Hongchao, S. | Search bioRxiv

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↗

bioRxiv2019

Cyniclomyces guttulatus is an opportunistic pathogen in rabbits with coccidiosis

Cyniclomyces guttulatus is a common inhabitant of the gastrointestinal tract in rabbits, and large numbers are often present in feces of diarrheic rabbits. However, its relation with rabbit diarrhea has not been clearly identified. We isolated a C. guttulatus Zhejiang strain from a rabbit with severe diarrhea and optimized the culture conditions in YPG medium. The sequenced 18S and 26S ribosomal DNA fragments were 1559bp and 632bp, respectively, and showed 99.8% homology with the 18S ribosomal sequence of the NRRL Y-17561 isolate from the dog and 100% homology with the 26S ribosomal sequence of the DPA-CGR1 and CGDPA-GP1 isolates from the rabbit and guinea pig. Our isolate was not pathogenic to healthy SPF rabbits. Instead, rabbits inoculated with the yeast had a slightly better body weight gain and higher food intake. Rabbits co-inoculated with C. guttulatus and the coccidian, E. intestinalis developed more severe coccidiosis as shown by clinical signs, and decreased body weight gain, diarrhea and death, associated with significantly higher fecal output of C. guttulatus vegetative cells but lower coccidian oocysts output than the rabbits inoculated with C. guttulatus or E. intestinalis alone. We also surveyed the prevalence of C. guttulatus in rabbits and found a positive rate of 83% in Zhejiang province. Our results indicate that C. guttulatus alone is not pathogenic to healthy rabbits, but could become an opportunistic pathogen when the digestive tract is damaged by other pathogens such as coccidia. Author summaryCyniclomyces guttulatus, a commensal yeast in rabbit gastrointestinal tract, is very commonly seen in diarrhea cases. However, it is unclear whether it causes or is a co-cause of diarrhea with other pathogens. Here, a C. guttulatus Zhejiang strain was firstly isolated from a rabbit with severe diarrhea and the culture conditions in YPG medium were optimized. Then, it was identified in morphology and molecular. It was agreed with the previous description in morphology and showed a closer phylogenetic relationship with other strains originated from herbivores than those from the carnivore. Finally, the C. guttulatus Zhejiang strain was inoculated to SPF rabbits singly or co-inoculated with Eimeria intestinalis. All of the results in animal assays show C. guttulatus alone is not pathogenic but seems a probiotic microorganism in rabbits. However, it could become an opportunistic pathogen when the digestive tract is damaged by other pathogens such as coccidia.

microbiology↗