplementation as a host-directed adjunctive intervention to mitigate pathology during toxoplasmosis.

The rapid expansion of cervid farming raises concerns about antimicrobial resistance (AMR) dissemination, yet its impact on the Cervidae gut microbiome remains poorly characterized. We integrated 89 newly sequenced fecal metagenomes with 599 publicly available datasets, comprising 285 metagenomes from farmed cervids and 370 from wild cervids, to construct a catalog of 15,494 non-redundant metagenome-assembled genomes (MAGs) representing 2,401 species. Our analysis demonstrates that farming profoundly reshapes the gut microbiome's functional composition. Specifically, farmed cervids exhibited significantly higher relative abundance, diversity, and heterogeneity of antimicrobial resistance genes (ARGs) compared to wild counterparts. We observed a robust synergistic relationship between ARGs, virulence factor genes, and mobile genetic element (MGE)-associated genes, identifying 70 ARG-MGE combinations as evidence of potential horizontal gene transfer. Plasmid profiling further suggested that a subset of ARGs may be associated with conjugative plasmids, with plasmid-associated ARGs being significantly more abundant in farmed than in wild cervids. Virome analyses indicated that bacteriophages, particularly Siphoviridae, may serve as mobile reservoirs for ARGs. Notably, Cervidae shared 268 ARG types with humans, including 23 high-risk genes associated with resistance to clinically important antibiotics (e.g. tetX1, vanRD, and bla-CTX-M-178), with Escherichia coli as a key cross-host carrier. These findings highlight that human-impacted cervid gut microbiomes are significant environmental reservoirs of clinically relevant AMR, underscoring the necessity for enhanced antibiotic stewardship and resistance surveillance in managed wildlife within a One Health framework.

Escherichia coli (E. coli) from food-producing animals serves as an important reservoir of antibiotic resistance genes (ARGs). To investigate the baseline genomic and antimicrobial resistance (AMR) profiles of bovine-associated E. coli from northern China, 143 fecal samples were collected across five provinces for analysis. A total of 112 E. coli isolates were recovered from 143 bovine fecal samples, with isolation rates ranging from 60 to 100

The livestock gut microbiota serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied. Here, we present a large-scale metagenomic analysis of 779 gut samples from Caprinae animals, primarily originating from China (95.38%), including Capra hircus (79.85%) and Ovis aries (17.33%). We reconstruct 17,023 metagenome-assembled genomes (MAGs), and identify 2,440 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). Escherichia coli represents a major host for both. Correlation analyses between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection mechanisms. Although MGEs were detected in only 1.45% of MAGs, likely reflecting limitations in identifying MGEs within incomplete assemblies, 19 ARGs are physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs are embedded within viral genomes, implicating bacteriophages in AMR dissemination. Comparative analyses reveal 184 distinct ARGs shared between Caprinae and humans, including 17 clinically critical genes such as tetX and van variants. These findings expand understanding of the Caprinae gut resistome and highlight its potential role in cross-host AMR transmission, and underscore the need for targeted AMR surveillance in this reservoir.

The role of gut microbiota in vitamin biosynthesis in wild birds, which is essential for understanding avian health and ecological adaptation, remains largely unexplored. In this study, metagenomic analysis was conducted on 10,455 metagenome-assembled genomes (MAGs) from 718 wild bird gut samples. After quality assessment and dereplication, 1947 MAGs were retained for systematic analysis of vitamin B and K2 biosynthesis potential. A total of 106,336 vitamin biosynthesis genes were identified, and 1164 MAGs (including 410 high-quality MAGs with >90% completeness and <5% contamination) were predicted to de novo synthesize at least one vitamin. Vitamin biosynthesis genes mainly originated from Pseudomonadota, Campylobacterota, Bacillota_A, and Actinomycetota, with dominant genera including Campylobacter_D, Escherichia, and Cutibacterium. Compared with chickens, the gut microbiota of wild birds was enriched in biotin, folate, and pantothenate biosynthesis genes, likely reflecting adaptation to diverse natural diets and fluctuating environments. Among all examined factors, host species explained the largest proportion of variation in vitamin biosynthesis gene composition, followed by environmental variables, while migratory behavior and primary diet showed relatively smaller but detectable associations. Dietary differences appeared to be associated with variations in vitamin biosynthetic potential, with crop- and insect-dominant birds tending to show higher representation of genes involved in the synthesis of multiple B vitamins, whereas aquatic-plant dominant birds exhibited relatively greater representation of folate biosynthetic pathways. Migratory birds exhibited significantly higher diversity but comparable relative abundance of vitamin biosynthesis genes compared with resident birds, suggesting a more flexible microbial metabolic potential to meet fluctuating nutritional demands during long-distance movement. Distinct microbial contributors were identified, with Escherichia and Pseudomonas_E being more prominent in migratory birds, and Campylobacter_D in resident birds. Collectively, this study provides novel insights into gut microbiota-driven vitamin biosynthesis in wild birds.

Escherichia coli (E. coli) is a common gut commensal and an important opportunistic pathogen in humans and animals. Here, we investigated antimicrobial resistance (AMR), virulence traits, and dissemination potential of E. coli from farmed foxes raised for fur production in northern China. From 248 fecal samples collected in Liaoning, Hebei, and Shandong, 109 E. coli isolates were recovered. We first performed phenotypic screening using four clinically important sentinel antibiotics (meropenem, polymyxin B, tigecycline, and ceftazidime) and then conducted in-depth characterization of the 34 screen-positive isolates, including extended susceptibility testing, PCR detection of resistance/virulence genes, conjugation assays, biofilm quantification, and whole-genome sequencing of 25 representative isolates. The screen-positive isolates showed widespread multidrug resistance and a diverse resistome; transfer of resistance determinants was observed in a subset of isolates. Targeted virulence screening detected only six virulence gene targets (irp2, fimH, fimC, fyuA, astA, and invE), and selected representative strains reduced survival in the Galleria mellonella infection model at high inocula. Biofilm formation varied across isolates, with a subset exhibiting strong biofilm-forming capacity. Whole-genome analysis further revealed abundant resistance determinants, virulence factors, and mobile genetic element–associated genes, highlighting the potential for persistence and dissemination within farm environments. Collectively, these findings provide an integrated view of AMR and virulence features of fox-derived E. coli and support ongoing surveillance and risk-mitigation efforts in fur-animal production systems.

The Tibetan antelope (Pantholops hodgsonii), an iconic species endemic to the Qinghai-Tibet Plateau, thrives at altitudes of 4,500–5,000 m under conditions of extreme hypoxia, cold, and limited nutrition. As a critical mediator of host physiology, the gut microbiome may play a key role in supporting these adaptations. This study presents the first genome-centric investigation of bile acid (BA) metabolism in the gut microbiome of the Tibetan antelope, unveiling unique microbial pathways that potentially facilitate survival in harsh environments. Comparative analysis of metagenome-assembled genomes revealed that the antelope’s BA-metabolizing microbiota is taxonomically distinct from that of other Caprinae species and humans, with only two of the top ten BA-producing genera shared across groups. Importantly, individuals infected with Blastocystis exhibited marked differences in BA-related KEGG ortholog (KO) profiles compared to uninfected counterparts. Our findings highlight that the proportion of bile salt hydrolase (K01442) genes in the gut microbiota of Tibetan antelopes is higher than that in other Caprinae species and humans. Among them, the genus Alistipes carries the highest proportion of K01442 in the Tibetan antelope’s gut microbiota. Additionally, infection-associated KO gene shifts were observed, suggesting a microbial contribution to the Tibetan antelope’s remarkable physiological resilience. In Tibetan antelopes, Alistipes was the dominant genus associated with bile acid synthesis. While bile acid synthesis KO distributions were broadly similar across species, K01442 higher proportion than other in Tibetan antelope gut microbiomes. Furthermore, Blastocystis infection altered three key bile acid synthesis KOs and induced distinct shifts in gut microbiome composition.

Klebsiella species are important opportunistic pathogens whose antimicrobial resistance and virulence evolution have attracted increasing attention. However, their prevalence and genomic characteristics in farmed sika deer remain unclear. A total of 69 Klebsiella isolates (13.40

Klebsiella pneumoniae is a significant opportunistic pathogen in animal farming. To investigate the occurrence of K. pneumoniae and associated antimicrobial resistance risk in foxes, this study collected 350 fecal samples from foxes across five northern Chinese provinces. A total of 163 K. pneumoniae isolates were recovered (isolation rate: 46.57%), and all isolates were classified as multidrug-resistant (MDR). All isolates were resistant to azithromycin and sulfisoxazole, with high resistance to enrofloxacin (98.16%), ciprofloxacin (87.12%), and tetracycline (70.55%). Resistance to tigecycline and polymyxin B was lower. Notably, all isolates were susceptible to meropenem. Antimicrobial resistance gene (ARG) analysis revealed high carriage rates of tet(E), aac(3)-IIa, and qnrS, alongside the colistin resistance genes mcr-1 and mcr-8. Whole-genome sequencing of 66 isolates revealed substantial genetic diversity: 45 sequence types (STs) were identified among 64 typeable isolates, with ST35 and ST603 being the most common (5/64, 7.81% each), and lineages previously reported in human clinical settings (e.g., ST307 and ST15) were also detected; however, no direct cross-host transmission was evaluated in this study. Capsular types KL22 (10/64, 15.63%) was the most common. Metagenomic analysis further showed that the fox gut microbiome harbored diverse ARGs, with 29 ARGs detected in both K. pneumoniae isolates and fox gut resistome datasets (descriptive overlap). Among these, 20 genes (e.g., blaCTX-M-55 and aac(3)-IIa) were located on predicted plasmids or transposons, suggesting potential mobility rather than confirmed transfer. Conjugation assays provided limited proof-of-concept evidence for plasmid-mediated transfer of tet(A) and tet(E). Collectively, these findings suggest that farmed foxes may serve as potential reservoirs of MDR K. pneumoniae and transferable resistance determinants, supporting the need for continued surveillance and prudent antibiotic use within a One Health framework.

Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.

Klebsiella pneumoniae is an important opportunistic pathogen of One Health concern, and its multidrug-resistant (MDR) and hypervirulent strains pose serious threats to public health. However, the epidemiological characteristics, antimicrobial resistance profiles, and virulence potential of K. pneumoniae circulating in farmed minks remain poorly understood. In this study, we integrated phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis to investigate the epidemiology, resistance determinants, and virulence characteristics of K. pneumoniae isolated from farmed minks in northern China. A total of 41 K. pneumoniae strains from 325 fecal samples (isolation rate: 12.62%), including three hypervirulent strains. All isolates exhibited multidrug resistance, with complete resistance to florfenicol, azithromycin, and sulfisoxazole, but remained highly susceptible to carbapenems and polymyxin B. Whole-genome sequencing revealed that the isolates harbored 241 antibiotic resistance genes (ARGs), including ESBL-associated genes and the plasmid-mediated mcr-1.1, along with 7,111 virulence factor genes (VFGs) and 135 mobile genetic elements (MGEs). Metagenomic analysis further revealed a complex resistome and virulome, with 7,259 ARGs and 6,701 virulence-related genes identified across samples. Antibiotic target alteration and efflux were the dominant resistance mechanisms, while effector delivery systems, metabolic functions, and adherence were the major virulence categories. MGEs were abundant, especially transposases, indicating active genetic mobility within the microbial community. Overall, this study provides a comprehensive characterization of antimicrobial resistance and virulence features of mink-derived K. pneumoniae and highlights the potential role of farmed minks as reservoirs of multidrug-resistant bacteria within the One Health framework, offering important insights for antimicrobial resistance surveillance and public health risk assessment.

Toxoplasma gondii infection remodels the gut microbiome, yet its impact on microbial vitamin biosynthetic potential and host redox metabolism remains unclear. Here, we integrated mouse gut metagenomes with publicly available metagenome-assembled genomes (MAGs) to construct a genome-resolved atlas of B-vitamin and vitamin K2 biosynthesis. From 45,697 MAGs, we curated 4,771 representative genomes, of which 2,682 met high-quality criteria (completeness ≥90%, contamination <5%). Functional annotation identified 229,717 vitamin-related genes corresponding to 177 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs across de novo pathways for eight B vitamins, thiamine (B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and vitamin K2. Among the high-quality genomes, 1,665 encoded complete de novo pathways for at least one vitamin, highlighting functional specialization and community-level complementarity. Transcripts per million-normalized metagenomic read counts revealed significant differences in KEGG ortholog abundances across six of the nine vitamin pathways. Reanalysis of metagenomic data from infected mice (acute, chronic, and control; n = 10 per group) revealed a stage-dependent reduction in α-diversity of vitamin biosynthesis pathways during acute infection, and a clear β-diversity separation from chronic and control groups. Core niacin biosynthesis genes (nadB, nadA, nadC) displayed phylum-specific redistribution, indicating selective remodeling of microbial NAD+ precursor production under infection-induced metabolic stress. These results suggest that T. gondii infection disrupts cooperative vitamin biosynthetic networks while specifically modulating niacin pathways linked to host NAD+ metabolism. IMPORTANCE:Gut microbes can synthesize essential vitamins, but how infection alters this function is poorly understood. By integrating mouse gut metagenomes with genome-resolved microbial data, we show that Toxoplasma gondii infection reshapes the vitamin biosynthetic potential of the gut microbiome in a stage-dependent manner. Acute infection reduces the diversity of vitamin biosynthesis pathways and shifts the taxonomic distribution of key niacin biosynthesis genes involved in microbial NAD+ precursor production. These findings identify vitamin metabolism, especially niacin-related pathways, as a sensitive functional axis of microbiome remodeling during infection. Our work links microbial taxonomic changes to functional metabolic consequences and suggests that microbiome-mediated regulation of NAD+-related metabolism may contribute to host redox adaptation during T. gondii infection.

Escherichia coli (E. coli) is one of the most common commensal bacteria in the intestinal tract of humans and animals. It serves as a major reservoir of antimicrobial resistance genes and may facilitate their horizontal transfer among different hosts. In this study, 212 fecal samples were collected from mink across four northern provinces of China, a total of 110 E. coli isolates were recovered (isolation rate, 51.89 %). Preliminary antimicrobial screening was conducted using four clinically critical antibiotics, including ceftazidime (CAZ), polymyxin B (PMB), meropenem (MEM), and tigecycline (TGC), with CAZ resistance being the most prevalent, followed by PMB, MEM, and TGC. Further antimicrobial susceptibility testing against ten commonly used antibiotics in 49 representative isolates revealed universal multidrug resistance (MDR), including 100 % resistance to imipenem, tetracycline, enrofloxacin, florfenicol, and sulfamethoxazole. Genetic screening identified multiple resistance genes such as aac(3')-IIa, blaCTX-M, tet(A), and mcr-1. Conjugation assays demonstrated that CAZ resistance was the most transferable. Virulence profiling revealed a low prevalence of classical pathogenic virulence factors, with only six virulence gene types detected, consistent with the results of Galleria mellonella infection assays. Whole-genome sequencing of 41 representative isolates revealed 87 unique antibiotic resistance genes (ARGs) types spanning 14 antibiotic classes including alinically important determinants such as blaCTX-M, tet, and mcr, and 71 unique virulence genes assigned to 65 functions. Metagenomic analysis further identified diverse ARGs within the mink gut microbiota, with 21 shared between whole-genome and metagenomic sequencing. Correlation analysis suggested co-occurrence patterns among ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs), particularly between ARGs and MGEs. Overall, mink-derived E. coli exhibited extensive MDR but limited classical pathogenic virulence, and the mink gut microbiota may represent an important reservoir and transmission hub for resistance genes in intensive farming ecosystems.

The gut microbiota of the Tibetan antelope (Pantholops hodgsonii) plays a vital role in host nutrition, particularly by contributing to the biosynthesis of essential micronutrients such as vitamins B and K2. In this study, we integrated existing P. hodgsonii gut metagenome-assembled genomes with healthy and Blastocystis-infected gut metagenomic samples to investigate microbial strategies for vitamins B and K2 production, as well as the potential modulation of these biosynthetic pathways in the gut of P. hodgsonii. From a total of 33,925 metagenome-assembled genomes, we identified 14,549 non-redundant genomes encoding 182 KEGG orthologs linked to vitamin biosynthesis. Among these, 2,115 high-quality genomes were predicted to synthesize at least one vitamin de novo, yet only 2.9% could produce four or more vitamins. Comparative analyses across multiple host species, including humans, chickens, cats, and mice, revealed that members of the phyla Bacillota_A and Bacteroidetes consistently serve as primary contributors to microbial vitamin biosynthesis. Blastocystis infection was associated with a significant increase in the abundance and diversity of vitamin biosynthesis genes, reflecting adaptive shifts in microbial metabolism. Detailed genomic analyses of the thiamine biosynthesis pathway highlighted the core contributions of Bacillota_A, Bacteroidota, Verrucomicrobiota, and Methanobacteriota, underscoring complex taxonomic cooperation. These results provide novel insights into the functional specialization and taxonomic composition of the P. hodgsonii gut microbiota, offering novel insights into microbial adaptation and metabolic cooperation that support host nutritional homeostasis and resilience in extreme environments.

Infectious bovine rhinotracheitis virus (IBRV), also known as bovine herpesvirus 1 (BoHV-1), is a globally important pathogen causing severe cattle diseases and substantial economic losses. However, the molecular mechanism by which IBRV induces host cell apoptosis through endoplasmic reticulum (ER)-mitochondria crosstalk remains largely unclear. In this study, Madin-Darby bovine kidney (MDBK) cells were used as an in vitro experimental model. Multiple experimental approaches including transmission electron microscopy, laser confocal microscopy, western blotting, flow cytometry, pharmacological inhibition, and siRNA interference, were applied to investigate the apoptotic mechanism triggered by IBRV infection. The results showed that IBRV infection destroyed ER ultrastructure and upregulated the expression of ER stress biomarker GRP78, accompanied by the full activation of three core branches of the unfolded protein response (UPR), including PERK, IRE1, and ATF6. Meanwhile, IBRV significantly promoted the formation of ER-mitochondrial membrane contact sites (MCSs) and triggered excessive Ca2+ release from the ER, leading to mitochondrial Ca2+ overload. Such Ca2+ dyshomeostasis further induced mitochondrial dysfunction, including reduced ATP production, collapsed mitochondrial membrane potential, and excessive reactive oxygen species accumulation, which ultimately activated caspase-dependent mitochondrial apoptosis. Inhibition of UPR signaling or ER-mitochondrial Ca2+ transport markedly alleviated mitochondrial damage, suppressed apoptosis, and reduced viral protein expression. Collectively, these findings demonstrate that the UPR-Ca2+-mitochondria axis serves as a key signaling pathway for IBRV-induced cell apoptosis, and that host UPR signaling is exploited by IBRV to support efficient viral replication, revealing a novel molecular pathogenic mechanism of IBRV and providing potential targets for the development of anti-IBRV therapeutic strategies.

As a zoonotic protozoan, Pentatrichomonas hominis has been implicated in gastrointestinal diseases, typically residing in the cecum or colon of diverse vertebrate hosts. Nevertheless, information regarding its prevalence and genotypic distribution in farmed foxes (Vulpes lagopus) remains limited. Fresh fecal samples (n = 352) from farmed foxes in northern China were analyzed for P. hominis via nested PCR. The overall prevalence was 15.62% (55/352). Infection rates were 12.09% (22/182) in adults and 19.41% (33/170) in juveniles. The prevalence exhibited seasonal fluctuations, ranging from 10.90% to 25.24%, with the highest prevalence observed in autumn. Foxes with diarrhea exhibited a significantly higher infection rate (33.78%, 25/74) than those without (10.79%, 30/278). Prevalence varied across regions, with the highest rates in Jilin (30.00%, 12/40), followed by Shandong (26.88%, 25/93), Hebei (12.90%, 12/93), Liaoning (6.33%, 5/79), and Heilongjiang (2.13%, 1/47). All positive samples were grouped into the zoonotic CC1 genotype based on phylogenetic analysis. This study offers novel epidemiological insights into P. hominis occurrence among farmed foxes in northern China and underpins the advancement of specific approaches for its detection and control.

Clostridium perfringens is a major pathogen threatening livestock health. This study investigated the antimicrobial resistance and genomic features of C. perfringens isolates from sheep in northern China. From October 2023 to June 2024, 70 strains were isolated from 467 fecal samples collected in Jilin, Heilongjiang, Liaoning, and Shandong provinces, with an overall isolation rate of 15.0%. The rate was significantly higher in diarrheic samples (18.07%) than in non-diarrheic ones (11.5%). Toxin gene typing identified 67.1% of isolates as type A and 32.9% as type D. Antimicrobial susceptibility testing showed that 94.3% of isolates were resistant to at least one antibiotic, with the highest resistance to gentamicin (GEN, 78.6%). Whole-genome sequencing identified seven classes of antimicrobial resistance, comprising 59 resistance genes. Additionally, 121 virulence-associated genes belonging to eight virulence factor categories were detected. Spearman correlation analysis revealed strong negative correlations between ARGs and VFGs in C. perfringens, including ErmQ vs. nagI (r_s = -1) and tetB(P) vs. cpe (r_s = -1), all remaining significant after multiple testing correction. These results suggest an adaptive trade-off in which resistance may be prioritized over virulence, highlighting a potential intrinsic antagonism between resistance and pathogenicity. Overall, C. perfringens isolates from sheep exhibit high resistance and genetic diversity, highlighting the importance of surveillance and prudent antimicrobial use to reduce potential public health risks.

Although gut microbiota-mediated bile acid (BA) metabolism is well characterized in mammals, its mechanisms in wild birds remain largely unknown, hindering our understanding of their ecological adaptation and health. In this study, metagenomic analysis was performed on 10,455 metagenome-assembled genomes (MAGs) derived from 718 wild bird gut samples, from which 1,034 high-quality non-redundant MAGs were selected for further analysis. Functional annotation analysis identified 755 MAGs encoding genes associated with BA biotransformation pathways, primarily derived from the phyla Bacillota_A, Bacteroidota, and Bacillota, with dominant genera including Helicobacter_G and Ligilactobacillus. Subsequent genomic analysis identified 379 MAGs encoding bile salt hydrolase (BSH), with phylogenetic classification demonstrating predominant affiliation to the Bacteroidota and Bacillota_A phyla. Compared to the BSH-producing microbiota in the human and chicken gut, the phylum Bacillota exhibited a notably higher relative abundance in wild birds. Within the wild bird gut microbiome, Helicobacter_G was identified as the predominant BSH-encoding genus, whereas its relative abundance was substantially lower in both humans and chickens. Moreover, migratory birds (MB) displayed significantly higher diversity of BA biotransformation genes than resident birds (RB), with Helicobacter_G being notably enriched at the genus level in MB, potentially associated with their heightened energy and nutritional demands during migration. Notably, in addition to residency status, host species emerged as the most influential factor shaping the compositional variation of BA biotransformation genes, followed by environmental factors and dietary habits. In summary, this study systematically elucidates the potential functions of gut microbiota in BA metabolism and their close associations with host ecological traits in wild birds, not only advancing our understanding of host-microbe interactions and metabolic adaptation mechanisms but also providing a theoretical foundation for future interventions targeting gut microbiota to improve wildlife health.

Wild rodent's gut microbiota serves as a crucial reservoir of antibiotic resistance genes (ARGs), where antimicrobial-resistant bacteria interact with mobile genetic elements (MGEs) to facilitate horizontal gene transfer. This study analyzed 12,255 gut-derived bacterial genomes from wild rodents to characterize the distribution of ARGs and virulence factor genes (VFGs), and to identify their bacterial hosts. A total of 8119 ARGs and 7626 VFGs were identified. The most prevalent ARGs conferred resistance to elfamycin, followed by those associated with multi-class antibiotic resistance. Enterobacteriaceae, particularly Escherichia coli, harbored the highest numbers of ARGs and VFGs. A strong correlation between the presence of MGEs, ARGs, and VFGs was observed, highlighting the potential for co-selection and mobilization of resistance and virulence traits. These findings underscore the importance of expanded surveillance to monitor and mitigate the risk of transmission of resistant and potentially pathogenic bacteria from wild rodents to human and animal populations.

Tibetan antelopes, native to high-altitude plateau regions, play an important role in the local ecosystem. Their gut harbors antimicrobial-resistant microbes, including potential pathogens. To explore this, we analyzed 33,925 metagenome-assembled genomes (MAGs), including 7,318 from 68 Tibetan antelopes sequenced in our laboratory. We first profiled the composition of antibiotic resistance genes (ARGs) and then examined their associations with virulence factor genes (VFGs). In total, 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being most prevalent. Two ARGs were located on phage-derived sequences, though their phage taxonomy could not be resolved. ARGs were significantly correlated with VFGs, particularly genes linked to adherence and effector delivery systems. Given potential dissemination risks, we further assessed associations between ARGs and mobile genetic elements (MGEs), finding that insertion elements accounted for the largest number of ARG-MGE links. Comparative analysis with other plateau animals and humans revealed seven ARGs uniquely present in Tibetan antelopes. In summary, this study provides the first comprehensive overview of ARG composition in Tibetan antelope gut microbiomes, establishing a baseline for future hypothesis-driven studies and antimicrobial resistance surveillance in wildlife. IMPORTANCE:Investigating the drug resistance of Tibetan antelope (Pantholops hodgsonii) gut microbiota serves as a critical biological indicator for assessing the impact of human activities (particularly antibiotic contamination) on the fragile ecosystem of the Qinghai-Tibet Plateau. This study untangles the invasion of antibiotic resistance genes (ARGs) into remote conservation areas, suggesting that Tibetan antelopes may act as potential vectors for ARG dissemination across plateau environments. Such findings not only highlight threats to wildlife health but also provide an ecological warning regarding the pervasive environmental risks posed by the global antimicrobial resistance crisis in natural ecosystems.