Yu, M.-Y. | bioRxiv Science

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↗

bioRxiv2024

Endophytic pyrroloquinoline quinone enhances banana growth and immunity against Fusarium wilt for plant-microbe mutualisms

Fusarium wilt has a substantial impact on global banana production, posing a threat to food security worldwide. However, breeding new Fusarium-resistant cultivars is difficult and time-consuming. Alternatively, endophytic biostimulants that could combat such pervasive plant diseases provide possible novel solutions. Our prior research demonstrated that a pyrroloquinoline quinone (PQQ)-producing endophytic bacterium, Burkholderia seminalis 869T2, can enhance the growth of various plant species and protect bananas from Fusarium wilt in the field. PQQ is a peptide-derived redox cofactor known to stimulate mitochondrial biogenesis and metabolism in animals, but its molecular roles, especially in plants, remain to be elucidated. In this study, multi-omics approaches were employed to explore the potential mechanisms through which PQQ influences banana plants. The result of in situ imaging mass spectrometry revealed that the endophytic metabolite PQQ does not function through direct antagonism against Fusarium. The follow-up transcriptomic profiling shows it could regulate plant respiration, TCA cycle, oxidative phosphorylation, NAD/NADP-dependent dehydrogenases, MAPK signalling, and various phytohormone signalling pathways. Furthermore, PQQ appeared to trigger plant systemic immunity, thereby enhancing plant health and resistance to biotic stress. Beyond that, the complete genome of 869T2 was determined for follow-up comparative genomics analyses, revealing its genetic contexts, potential evolutionary events of PQQ operons among the Burkholderia species, and the absence of human virulence-facilitating genes within those PQQ-producing agricultural isolates. In summary, this study facilitates our understanding of PQQ in plant-microbe mutualisms and provides scientific evidence for its future application in agriculture. Significance StatementFusarium wilt is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a notorious soil-borne pathogen that attacks bananas vascular system, which critically threatens global banana production and food security. A potential PQQ-producing endophytic strain has been confirmed to protect bananas through in planta biocontrol, reducing the morbidity of Banana Fusarium Wilt (BFW) disease in the field and promoting the growth of banana plants simultaneously. Our results revealed that the endophytic metabolite PQQ does not function through direct antagonism but triggers plant systemic immunity and coordinates energetic metabolisms, thereby improving the overall health of host plants and enhancing their resistance against Fusarium wilt.

plant biology↗