Biology subjects

Ni, H.-B.

Publications and source records attributed to Ni, H.-B..

4 recordsLinked to original sources

bioRxiv2025

Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes

Tibetan antelopes, native to high-altitude plateau regions, play a vital role in the local ecosystem. However, their gut microbiota harbors diverse antibiotic resistance genes (ARGs) and virulence genes (VFGs), raising concerns about the potential spread of antibiotic resistance in wildlife. In this study, in addition to collecting 26,608 metagenome-assembled genomes (MAGs) from public databases, we performed gut metagenomic sequencing on 68 Tibetan antelopes and obtained 7,318 MAGs through binning. A total of 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being the most prevalent. Comparative analysis revealed 7 ARGs unique to Tibetan antelopes, suggesting species-specific adaptations. Additionally, during the analysis of shared antibiotic resistance profiles between Tibetan antelopes and humans, two bacterial strains were identified within the Tibetan antelope gut microbiota: Enterococcus gallinarum exhibiting resistance to extended-spectrum class A beta-lactamases and Klebsiella grimontii demonstrating vancomycin resistance. Mobile genetic elements played a key role in ARG dissemination. ARGs were significantly correlated with VFGs, particularly those linked to adherence and effector delivery systems. These findings underscore for the first time the potential ecological and health implications of ARG dissemination in Tibetan antelopes, highlighting the need for further surveillance to assess its impact on wildlife and environmental resistomes.

microbiology↗

bioRxiv2025

Integrated metagenome-resolved profiling of the resistome, virulome, and mobilome in the gut microbiota of wild birds

Wild birds, with their extensive geographic distributions and high mobility, are increasingly recognized as important players in the dissemination of antimicrobial resistance. Their gut microbiota, shaped by exposure to diverse environments, may act as both reservoirs and vectors of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and mobile genetic elements (MGEs). In this study, we reconstructed 2,516 high-quality metagenome-assembled genomes (MAGs) from 718 gut metagenomes of wild birds to comprehensively profile their resistome and virulome. We identified 5,596 ARG-encoding proteins across 389 distinct ARG types, with multidrug resistance emerging as the most dominant category. Escherichia coli was the principal carrier of ARGs, and genes conferring resistance to elfamycin antibiotics via target alteration were notably widespread--indicating persistent antibiotic selection pressures in avian habitats. Co-occurrence analyses revealed extensive genetic linkage between ARGs, VFGs, and MGEs. Critically, we detected 25 ARG-MGE co-localization events within 5-kilobase genomic regions, highlighting a strong potential for horizontal gene transfer and accelerated resistance dissemination within microbial communities. Of particular concern was the detection of the tetX1 gene--conferring resistance to tigecycline, a last-resort antibiotic--in the gut microbiota of Chroicocephalus ridibundus and Cygnus cygnus. This finding strongly implicates anthropogenic pollution in the spread of clinically relevant ARGs into wildlife and emphasizes the risk of environmental transmission to other hosts, including humans. These results underscore the critical ecological role of wild birds in the global antimicrobial resistance network. As both reservoirs and potential vectors of ARGs, they represent a significant but under-monitored interface between environmental and clinical resistance pathways. Enhanced surveillance and mitigation strategies targeting wildlife are urgently needed to curb the environmental propagation of antimicrobial resistance.

microbiology↗

bioRxiv2025

Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species

The gut microbiota of livestock serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied in this context. In this comprehensive metagenomic study, we analyzed 779 gut samples from Caprinae animals and reconstructed 17,023 high-quality metagenome-assembled genomes (MAGs). From these, we identified 4,685 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). Escherichia coli emerged as a major host carrying high burdens of both ARGs and VFGs. Strong positive correlations between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection and genetic linkage. Although MGEs were found in only 1.45% of MAGs, 23 ARGs were physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs were embedded within viral genomes, two of which were associated with Myoviridae phages and one with an unclassified viral source, implicating phages in AMR dissemination. Comparative analyses revealed 292 ARG types shared between Caprinae and the human gut microbiota, including 20 genes representing six clinically critical resistance types: tetX1, tetX4, tmexD3, vanD, vanR, and vanS--conferring resistance to tigecycline, vancomycin, and polymyxins. These findings expand our understanding of the resistome and virulome in Caprinae animals and highlight potential zoonotic transmission pathways, underscoring the need for targeted AMR surveillance and mitigation strategies.

microbiology↗

bioRxiv2025

Expanding the chicken gut virome: Uncovering viral diversity, host interactions, and regional variations across the intestinal tract

Chicken gastrointestinal virome comprises a complex and diverse viral community with significant implications for host health and microbiome function. We analyzed 3,312 publicly available chicken gut metagenomic datasets to establish the chicken gastrointestinal virome collection (CGVD), which includes 39,380 non-redundant viral operational taxonomic units (vOTUs); notably, 84.90% (33,433/39,380) represent novel sequences absent from current databases. Over half of the CGVD vOTUs were classified as bacteriophages, predominantly from the order Caudovirales. The predicted hosts were mainly prokaryotes, particularly Bacillota and Bacteroidota, revealing a multifaceted landscape of virus-host interactions. Many vOTUs infected multiple bacterial phyla, indicating high adaptability and broad ecological impact. In addition, lifestyle prediction showed that 28.28% (11,137 /39,380) of the vOTUs in CGVD were identified as lytic phages. Functional annotation demonstrated that viral genes contribute to key metabolic processes, including nucleotide and amino acid metabolism, thereby facilitating viral replication and host adaptation. The detection of auxiliary metabolic genes and carbohydrate-active enzymes underscores the role of viruses in modulating the gut microbiome. Although antibiotic resistance genes and mobile genetic elements were present, their contribution to horizontal gene transfer appears limited. Additionally, marked regional differences in virome composition were observed between the small and large intestines, particularly in the abundance of families such as Siphoviridae and Myoviridae. CGVD not only highlights the key role of viruses in shaping the chicken gut microbiome and influencing microbial dynamics and metabolic pathways, but also provides new resources and insights for future research.

microbiology↗