Institute of Microbiology

Objective: This study aimed to investigate antimicrobial resistance (AMR) in Escherichia ( E. ) coli , a recognized indicator bacterium for drug resistance, across animal, environmental and human compartments on Zhongyangshan Island under natural conditions. Methods: A total of 51 E. coli strains were isolated and identified from animal, environmental, and human samples on Zhongyangshan Island between 2022 and 2023. The drug resistance status of E. coli was analyzed using antimicrobial susceptibility testing, whole-genome sequencing analysis, multilocus sequence typing and pulsed-field gel electrophoresis. Results: Antimicrobial susceptibility testing revealed that the resistance rate of E. coli across the “animal-environment-human” interface on Zhongyangshan Island was ≤50%. Overall, AMR levels were low, with isolates from human sources exhibiting higher resistance to seven antibiotics and a higher prevalence of multidrug resistance compared to those from animal sources, while environmental isolates showed the lowest resistance levels. Of the 51 “animal-environment-human” E. coli strains, 31.37% (16/51) harbored five or more different antimicrobial resistance genes. Additionally, 78 transposons were detected, including 72 insertion sequences (IS), 3 compound transposons (Tn), and 3 other types of transposons, along with 18 plasmid replicon sequence types associated with AMR. Multilocus sequence typing and pulsed-field gel electrophoresis-based evolutionary analyses indicated the E. coli strains from the “animal-environment-human” continuum exhibited diverse sequence types and limited genetic relatedness. Further analysis of broiler-derived E. coli from Zhongyangshan Island showed significantly lower resistance rates to 12 out of 14 tested antibiotics and a lower overall multidrug resistance rate (46.67%), compared with isolates from intensive broiler farms in Zhejiang Province, except for amoxicillin/clavulanic acid and meropenem. whole-genome sequencing analysis confirmed that these strains carried fewer AMR genes. Conclusions: E. coli , serving as an indicator organism for AMR within the “animal-environment-human” system on Zhongyangshan Island, exhibits low AMR prevalence and limited clonal relatedness. These findings provide a valuable baseline for investigating the ecological mechanisms underlying antimicrobial resistance emergence and transmission under the “One Health” framework.

Ericoid mycorrhizal (ERM) fungi are essential mediators of nutrient cycling in heathland ecosystems, helping host plants access organic nutrients in nutrient-poor conditions. Traditionally, these fungi are regarded as mutualists; they also possess saprotrophic capabilities that may become increasingly important under changing environmental conditions. Such climate-driven lifestyle flexibility could reshape soil carbon cycling and feedbacks to the atmosphere. Yet, how these lifestyle shifts reshape ERM and broader fungal community composition, and their consequences for soil carbon dynamics, remain poorly understood.This study examines the impact of climate change on the decomposer activity and carbon allocation dynamics of ERM fungi using DNA-Stable Isotope Probing (DNA-SIP). Experiments were conducted within climate manipulation mesocosms representing past (2009-2013) and future (2080-2089) climate scenarios. Two complementary DNA-SIP experiments were employed. In the first experiment, mesh bags containing 13C-labeled cellulose or hemicellulose were used to trace the capacity of ERM fungi to decompose plant polymers. Samples were collected at 2 and 7 days post-labeling to capture the early and later stages of substrate utilization. In the second, entire mesocosms were fumigated with 13CO2 for 5 days, and samples were collected 2, 7, and 15 days post-fumigation to quantify carbon transfer from plants to ERM fungi and evaluate shifts in belowground carbon allocation under future climate conditions.By linking isotopic enrichment in fungal DNA with molecular community profiling, this project aims to identify which ERM taxa actively assimilate carbon from distinct sources under varying climates. We expect that future climate conditions will promote ERM taxa with greater saprotrophic potential and modify the temporal dynamics of carbon flow from plants to mycorrhizal fungi. Such shifts are likely to influence fungal community composition, intensify interactions with saprotrophic decomposers, and accelerate the turnover of soil organic matter.Understanding these potential lifestyle shifts is crucial for predicting how ERM fungi mediate soil carbon balance and ecosystem resilience in response to ongoing climate change.

<title>Abstract</title> Deep-sea microorganisms comprise the Earth's largest and least explored microbiome, yet the vast majority remain uncultivated due to challenges of preserving in situ high hydrostatic pressure and preventing loss of viability and diversity during recovery, which limits our ability to explore their ecological functions and adaptive strategies. Here, we introduce DeepDrop, a microfluidics platform that enables high-throughput single-cell cultivation under pressures spanning the full ocean depth directly aboard research vessels, following direct colony formation via pipette-generated double emulsions. Applying to hadal samples, DeepDrop recovered &gt;50% more microbial diversity than conventional high-pressure bulk cultivation, including rare taxa with streamlined genomes and distinctive genetic features associated with pressure adaptation. Combined metagenomic and transcriptomic analyses revealed that DeepDrop enriched pressure-adapted taxa carrying key stress-related genes and induced coordinated transcriptional reprogramming, characterized by upregulation of stress pathways and repression of motility. By integrating shipboard deployment, pressure-stable droplet cultivation, and efficient recovery, DeepDrop offers a powerful platform for accessing deep-sea microbial dark matter and illuminating microbial life strategies under extreme environmental constraints.

Macrophages are essential for host defense, yet how parenchyma-residing macrophages detect pathogens without direct contact remains unclear. Cryptococcus neoformans is an encapsulated fungal pathogen that infects the brain. Using in situ imaging of mouse model, we showed that brain-resident microglia vigilantly detect capillary-residing C. neoformans prior to its blood-brain barrier transmigration, but are less responsive to nonencapsulated fungi or parenchyma-injected C. neoformans. Microglia migrate to and enwrap leaky capillaries harboring fungi, leading to fungal uptake but not clearance, instead promoting fungal growth. Microglial response is triggered by released capsule components, rather than the assembled capsule. In particular, glucuronoxylomannan (GXM) plays a critical role by activating endothelial cells to release nucleotides which act on microglia P2Y12. Our findings revealed a novel paradigm by which microglia detect pathogens without direct contact, offering new insights for microglia-directed antifungal therapies.

Human galectin-1 (hGal-1) is an abundant β-galactoside-binding animal lectin that plays an essential role in promoting the immunosuppressive tumor microenvironment. Although hGal-1 has been identified as a promising target for pharmacological inhibition, developing potent and selective hGal-1 inhibitors has been complicated by the high degree of sequence similarity of the glycan-binding site across the galectin family. Herein, we present potent nanomolar hGal-1 inhibitors with unprecedented selectivity of 2 to 3 orders of magnitude over human galectin-3 (hGal-3). Their primary structural feature is the modification of a thiodigalactoside scaffold at the 3- and 3'-positions with a half-sandwich ruthenium(II) arene complex containing a bidentate 4-(2-pyridyl)-1H-1,2,3-triazol-1-yl ligand. The most potent inhibitor in the series efficiently blocked the binding of hGal-1 to the surface of MDA-MB-231 tumor cells, reduced their viability, and completely suppressed hGal-1-induced phosphatidylserine exposure in Jurkat cells, a process previously described as preaparesis rather than classical apoptosis.

<title>Abstract</title> Individual variation in human attractiveness to mosquitoes critically influences vector-borne disease transmission, but the mechanistic basis remains unclear. This study integrated human skin microbiome profiling, non-human primate in situ intervention, and volatilomics to uncover a microbial-mediated mechanism underlying host-specific mosquito repellency. We established that <italic>Bacillus</italic> species were a core microbial signature associated with reduced mosquito attraction in humans. Targeted Intervention of <italic>B. licheniformis</italic> and <italic>B. paralicheniformi</italic> s on primate skin was sufficient to significantly reduce mosquito attraction, thereby establishing a causal microbial contribution beyond descriptive correlations. Mechanistic analyses revealed that <italic>Bacillus</italic> enrichment reprogramed the skin volatilome, specifically increasing the abundance of aromatic and fatty acid-derived effectors, such as p-Cresol and decanoic acid, which associated with repellency phenotypes. Together, these findings revealed a conserved role of skin commensals in shaping mosquito host-seeking behavior, providing a molecular basis for microbiome-informed and bio-inspired strategies for mosquito disease control.