The bacterial pathogen Legionella pneumophila delivers more than 330 effector proteins into host cells through its Dot/Icm type IV secretion system (T4SS) to facilitate its intracellular replication. A number of these effectors modulate organelle trafficking pathways to create a membrane-bound niche called the Legionella-containing vacuole (LCV). In this study, we found that L. pneumophila induces F-actin accumulation in the host cell cortex by its Dot/Icm substrate RavJ (Lpg0944). RavJ harbors a C₁₀₁H₁₃₈D₁₇₀ motif associated with human tissue transglutaminases (TGs). We show that RavJ catalyzes a covalent linkage between actin and members of the Motin family of proteins, including Angiomotin (AMOT) and Angiomotin-like 1 (AMOTL1), which are known to regulate cell migration and contribute to the formation of cellular structures such as endothelial cell junctions and tubes. Further study reveals that RavJ-induced crosslink between actin and AMOT occurs on its Gln₃₅₄ residue. Crosslink between actin and AMOT significantly reduces the binding between actin and its binding partner cofilin, suggesting that RavJ inhibits actin depolymerization. We also demonstrate that the metaeffector LegL1 directly interacts with RavJ to antagonize its TG activity, leading to reduced crosslinks between actin and Motin proteins. Our results reveal a novel mechanism of modulating the host actin cytoskeleton by L. pneumophila.

Probiotics can reduce the incidence of respiratory syncytial virus (RSV) disease in premature infants; this approach is resource-intensive and less expensive than other strategies and easier to implement than most current methods worldwide. Traditional lactic acid-producing bacteria are the main probiotics that have been studied for RSV treatment. Marine probiotics promote the survival, immunity, and disease resistance of aquatic plants and animals. However, relatively little research has been conducted on viral infections in humans. Here, we report a slightly halophilic and extremely halotolerant marine bacterium, Paraliobacillus zengyii, which has antiviral activity and grows at a relatively low temperature (28°C). We found that P. zengyii inhibited RSV infection by regulating the interferon (IFN) response both in vitro and in vivo. P. zengyii significantly increased the RSV-induced phosphorylation of TBK1 and IRF3 and the expression of antiviral factors interferon-induced transmembrane protein 1 (IFITM1) and interferon-induced transmembrane protein 3 (IFITM3). Furthermore, P. zengyii upregulated Sendai virus (SeV)- and poly(I:C)-induced IFN-β expression. These results indicate that the marine bacterium P. zengyii inhibits RSV infection and increases IFN-β production in response to RSV, SeV infection, or poly(I:C) stimulation. Consequently, P. zengyii has potential as a broad-spectrum anti-RNA virus probiotic.

Gram-negative bacteria are particularly prone to developing antimicrobial resistance (AMR), as evidenced by the WHO's ESKAPEE list of high-priority pathogens. One strategy that has increased is the use of antibiotic enhancers, which can re-empower abandoned or poorly active antibiotics against the resistant strain of interest. In this study, the polyamino-isoprenyl antibiotic enhancer, NV716, was tested in combination with two families of multi-target Ser/Cys-based enzyme inhibitors, the oxadiazolone derivatives (OX) and the Cyclipostins and Cyclophostin analogs (CyC), which are inactive against Gram-negative ESKAPEE bacteria, to potentiate their antibacterial activity and thus make them active against these bacteria. We demonstrated that NV716 potentiates some OX and CyC compounds by permeabilizing the outer membrane and thus by increasing the inhibitor accumulation, as shown by fluorescence microscopy. By using the click-chemistry activity-based protein profiling (ABPP) approach coupled with proteomic analysis, we also confirmed the multi-target nature of the best OX and CyC inhibitors by identifying their target proteins on a bacterial culture of Enterobacter cloacae. Remarkably, a large set of these identified proteins had already been captured in previous ABPP experiments conducted on Mycobacterium tuberculosis and/or Mycobacterium abscessus culture. Furthermore, we showed that five of the identified target proteins were present in a total lysate of Pseudomonas aeruginosa. Importantly, these latter enzymes are highly conserved among Gram-negative bacteria, with two of them annotated as essential for bacterial survival. These results provide proof of concept that both OX and CyC, if successfully potentiated, could be used against ESKAPEE Gram-negative bacteria.

The emergence and spread of antibiotic-resistant pathogens in food animals pose a major threat to global public health. Carbapenem-resistant Enterobacteriaceae (CRE), particularly those producing New Delhi Metallo-β-lactamase (NDM-CRE), are prevalent in livestock and have acquired resistance to nearly all commonly used β-lactam antibiotics. This study evaluated the efficacy of the antimicrobial peptide BMAP-27B, a derivative of the cathelicidin family, against NDM-CRE strains in food animals. BMAP-27B showed potent antibacterial activity and rapid bactericidal effects against CRE, as well as comparable effects against human carbapenem-resistant Acinetobacter baumannii. Furthermore, BMAP-27B effectively penetrated and cleared biofilms formed by virulent strains of Escherichia coli and Klebsiella pneumoniae. Mechanistic studies indicated that BMAP-27B exerts its antibacterial activity by disrupting bacterial membranes and inhibiting bacterial energy metabolism. BMAP-27B effectively enhances the efficacy of carbapenems against NDM-positive isolates by inhibiting efflux pump activity and chelating Zn²⁺ to inhibit NDM proteases, thus reversing carbapenem resistance in NDM-CRE. Importantly, BMAP-27B maintained excellent antimicrobial stability under extreme pH changes and high salt concentrations, along with resistance to serum and protease degradation. Investigations revealed that BMAP-27B also shows ideal biocompatibility and therapeutic efficacy in vivo. In summary, the highly potent antibacterial activity of BMAP-27B, along with its potential role as a broad-spectrum antibiotic adjuvant, makes it a promising candidate for combating infections caused by foodborne NDM-CRE and preventing pathogen transmission at the animal-human-environment interface.

Understanding microbial community assembly in plants is critical for advancing agricultural sustainability. This study investigated microbial diversity and community assembly mechanisms across six compartments of tomato plants: bulk soil, rhizosphere, root, stem, flower, and seed. Using 16S rRNA amplicon sequencing, we observed that microbial richness was highest in the bulk soil and rhizosphere, with significant reductions in internal plant tissues. Co-occurrence network analysis identified distinct microbial hubs in each compartment, such as Bacillus in the root and seed, highlighting critical interactions influencing microbial dynamics. Ecological process modeling revealed that deterministic processes, such as selection, dominated in below-ground compartments, whereas stochastic processes like drift were more influential in above-ground tissues, reflecting differences in niche specificity and ecological stability. Dispersal limitation emerged as a key driver in soil-associated compartments, structuring microbial diversity. These findings advance our understanding of the ecological mechanisms shaping plant microbiomes and suggest targeted microbiome management strategies to enhance crop health, productivity, and resilience. Future research integrating functional genomics, temporal dynamics, and environmental factors is necessary to uncover the broader implications of plant-associated microbiomes.

Microbial biogeography and its controlling mechanisms are central themes in microbial ecology. However, we still lack a comprehensive understanding of how habitats and lifestyles affect microbial biogeography across complex environmental gradients. In this study, we investigated the planktonic (including free-living [FL] and particle-associated [PA] lifestyles) and benthic prokaryotic communities along a river–estuary–sea continuum of the Changjiang River to explore their distinct spatial dynamics. We observed greater community variability across spatial distances than between habitat and lifestyle types. Spatial variations were evident in FL, PA, and benthic communities, with the highest turnover rates observed in benthic communities, followed by PA, and the lowest turnover rates observed in FL. The replacement effect dominated PA and benthic community variations, whereas the richness effect was more significant in FL communities. Microbial assembly was primarily governed by homogeneous selection and dispersal limitation regardless of habitats/lifestyles, with their ratios decreasing as the spatial distance increased, particularly in the FL fraction. Dispersal limitation had a stronger effect on benthic communities compared to planktonic communities. While heterogeneous selection generally played a minor role, its influence became more pronounced over larger spatial distances and with increasing salinity differences. Finally, we showed that abiotic and biotic factors individually exerted a greater influence on PA communities, whereas their interactions had a stronger effect on FL communities. Our results revealed complex spatial dynamics and assembly mechanisms among microorganisms across different habitats and lifestyles, providing insights into the spatial scaling of community assembly across complex environmental gradients.

Dissolved organic matter (DOM) contains thousands of molecules and is key for biogeochemical cycles in aquatic and terrestrial ecosystems by interacting with microbes. Over the last decade, the study of DOM has been advanced and accelerated with the developments of instrumental and statistical approaches. However, it is still challenging in statistical analyses, data visualization, and theoretical interpretations largely due to the complexity of molecular composition and underlying ecological mechanisms. In this study, we developed an R package iDOM with functions for the basic and advanced statistical analyses and the visualization of DOM derived from Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). The package could handle various data types of DOM, including molecular compositional data, molecular traits, and uncharacterized molecules (i.e., dark matter). It could integrate explanatory data, such as environmental and microbial data, to explore the relationships between DOM and abiotic or biotic drivers. To illustrate its use, we presented case studies with an example dataset of DOM and microbial communities under experimental warming. We included case studies of basic functions for the calculation of molecular traits, the assignment of molecular classes, and the compositional analyses of chemical diversity and dissimilarity. We further showed the case studies with advanced functions to quantify DOM assembly processes, assess the effects of dark matter on molecular interactions, analyze the ecological networks between DOM and microbes, and explore their response to warming. The source code and example dataset of iDOM are publicly available on https://github.com/jianjunwang/iDOM. We expect that iDOM will serve as a comprehensive pipeline for DOM statistical analyses and bridge the gap between chemical characterization and ecological interpretation in a theoretical framework.