FEMS microbes最新文献

Urinary tract infections (UTI) are very common infections. To study UTI, researchers often use animal models, but studying certain phenotypes is difficult and comes with ethical and administrative challenges. To address these challenges, we developed a reproducible and cost-effective model to study UTI using donated mouse bladders that would otherwise be discarded. This model, which is easily mastered, supports study of interactions between the host and bacteria in a controlled environment. We found that uropathogenic Escherichia coli colonization and invasion in our model was comparable to in vivo mouse models. To optimize reproducibility, we tested variables including incubator conditions, and biological factors like donor mouse sex or pregnancy. Our method allows assessment of early host-pathogen interactions, immune cell uptake, the impact of age and sex, and diverse bacterial strains or treatments. In some countries, sharing material from animals sacrificed for other reasons does not require additional ethical approval, providing a resource for labs without animal access and reducing administrative burden. Given the breadth of the model to test sex, age, mouse and bacterial strain, or any parameter that can be adapted to a 96-well plate, this model has potential application beyond infection or even beyond the bladder to other tissues.

Clostridioides difficile infection (CDI) is a toxin-mediated gastro-intestinal disease. Yet, C. difficile is a phylogenetically diverse species that includes many non-toxigenic strains. In general, these are understudied, despite having significant potential impact for our understanding of the colonization process and as therapeutic modalities. Here, we present an in-depth characterization-including the complete genome sequence-of the non-toxigenic C. difficile strain L-NTCD03. This strain belongs to PCR ribotype 416, clade 4 and multilocus sequence type 39. It is resistant to multiple antimicrobials, but not those used for treatment of CDI. We validated the relevance of the cfr(B) gene from this strain in antimicrobial resistance to clindamycin, linezolid, retapamulin, and streptogramin A. We found the L-NTCD03 strain to be non-toxic in various assays. Altogether, L-NTCD03 is a promising candidate for developing into a live biotherapeutic product.

MtxX, also known as Methanogen Marker Protein 4 (MMP4), is a member of the group of proteins conserved in archaeal methanogens called the Methanogen Marker Proteins (MMPs). Owing to this taxonomic distribution the MMPs are presumed to have roles related to methanogenesis or are evidence for an evolutionary history associated with methanogenic processes. MtxX is sequence-annotated as either a methyltransferase (EC 2.1.1.-) or a phosphate acetyl/butyryltransferase (EC 2.3.1.8/2.3.1.19). Gene synteny analysis shows mtxX is located next to other MMP genes in Methanomicrobiales, Methanotrichales, and Methanocaldococcus genomes, while in Methanobacteria and Methanococci it is positioned adjacent to undecaprenyl pyrophosphate synthase, a cell wall biosynthesis enzyme. We describe the crystal structure for MtxX from Methanothermobacter thermautotrophicus ΔH showing that it has a protein fold homologous to phosphate acetyltransferases and decarboxylating NAD(P)-dependent dehydrogenases. The MtxX structure has a conserved binding cleft which is the presumptive functional site based on crystallographic symmetry-related molecular binding interactions and structural homology.

Gram-negative bacteria utilize type VI secretion systems (T6SS) for microbial competition and host interaction. While most pathogens rely on the canonical T6SSⁱ, Francisella species uniquely possess T6SSⁱⁱ. The highly virulent human pathogen Francisella tularensis harbors a distinct T6SSⁱⁱ variant that includes pdpC, encoding a putative effector protein. Bioinformatic analysis revealed a conserved amino acid triad in PdpC, homologous to motifs found in Make Caterpillars Floppy family toxins. To investigate the functional relevance of this triad, site-directed mutagenesis was performed in the live vaccine strain of F. tularensis, substituting each residue with alanine. Mutants showed impaired phagosomal escape, reduced intracellular replication, and marked attenuation in the mouse infection model. Equivalent mutations introduced into F. novicida, a model for T6SS-mediated secretion, confirmed the triad's importance. Mass spectrometry analysis demonstrated that PdpC is secreted in a T6SS-dependent manner. Importantly, the mutations did not affect secretion, and deletion of pdpC did not alter the overall secretion profile. These findings indicate that the conserved triad is essential for PdpC's effector function but dispensable for its secretion. This study highlights a critical motif required for Francisella virulence and provides new insights into the specialized mechanisms of T6SSⁱⁱ effectors.

Candida glabrata is a clinically significant cause of candidemia, yet how it supplies uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) for cell-wall chitin synthesis remains unclear. Here, we identify an N-acetylglucosamine (GlcNAc) kinase encoded by CAGL0M00682g and designated CgNgk1. In vitro, purified CgNgk1 preferentially phosphorylated GlcNAc with markedly higher catalytic efficiency than other sugars and accepted multiple nucleoside triphosphates, including ATP, as phosphoryl donors. Site-directed mutagenesis indicated that Asp197 and Lys155 are required for catalysis and ATP binding, respectively. In vivo, CgNgk1 overexpression in C. glabrata increased intracellular UDP-GlcNAc in a GlcNAc dose-dependent manner, whereas the kinase-dead D197N variant had no effect. CgNgk1-mediated GlcNAc phosphorylation elevated cell-wall chitin and heightened sensitivity to sodium dodecyl sulfate, heat, and low pH, but did not affect β-1,3-glucan-related phenotypes such as zymolyase or caspofungin sensitivity. Under GlcNAc supplementation, CgNgk1-overexpression specifically decreased cellular susceptibility to flucytosine, while responses to voriconazole and amphotericin B were unchanged. Overexpression of the putative hexosamine-pathway regulator CgIsr1 lowered intracellular UDP-GlcNAc, consistent with an intact endogenous pathway. These findings demonstrate that imported GlcNAc is routed via CgNgk1 to UDP-GlcNAc to promote chitin biosynthesis, and that quantitative control of this route shapes cell-wall integrity and modulates responses to host-relevant stresses and antifungal agents.

Marine microbial communities are vital to biogeochemical cycling, yet their dynamics in regions of ecological and industrial significance, such as the Santos Basin (SB), Brazil's largest offshore oil-producing basin, remain poorly resolved. To address this gap, we combined 16S rRNA amplicon sequencing, flow cytometry, and a hybrid machine learning framework (Self-Organizing Maps and Random Forest) to analyze microbial community stratification across pelagic depths in the SB. We identified five depth-specific microbial associations predicted with 86% accuracy, driven primarily by temperature, salinity, water density, and nutrient availability. Shallow epipelagic and mesopelagic zones were dominated by temperature-driven assemblages, while deeper bathypelagic communities responded to salinity and density gradients. Temporal and spatial patterns further highlighted the influence of regional oceanographic processes, including the Cabo Frio upwelling and Rio de la Plata plume. Microbial diversity increased with depth, contrasting with higher cell abundances in nutrient-rich shallow waters. We provided new insights into the relative importance of oceanographic processes, suggesting that vertical stratification and regional hydrography may play a more central role shaping microbial communities than previously recognized. We also established a predictive framework for microbial dynamics in marine ecosystems, with direct implications for assessing anthropogenic impacts in industrially active regions like the SB.

The rapid emergence of multidrug-resistant (MDR) bacteria has severely compromised the efficacy of conventional antibiotics and intensified the global antimicrobial resistance crisis. Antimicrobial peptides (AMPs) have attracted considerable interest as adjunctive agents due to their membrane-active mechanisms and immunomodulatory properties; however, their clinical use as monotherapy remains limited by instability, toxicity, and pharmacokinetic constraints. Combining AMPs with conventional antibiotics has emerged as a promising strategy to enhance antibacterial efficacy, restore antibiotic susceptibility, and modulate resistance development. This review critically examines the mechanistic basis of AMP-antibiotic synergy, integrating evidence from in vitro and in vivo studies. Particular emphasis is placed on determinants that govern synergistic outcomes, including membrane permeability, porin-dependent antibiotic uptake, resistance-associated adaptations, and host-related factors that cannot be captured in vitro. In addition, we discuss key translational barriers limiting clinical implementation, such as immune modulation, pharmacokinetic mismatch, peptide instability, and strain-dependent variability in synergistic responses. By linking molecular mechanisms to experimental and translational outcomes, this review provides a focused framework for rational design and optimization of AMP-antibiotic combination therapies against MDR bacterial infections.

Toxoplasma gondii is remarkable for its intermediate host range, which includes most warm-blooded animals so far tested. Being such a generalist poses challenges for how the parasite can be optimized for growth in cell types that might be radically different in their metabolism and other aspects, including host defenses and microenvironments. To explore how the parasite might adapt to finding itself in a different host, we started with a Type II line of T. gondii (ME49) that had been grown for at least the past 20 years exclusively in vivo. This line was then used to repeatedly infect two cell lines in vitro, human foreskin fibroblasts and Madin-Darby bovine kidney cells. After at least 70 such passages in one or other host cell type, the resulting lines were compared with respect to growth differences, secretion of an important adhesin (MIC2), and transcriptome. The results showed that passage on these two host cell lines results in profound and reproducible differences in parasite phenotype, including attachment/invasion, MIC2 secretion, and gene expression. The transcriptomic differences were especially pronounced for parasite surface antigen genes. The implications of these results for how T. gondii deals with its breadth of possible intermediate hosts are discussed.

Fermented foods represent complex microbial ecosystems that contribute to food quality, functionality, and potential health benefits, yet many traditional fermented foods remain poorly characterized. The aim of this study was to study microbial diversity, and functional potential of underexplored traditional Indonesian fermented food. The fermented products displayed substantial variation in bacterial richness, ranging from 65 to 614 bacterial amplicon sequence variants across samples. The microbial communities were dominated by bacterial taxa affiliated with the orders Bacillales and Lactobacillales, alongside fungal taxa from the order Mucorales. The plant-based products i.e. tape ketan and tape singkong had a higher bacterial abundance but lower diversity than animal-based terasi. We found significant correlations between bacterial and fungal communities dominated by positive cooccurrence patterns and highly complex networks especially in terasi. Each food product was characterized by a unique functional profile of genes linked to beneficial metabolic functions (biosynthesis of bacteriocins, short-chain fatty acids, and vitamins) but tape ketan samples demonstrated the highest diversity and abundance of them. Metagenome assembled genomes reflect a high diversity of health beneficial properties as well as substrate-specific degradation capabilities. Traditional Indonesian fermented foods harbour functionally redundant but phylogenetically diverse taxa offering a potential source for probiotic traits and functional food development.

Studies in model organisms and wild populations have uncovered manifold links between the gut microbiome and sociality, which, considering the adaptiveness of social behaviour, suggest a potentially generalized coevolution between microbiomes and social behaviour. Here, we leverage phylogenetically and ecologically diverse data from the Earth Microbiome Project to test the generality of the links between sociality and the gut microbiome in wild animals. We find evidence of a small but significant link between sociality and microbiome beta diversity, but not alpha diversity, in mammalian taxa, potentially due to socially mediated microbial transmission. Our work highlights the value of leveraging large-scale multi-study datasets to test fundamental questions about the role of sociality in host-microbiome coevolution.