{"title":"Fluorescent protein sensors illuminate cellular pH changes in Enterobacter cloacae: unravelling the mechanisms of TolC-dependent acid survival.","authors":"Sanchari Chowdhury, Harapriya Mohapatra","doi":"10.1093/femsle/fnag070","DOIUrl":"10.1093/femsle/fnag070","url":null,"abstract":"<p><p>TolC is the outer membrane component of the tripartite RND efflux pump AcrAB-TolC. The underlying mechanism of TolC-dependent acid survival at physiological pH remains unclear. The present study aimed at understanding mechanism of TolC mediated acid survival in logarithmic phase culture of Enterobacter cloacae subsp. cloacae ATCC 13047 not preconditioned to acidic pH. Of the three distinct loci encoding tolC and tolC like proteins, only ECL_04 363 (hereafter referred to as EctolC2) exhibited 86% identity with TolC protein from E. coli K12; deletion of which compromised survival at pH 4.0. Tracking the periplasmic and cytoplasmic pH changes with fluorescent protein sensors indicated deletion of EctolC2 resulted in sustained cytoplasmic acidification and loss of pH homeostasis causing cell death. Exogenous supplementation of lysine significantly rescued acid induced lethality in EcΔtolC2 mutants. ΔmarRAB mutants exhibited slower death rate compared to Δrob mutants; underpinning role of the latter in upregulating EctolC2 at early time point of growth at pH 4.0. Results of the study construe that EctolC2 provides reinforcement to the outer membrane preventing extreme acidification of the periplasm and thereby restoring cytoplasmic pH homeostasis. This study provides significant insight into mechanism of TolC dependent acid survival in E. cloacae.</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":"148239246","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}
Aimen Firdous, Fathima Salam, Vasanthi Kalli, Manjusha Lekshmi, Sanath H Kumar, Indrani Karunasagar, Binay B Nayak
{"title":"Distribution of Arcobacter butzleri and its correlation with faecal contamination in the aquatic environment.","authors":"Aimen Firdous, Fathima Salam, Vasanthi Kalli, Manjusha Lekshmi, Sanath H Kumar, Indrani Karunasagar, Binay B Nayak","doi":"10.1093/femsle/fnag009","DOIUrl":"10.1093/femsle/fnag009","url":null,"abstract":"<p><p>Arcobacter butzleri, a foodborne pathogen of increasing public health relevance and associated with the gut of warm blooded animals is widely distributed in aquatic environments. Its association with the extensively studied faecal indicator, Escherichia coli remains unclear, yet is important for clarifying the ecology of pathogens and assessing risks. This study evaluated the prevalence and correlation between A. butzleri and E. coli in finfish, shellfish, and water sampled across multiple contamination points- markets, landing centres, and fishing vessels in Mumbai, India. A total of 70 samples (30 finfish, 30 shellfish, and 10 water) were tested using a miniaturized most probable number-quantitative polymerase chain reaction, which bypasses lengthy culture procedures and offers a reliable approach in the absence of a standard isolation method for A. butzleri. Arcobacter butzleri was present in 73% of the samples and E. coli in 81% samples indicating a high microbial burden of both organisms within this seafood ecosystem. Contamination varied by source, with market samples showing highest levels, followed by landing centres and lowest from on-board vessels, indicating post-harvest contamination influenced by nearshore water pollution. Regression analysis indicated positive correlation between A. butzleri and E. coli (ρ = 0.88, R² = 0.78, P < 0.001) and particularly robust associations were observed in shellfish and water matrices. This supports the close association of A. butzleri with sewage-impacted environments and its potential role as a supplementary indicator of fecal contamination.</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":"146009516","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}
Oleksandra Rudenko, Laura Baseggio, Andrew C Barnes
{"title":"The Type III Secretion System plasmid pPHDPT3 of Photobacterium damselae subsp. piscicida is stable in Australian isolates due to conserved non-repetitive genomic architecture.","authors":"Oleksandra Rudenko, Laura Baseggio, Andrew C Barnes","doi":"10.1093/femsle/fnag074","DOIUrl":"10.1093/femsle/fnag074","url":null,"abstract":"<p><p>Photobacterium damselae subsp. piscicida (Pdp) is a host-adapted primary pathogen impacting finfish aquaculture worldwide, whose virulence evolution is driven by the mobilome. The pPHDPT3 plasmid encoding a type III secretion system is critical for Pdp virulence but unstable in vitro in European and Japanese isolates. Here we show that a stable ancestral variant is conserved in Australian isolates. The elusive pPHDPT3 variant has undergone gene loss and accumulated a ∼5.5 kb quadruple direct repeat, which could explain plasmid loss via the classic dimer catastrophe scenario. In addition, we hypothesize that a 189-aa serine recombinase encoded within this repeat, and also on pPHDP10 plasmid, may act as a plasmid resolvase, with its frequent loss further exacerbating the dimer catastrophe.</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/PMC13347740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148307924","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}
Laura Losada Calderón, Sergio Andres Castañeda Garzon
{"title":"Identification of differentially abundant micro-organisms associated with Sjögren's syndrome: a 16S rRNA sequencing data mining approach.","authors":"Laura Losada Calderón, Sergio Andres Castañeda Garzon","doi":"10.1093/femsle/fnag094","DOIUrl":"10.1093/femsle/fnag094","url":null,"abstract":"<p><p>Manifestations of Sjögren's syndrome (SS) considerably affect the quality of life. Owing to the multifactorial nature of the syndrome, some individuals present alterations in oral microbiota profiles. This study analyzed the oral cavity microbiota profiles of 242 samples-168 from pSS group and 74 from control group-using metabarcoding technique based on sequencing of 16S rRNA gene. Data processing, amplicon sequence variants, and taxonomic assignment were performed using DADA2. Statistical and microbial diversity analyses were performed using phyloseq in R. Alpha and beta diversity metrics were evaluated, as well as the identification of enriched taxa using Linear discriminant analysis effect size analysis. Results revealed no significant differences in the composition and structure of the microbiota between groups. However, differential abundance analysis allowed the identification of 27 microbial taxa, including species Actinomyces dentocariosa; genera Streptococcus, Leptotrichia, Veillonella, Fusobacterium, and Alloprevotella; and phyla Actinobacteriota and Fusobacteriota, in pSS group. Although no direct associations have yet been established between oral microbiota and SS, some of the identified genera have been documented to possess pathogenic factors that induce immune responses. Accordingly, this study lays the groundwork for future analyses of oral microbiota profiles in SS to identify potential microbial biomarkers of disease.</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/PMC13536491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148790005","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}
Rachel C Beaver, Cailyn M Perry, Chang Seok Kim, Josh D Neufeld
{"title":"Low bentonite biomass leads to inconsistent culture-based estimates of microbial abundances.","authors":"Rachel C Beaver, Cailyn M Perry, Chang Seok Kim, Josh D Neufeld","doi":"10.1093/femsle/fnag003","DOIUrl":"10.1093/femsle/fnag003","url":null,"abstract":"<p><p>Bentonite is an important component of deep geological repositories for long-term storage of used nuclear fuel. Studying the microbiology of bentonite exposed to various conditions is relevant because certain microorganisms (e.g. those that produce corrosive sulfide or gaseous metabolites) could lead to deterioration of engineered barrier components of the repository. In previous research, a high degree of variability in the abundance of culturable microorganisms among replicate samples has been observed. The purpose of this study was to test whether experimental technique (e.g. inadequate mixing of bentonite) or extremely low biomass represent mechanisms to explain such variability. Using a combination of cultivation- and DNA-based techniques to study six replicate hydrated bentonite microcosms, as well as six replicate bentonite aliquots originating from the same hydrated bentonite microcosm, the results of this study demonstrate that observed heterogeneity is likely not due to inadequate bentonite mixing. Instead, the data indicate that low biomass of as-received bentonite leads to unique populations of culturable bacteria associating with each sample, or to a lesser degree within different areas of a single bentonite sample used to establish a microcosm. Because some microorganisms that grow in bentonite are culturable under commonly used cultivation conditions and others are not, this can lead to differences in culture-based abundance estimates among replicate samples. Although cultivation is a useful technique to demonstrate viability of microorganisms in bentonite, the results of this study highlight the importance of a multifaceted experimental approach (i.e. coupling cultivation to DNA-based analysis) and careful analysis of replicates when working with such low biomass samples.</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/PMC12850535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145958955","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}
Elisabeth Williamson, Kelly Hill, Raphael Eisenhofer, Katja Hogendoorn
{"title":"Experimental evidence for the absence of a functional gut microbiome in the solitary bee Megachile tosticauda.","authors":"Elisabeth Williamson, Kelly Hill, Raphael Eisenhofer, Katja Hogendoorn","doi":"10.1093/femsle/fnag012","DOIUrl":"10.1093/femsle/fnag012","url":null,"abstract":"<p><p>The eusocial honey bee is a model for insect microbiome research, with socially transmitted gut communities that play key roles in health and development. In contrast, solitary bees lack social transmission pathways and often have an environmentally acquired microbiome, which may or may not be functionally important. Using 16S rRNA gene metabarcoding, previous work has described the bacterial communities in the solitary resin bee Megachile tosticauda pollen provisions, brood, and adult bees, but their functional significance has yet to be studied. Here, we investigate the importance of live bacteria for larval development and survival with an antibiotic-feeding experiment, and test whether bacteria are present in adult guts using scanning electron microscopy. Removing live bacteria in the food and gut of feeding larvae had no significant effect on survival or growth. Microscopy revealed no bacterial colonization of the adult gut, and the dominant taxon detected in larval pollen could not be cultured under targeted conditions. These results suggest an absence of a beneficial gut microbiome in M. tosticauda. Based on our findings, we propose that some bacteria detected by DNA-based methods in M. tosticauda may represent relic DNA, surface-associated or transient bacteria. Our findings highlight fundamental differences in the bacterial associations between social and solitary bees.</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/PMC13016869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146085009","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":"Functional hierarchy and redundancy organize phosphorus cycling potential in Peltigera lichen microbiomes.","authors":"Constanza Soto, Katerin Almendras, Julieta Orlando","doi":"10.1093/femsle/fnag029","DOIUrl":"10.1093/femsle/fnag029","url":null,"abstract":"<p><p>Lichen symbioses host complex microbial communities whose functional organization remains poorly understood. In Peltigera lichens, bacterial partners mediate key nutrient transformations, but it is unclear whether the spatial distribution of phosphorus-cycling functions follows the hierarchical control previously observed for community composition. We hypothesized that Peltigera microbiomes follow a thallus-to-soil gradient of control, in which host-driven specialization within thalli transitions toward environmentally driven reconfiguration in the substrate and soil. To test this, we quantified five bacterial genes involved in phosphorus turnover (gcd, phoD, phoN, phnX, and appA) across thalli, underlying substrates, and adjacent soils of several Peltigera species collected along contrasting Patagonian bioclimates. Absolute and relative gene abundances, together with diversity and variance partitioning analyses, were used to evaluate the influence of host identity, edaphic properties, and climate. Gene profiles revealed a shift from host-associated specialization to environmentally filtered assemblages, indicating that symbiotic and abiotic factors jointly structure phosphorus-cycling potential. The coexistence of functional specialization and redundancy provides a plausible mechanism for sustaining phosphorus turnover under changing environmental conditions.</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":"147503477","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}
Caroline Kihara Cornachini, Letícia Pereira de Souza, Dirlei Gomes Martins Salvador, Kauany Damiane Silva, Joyce Marinho de Souza
{"title":"Gut microbiota-skin axis in melasma: microbial metabolites and hormonal crosstalk.","authors":"Caroline Kihara Cornachini, Letícia Pereira de Souza, Dirlei Gomes Martins Salvador, Kauany Damiane Silva, Joyce Marinho de Souza","doi":"10.1093/femsle/fnag036","DOIUrl":"10.1093/femsle/fnag036","url":null,"abstract":"<p><p>The gut microbiota is increasingly recognized as a systemic regulator of host physiology, extending its influence to the skin. Microbial metabolites-including short-chain fatty acids, exopolysaccharides, β-glucuronidase, and S-equol-modulate key processes such as inflammation, estrogen metabolism, and cellular senescence. In melasma, a chronic hyperpigmentation disorder with inflammatory features, dysbiosis alters immunometabolic pathways that sustain disease persistence. Beneficial taxa such as Faecalibacterium prausnitzii, Bacteroides thetaiotaomicron, Lactobacillus, and Bifidobacterium generate bioactive products that inhibit NF-κB signalling, suppress the senescence-associated secretory phenotype, and mitigate melanogenic stimuli. Conversely, β-glucuronidase-producing microbes enhance estrogen recycling and oxidative stress, favouring hyperpigmentation. This mini-review highlights microbial drivers of gut-skin crosstalk in melasma and underscores the microbiota as a source of potential biomarkers and therapeutic targets. We propose that gut dysbiosis contributes to melasma pathogenesis through microbiota-derived metabolites that modulate estrogen signalling and cellular senescence pathways, establishing a mechanistic framework linking immunometabolic dysregulation to persistent hyperpigmentation.</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":"147591141","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}
Júlio César Silva, Vitória Beatriz Roberto Silva, Luís Pereira-de-Morais, Raimundo Luiz Silva Pereira, Isaac Moura Araújo, Thiago Mielle Brito Ferreira Oliveira, Cícera Datiane de Morais Oliveira-Tintino, João Arthur de Oliveira Borges, Nair Silva Macedo, Henrique Douglas Melo Coutinho, Francisco Nascimento Pereira Junior
{"title":"Ammonium polyoxomolybdate modulates antibiotic activity against resistant Staphylococcus aureus and Escherichia coli.","authors":"Júlio César Silva, Vitória Beatriz Roberto Silva, Luís Pereira-de-Morais, Raimundo Luiz Silva Pereira, Isaac Moura Araújo, Thiago Mielle Brito Ferreira Oliveira, Cícera Datiane de Morais Oliveira-Tintino, João Arthur de Oliveira Borges, Nair Silva Macedo, Henrique Douglas Melo Coutinho, Francisco Nascimento Pereira Junior","doi":"10.1093/femsle/fnag038","DOIUrl":"10.1093/femsle/fnag038","url":null,"abstract":"<p><p>This study investigated the antibacterial and potentiating activity of ammonium polyoxomolybdate tetrahydrate (NHMO; (NH4)6Mo7O24·4H2O; 1235.86 g/mol), particularly in combination with ampicillin against Staphylococcus aureus and Escherichia coli strains. Spectroscopic characterization by attenuated total reflectance Fourier transform infrared spectroscopy and microdilution tests with resazurin were used. NHMO showed no direct antibacterial activity, with a minimum inhibitory concentration (MIC) ≥1024 μg/mL (≈0.83 mM). However, when used at a subinhibitory concentration (MIC/8, 128 μg/mL; ≈0.10 mM) with antibiotics initially tested at 1024 μg/mL, NHMO reduced the MIC of ampicillin by ~50% for both bacterial strains. Sulbactam, a known β-lactamase inhibitor, showed superior results, confirming the presence of enzymatic resistance. NHMO also demonstrated a resistance-reversal effect in β-lactamase-producing S. aureus strains, lowering the MIC of ampicillin from 20.16 to 16 μg/mL in K4100 and from 322.54 to 256 μg/mL in K4414. Ciprofloxacin did not show relevant modulation, whereas gentamicin potentiation was observed against S. aureus 10. These findings indicate that NHMO can enhance the activity of antibiotics, particularly ampicillin and gentamicin, in resistant bacterial strains. Its action in β-lactamase-related assays suggests that it is a promising candidate in the search for alternatives to combat antimicrobial resistance.</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":"147632906","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":"Oral examination as a tool for mastery learning in undergraduate microbiology.","authors":"Andrew R St James, Camille Widener","doi":"10.1093/femsle/fnag010","DOIUrl":"10.1093/femsle/fnag010","url":null,"abstract":"<p><p>Undergraduate courses in general microbiology often have high content and cognitive loads, making it challenging for students to achieve content mastery of the whole curriculum. Thus, the development of manageable mastery learning interventions that work within these contexts should benefit microbiology education broadly. In this work, we describe an oral examination intervention implemented within a modified Bloom's Learning for Mastery framework that significantly improves retention of course material across low-performing students in an undergraduate general microbiology course. The intervention consumed a relatively small amount of instructor time to administer (less than 15 min per student) and resulted in no distinguishable differences in knowledge retention on the final exam between students who initially mastered the content and did not participate in the intervention and those who participated in the intervention after failing to initially master the content. Students reported overwhelmingly positive experiences with the intervention, including increased perceptions of their own content retention, increased feelings of self-pride after participating in the intervention, and a general feeling that the intervention was fair. We conclude that oral examinations are an effective mastery learning tool in the microbiology classroom and can be easily implemented by the instructor alone in small- to medium-sized courses.</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/PMC13130396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146040590","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}