Fems Microbiology Letters最新文献

{"title":"Identification and genomic characterization of Shiga toxin subtype 2j-producing Escherichia coli isolated from an asymptomatic carrier in Japan.","authors":"Yuki Wakabayashi, Koichi Kojima, Shunya Nishijima, Tetsuya Harada, Takahiro Yamaguchi, Junko Sakata, Sadanori Sekiya, Shinichi Iwamoto, Koichi Tanaka, Takao Kawai","doi":"10.1093/femsle/fnag018","DOIUrl":"10.1093/femsle/fnag018","url":null,"abstract":"<p><p>Shiga toxin (Stx) is the primary virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx is categorized into Stx1 and Stx2 and further classified into several subtypes based on amino acid sequence variations. During routine surveillance of STEC isolates in Japan, we identified strain 2021H102 which harbored an uncommon stx subtype. Whole genome sequencing combined with matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysis revealed that 2021H102 was a Stx2j-producing E. coli. Despite similarity among the sequences of Stx2j encoding prophages, phylogenetic analysis revealed that stx2j-positive E. coli genomes are diverse. 2021H102 clustered with genomes identified in the United States by core-genome single nucleotide variant-based phylogenetic analysis, implying that 2021H102 may have been an imported case. Several detection PCR primers failed to amplify stx2j, implying that stx2j-positive STEC might not be detected in some clinical laboratories. To our knowledge, this is the first report of Stx2j-producing E. coli isolated from outside of North American continent.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146131645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aromatic metabolites regulate prodigiosin production in Serratia marcescens through SlyA.","authors":"Faviola Tavares-Carreón, Yossef López de Los Santos, Bryant U Trejo, Orlando Flores-Maldonado, Miguel A Becerril-García, Rogelio J Treviño-Rangel, Angel Andrade","doi":"10.1093/femsle/fnag041","DOIUrl":"10.1093/femsle/fnag041","url":null,"abstract":"<p><p>Some Serratia marcescens (Sm) strains produce the red pigment prodigiosin, which exhibits immunosuppressive, antimicrobial, and antitumoral properties. Prodigiosin biosynthesis is controlled by a complex regulatory network that includes SlyA, a MarR-family transcriptional regulator. However, the molecular mechanism by which SlyA regulates prodigiosin production remains largely unknown. Here, we showed that methyl benzoate, paeonol, salicylic acid, and p-coumaric acid reduce pigment production in Sm. Given previous evidence that small aromatic molecules can allosterically regulate MarR-family proteins, we generated a homodimeric structural model of Sm SlyA. Molecular docking analyses suggested that these aromatic metabolites bind within the two cavities of the SlyA homodimer, and molecular dynamics simulations identified methyl benzoate as the most stable ligand. Consistently, in vitro assays showed that the binding of recombinant SlyA to the prodigiosin promoter was altered in the presence of methyl benzoate and phenolic metabolites. Finally, exogenous methyl benzoate, paeonol, and salicylic acid significantly reduced pigA-gfp transcription in Sm, and this effect became more pronounced upon expression of slyA from a multicopy plasmid. Together, these findings support a model in which SlyA functions as an allosterically regulated sensor, coupling the perception of aromatic carbonyl compounds to the control of prodigiosin biosynthesis in Sm.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":"373 ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics of Lacticaseibacillus paracasei strain 69Bis reveals encoded probiotic traits and genomic specificities.","authors":"Mokhtar Eddine Djouad, Mohammed El Amine Bendaha, Hadj Ahmed Belaouni, Farid Bensalah","doi":"10.1093/femsle/fnag060","DOIUrl":"10.1093/femsle/fnag060","url":null,"abstract":"<p><p>This study provides a comprehensive characterization of Lacticaseibacillus paracasei strain 69Bis, isolated from traditional fermented goat milk collected in Biskra (southeast Algeria). Phenotypic investigations revealed robust probiotic traits across all isolates, including NaCl tolerance at 10%, acid resistance at pH 2.0 for 3 h, bile tolerance at 0.3%, and survival in simulated gastrointestinal digestion. Adhesion properties included high auto-aggregation and hydrophobicity. The strain exhibited potent antimicrobial activity, particularly against Pseudomonas aeruginosa. Whole-genome sequencing yielded a genome of 2.9 Mbp, with 46.38% GC and 2969 protein-coding sequences, enriched in carbohydrate and amino acid metabolism. Functional annotation highlighted genomic features associated with probiotic functions, including adhesion factors (acm, fimA, lapA), stress response pathways, and exopolysaccharide synthesis (eps gene family). Three biosynthetic gene clusters were detected, encoding bacteriocins and terpene synthesis. The absence of known acquired antimicrobial resistance genes and the susceptibility to all tested antibiotics indicate a favourable safety profile. The presence of CRISPR-Cas systems was confirmed, which may contribute to genomic stability and protection against phages. Comparative genomics, through genome-based taxonomy, confirmed the assignment to L. paracasei. Pan-genome analysis of 122 genomes from the same species (including 69Bis) revealed an open pan-genome (6878 genes, 25.76% core), along with several unique and rare determinants linked to probiotic traits in 69Bis. Overall, these results position strain 69Bis as a promising candidate for use in functional foods, particularly in the context of nutrition in arid regions.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147971852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel NADP+-dependent meso-diaminopimelate dehydrogenase from Candidatus Syntrophocurvum alkaliphilum: a promising biocatalyst for d-amino acid production.","authors":"Hironaga Akita, Ryo Hasegawa, Tomoe Komoriya","doi":"10.1093/femsle/fnag083","DOIUrl":"10.1093/femsle/fnag083","url":null,"abstract":"<p><p>The demand for d-amino acids is increasing as their unique physiological role continues to be elucidated. meso-Diaminopimelate dehydrogenase catalyzes the reversible NADP+-dependent oxidative deamination of meso-diaminopimelate to produce l-2-amino-6-oxopimelate. Moreover, a few enzymes show a broad range of reductive amination activity toward 2-oxo acids, synthesizing d-amino acids. Here, we report the identification and characterization of a novel NADP+-dependent meso-diaminopimelate dehydrogenase from Candidatus Syntrophocurvum alkaliphilum (CSaDAPDH). The purified enzyme exhibited oxidative deamination activity toward meso-diaminopimelate, as well as reductive amination activity toward several 2-oxo acids to produce the corresponding d-amino acids. The optimum pH and temperature for oxidative deamination of meso-diaminopimelate were 9.0 and 45°C, respectively. The optimum pH for reductive amination of pyruvate was 6.5, which was the lowest optimum pH among known enzymes, and thus, may lead to the development of new enzymatic methods for d-amino acid production. CSaDAPDH retained more than 60% of its activity after incubation for 30 min at 50 °C (pH 7.0) or at pHs ranging from 5.5 to 7.0 (50°C). Moreover, using known enzymes as comparisons, the coenzyme and substrate recognition mechanisms of CSaDAPDH were elucidated based on a multiple sequence alignment and the homology model.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148519861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intercellular signal transduction within the mother cell compartment during Bacillus subtilis sporulation.","authors":"Nobuki Kuwabara, Masato Anzue, Shin-Ichi Miyoshi, Tsutomu Sato, Daisuke Imamura","doi":"10.1093/femsle/fnag055","DOIUrl":"10.1093/femsle/fnag055","url":null,"abstract":"<p><p>Intercellular signaling contributes to the spatiotemporal regulation of gene expression during sporulation in Bacillus subtilis. The mother cell transcription factor σE is initially produced as an inactive precursor protein pro-σE and activated by the processing enzyme SpoIIGA in response to the forespore-produced putative signaling molecule SpoIIR. However, the mechanism underlying the SpoIIR-mediated signal transduction remains poorly understood. In this study, we showed that the spoIIR-positive, spoIIGA-deleted strain was able to induce SpoIIGA-dependent pro-σE processing in co-cultured spoIIR-deleted, spoIIGA-positive strains. This signaling was dependent on SpoIIR expression and did not involve DNA transfer. Extracellular materials including secreted proteins and membrane vesicles were unlikely to be involved in this signaling pathway. Interestingly, cessation of co-incubation shaking enhanced the signaling, while the addition of membrane-solubilizing detergent abolished it. In addition, SpoIIR signaling did not necessitate release from the forespore membrane or extracellular translocation. A SpoIIR variant lacking the putative signal peptide-like hydrophobic domain produced solely in the mother cell compartment was still able to activate pro-σE. Overall, the study findings suggested that the forespore-produced SpoIIR is neither secreted nor externally translocated. Instead, SpoIIR appeared to be transferred into the mother cell compartment and interacts with the SpoIIGA cytoplasmic domain to trigger pro-σE processing.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13174948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147835811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic support of pebS as a phage-exclusive auxiliary metabolic gene.","authors":"Nina Baeuerle, Nicole Frankenberg-Dinkel, Anne Kupczok","doi":"10.1093/femsle/fnag053","DOIUrl":"10.1093/femsle/fnag053","url":null,"abstract":"<p><p>Marine picocyanobacteria, including the genera Prochlorococcus and Synechococcus, are major contributors to oceanic photosynthesis and global primary production. Their populations are influenced by T4-like cyanophages, which frequently encode auxiliary metabolic genes (AMGs) capable of altering host metabolism during infection. One such AMG, pebS, encodes a ferredoxin-dependent bilin reductase (FDBR) phycoerythrobilin (PEB) synthase, which converts biliverdin IXα to PEB. In contrast, cyanobacteria perform a two-step reaction using the FDBR enzymes PebA (15,16-dihydrobiliverdin: ferredoxin oxidoreductase) and PebB (PEB:ferredoxin oxidoreductase), whereas pebS has not been reported in cyanobacterial genomes. Here, we re-evaluated whether pebS is truly restricted to cyanophages by searching the Ocean Gene Atlas (OGA) and all available cyanobacterial genomes at National Center for Biotechnology Information (NCBI) using a cyanophage-derived PebS sequence as query. Using protein phylogenies, we found that most search hits group with PebA or PebB, while few sequences from cyanobacterial genome assemblies were confirmed to belong to PebS based on phylogenetic placement. However, genomic context analysis of these pebS sequences revealed their phage origin, consistent with cyanophage infection at the time of sampling. In conclusion, our results support that pebS is absent in cyanobacterial genomes, raising questions about the evolutionary and biochemical causes for the two-step reduction of biliverdin IXα to PEB in these organisms.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13198022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotypic and phenotypic comparison of Neisseria meningitidis carriage and invasive disease isolates contemporaneously collected in the Netherlands.","authors":"Charles H Jones, Zhenghui Li, Li Hao, Arie van der Ende, Paul A Liberator, Annaliesa S Anderson, Ashlesh K Murthy","doi":"10.1093/femsle/fnaf140","DOIUrl":"10.1093/femsle/fnaf140","url":null,"abstract":"<p><p>Neisseria meningitidis (Nm), a commensal that colonizes the nasopharynx of 4.5%-24% of healthy humans, can cause invasive meningococcal disease (IMD). We hypothesized that distinct genotypic and/or phenotypic signatures might be found in carriage vs. invasive isolates. Carriage isolates were cultured from nasopharyngeal swabs (n = 267) collected from healthy students (aged 13-21 years) during the 2013 and 2014 school years in the Netherlands. Invasive isolates (n = 214) were cultured from all reported disease cases in the Netherlands from 2012 to 2014. Whole core genome sequences were determined for all isolates and comparisons of selected genotypic markers and phylogenomic associations between carriage and disease isolates were analyzed. While 30% of carriage isolates could not be assigned a genogroup, all the invasive isolates were successfully genogrouped. Genogroup B (MenB) predominated, representing 27% of carriage and 75% of IMD isolates. Sequence type (ST) complex diversity was dominated by four STs (ST-41/44, ST-213, ST-32, and ST-269) in both carriage and disease isolates. FHbp subfamily A variants were prevalent (79%) in carriage, whereas subfamily B variants were more frequent (69.6%) in disease. Carriage and IMD-causing Nm strains display similar ST and phylogenomic profiles; however, an increased FHbp subfamily B prevalence and an enhanced level of FHbp surface expression were noted in MenB disease-causing isolates.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12794619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145762557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparative study on the effects of emulsification methods on the antimicrobial activity of essential oil emulsions.","authors":"Paul G Kamau, Paola Alzate, Malco Cruz-Romero, Michael A Morris, Joe P Kerry","doi":"10.1093/femsle/fnaf144","DOIUrl":"10.1093/femsle/fnaf144","url":null,"abstract":"<p><p>A 3 × 3 factorial design was used to systematically evaluate the impact of three widely used emulsification methods [ultrasonication (UT), high-shear homogenization (HSH), or vortex mixing (VM)] at three treatment times (30, 60, or 120 s) on the antimicrobial efficacy of sage (SEO) and garlic (GEO) essential oil emulsions. Independent of essential oil used, antimicrobial activity was significantly (P < 0.05) influenced by both emulsification method and treatment time, with Gram-negative bacteria showing greater resistance. From the tested methods, emulsions prepared by UT or HSH for at least 60 s exhibited significantly (P < 0.05) higher antimicrobial activity, which might be associated with their significantly (P < 0.05) smaller particle size and polydispersity index. Additionally, UT and HSH produced more stable SEO emulsions, while GEO required ≥60 s treatment for stability and VM led to rapid destabilization regardless of oil or time. This study highlights the importance of selecting an appropriate emulsification method for producing essential oil emulsions with enhanced antimicrobial activity, which is important not only for antimicrobial testing but also for the overall functional performance of the emulsion.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13017692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147473078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA replication and cell division complexes remain physically associated throughout the cell cycle in Helicobacter pylori.","authors":"Priyanka Dubey, Anjali Yadav, Salman Khan, Fatima Akhtar, Mohammad Kamran, Inderjeet Kaur, Suman Kumar Dhar","doi":"10.1093/femsle/fnag037","DOIUrl":"10.1093/femsle/fnag037","url":null,"abstract":"<p><p>The occurrence of drug-resistant strains exacerbates the difficulty of treating stomach cancer caused by Helicobacter pylori. DNA replication and cell division offer attractive targets for the development of antibacterial therapies. Both DNA replication and cell division in H. pylori start at one of the poles and terminate at the middle of the cell. The absence of a SlmA homolog and the presence of a unique Min CDE system may explain polar divisome assembly in Helicobacter. We previously observed the co-localization of replisome and divisome proteins; however, it is unclear if they interact directly. We report, for the first time, the interaction between two complexes in vitro and in vivo. These results highlight the mechanistic aspects of the unique polar co-assembly of the replisome/divisome complex in Helicobacter, through interactions among members of each component, which might be useful for identifying new targets.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147632964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Galleria mellonella as a novel invertebrate model for studying Ehrlichia ruminantium pathogenesis and host-pathogen interactions.","authors":"Maëlle Bayet, Christina Nielsen-Leroux, Valérie Rodrigues, Damien F Meyer","doi":"10.1093/femsle/fnag113","DOIUrl":"10.1093/femsle/fnag113","url":null,"abstract":"<p><p>Ehrlichia ruminantium, the causative agent of heartwater disease, is an obligate intracellular bacterium that poses significant economic threats to livestock production in endemic regions. Current research models present substantial ethical, logistical, and economic constraints, particularly for studying host-pathogen interactions within arthropod vectors. Here, we establish Galleria mellonella larvae as a tractable invertebrate infection model for Ehrlichia ruminantium, enabling experimental investigation of pathogen persistence and host-pathogen interactions in an arthropod system. Following infection, G. mellonella proved susceptible to E. ruminantium with moderate mortality and remarkable bacterial persistence. Using rhodamine-labeled bacteria and fluorescence microscopy, we tracked bacterial dissemination from injection sites to systemic distribution in characteristic segmental patterns throughout the larval body. Rhodamine-labeled bacteria were consistently associated with hemocytes, the primary immune cells of G. mellonella, although widefield imaging cannot establish intracellular localization. Quantitative PCR revealed stable bacterial loads over the study period, and bacteria recovered from infected larvae remained viable and infectious for endothelial cells. These findings show that E. ruminantium persists in G. mellonella for at least two weeks without inducing a detectable melanization response. The fluorescence adopted a reproducible segmental distribution whose biological basis remains to be determined. This model offers significant advantages: ethical acceptability, cost-effectiveness, experimental tractability, and compatibility with high-throughput screening approaches. The G. mellonella system represents a valuable complement to existing mammalian models and provides a unique platform for investigating arthropod-specific aspects of E. ruminantium biology, screening antimicrobial compounds, and testing hypotheses of immune evasion that may inform strategies for heartwater disease control.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13656321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149106384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}