Microbiology spectrum最新文献

{"title":"Application value of metagenomic next-generation sequencing based on protective bronchoalveolar lavage in nonresponding pneumonia.","authors":"Yingchen Pang, Junjin Qiu, Hong Yang, Junbao Zhang, Jianming Mo, Wendi Huang, Chao Zeng, Ping Xu","doi":"10.1128/spectrum.03138-24","DOIUrl":"https://doi.org/10.1128/spectrum.03138-24","url":null,"abstract":"<p><p>This study aims to explore the application value of metagenomic next-generation sequencing (mNGS) of protective bronchoalveolar lavage fluid in the differential diagnosis and pathogenetic identification of nonresponding pneumonia. This study analyzed patient symptoms, auxiliary examinations including pathogen detection, and treatment response to identify the reasons for the lack of response to initial treatment and the pathogenetic diagnosis of pulmonary infections. The diagnostic efficacy of pathogen culture and mNGS was statistically analyzed and compared based on the clinical diagnosis criteria. (1) The two most common reasons for the ineffectiveness of initial treatment in nonresponding pneumonia cases are that (i) the initial treatment did not cover the pathogenic bacteria in pulmonary infection cases and that (ii) non-infectious pulmonary diseases were responsible. The most common pathogens in pulmonary infection cases of nonresponding pneumonia are <i>Mycobacterium tuberculosis</i> (MTB), <i>Pneumocystis jirovecii</i>, <i>Aspergillus</i>, and <i>Pseudomonas aeruginosa</i>. (2) In pulmonary infectious cases, mNGS demonstrated a higher detection sensitivity for pathogenic bacteria than pathogen cultures. mNGS combined with protective bronchoalveolar lavage has good clinical application value in the accurate diagnosis of pathogens and identification of non-infectious diseases.IMPORTANCEThe combination of mNGS and the protective BAL technique demonstrates significant utility in accurately diagnosing pathogens and identifying non-infectious diseases. Misdiagnosis of non-infectious lung diseases as infectious lung diseases is a common factor contributing to the lack of response to initial treatment in nonresponding pneumonia patients. The most common pathogens in pulmonary infection cases of nonresponding pneumonia are MTB, <i>Pneumocystis jirovecii</i>, <i>Aspergillus</i>, and <i>Pseudomonas aeruginosa</i>.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0313824"},"PeriodicalIF":3.7,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-strain, biofilm-forming cocktail of <i>Bacillus</i> spp. and <i>Pediococcus</i> spp. alters the microbial composition on polyethylene calf housing surfaces.","authors":"C A Reynolds, R A Scuderi, A L Skidmore, L Duniere, S Y Morrison","doi":"10.1128/spectrum.03302-24","DOIUrl":"https://doi.org/10.1128/spectrum.03302-24","url":null,"abstract":"<p><p>Application of a beneficial microbial cocktail of <i>Bacillus</i> spp. and <i>Pediococcus</i> spp. was evaluated first for adherence to polyethylene calf hutch material, and second, to determine if application <i>in situ</i> to individual calf hutches post-cleaning influenced surface recolonization by enteric pathogens. Three treatments were utilized: (i) no application (<b>NC</b>), (ii) chlorine-free, distilled water (<b>DW</b>), or (iii) an application of a microbial inoculant containing <i>Bacillus</i> spp. and <i>Pediococcus</i> spp. at a concentration of 0.4 g/m² of hutch space (<b>LF</b>). Thirty-six 15 × 15 cm pieces of naïve, sterile polyethylene calf hutch material received either NC or LF and were incubated at 28°C, and bacterial growth was evaluated by total aerobic plate counts at 24, 48, and 72 h post-application. Thirty polyethylene calf hutches (<i>n</i> = 10/treatment) were randomized to NC, DW, or LF 24 h after cleaning. Calves were placed in the hutches 24 h after treatment application and monitored daily for 28 d. <i>In situ</i> surface samples were randomized by time from five unique locations within the calf hutch interior: 24 h post-cleaning and then 24 h, 7 d, 14 d, and 21 d post-application. Total aerobic plate counts and culture-independent approaches RT-qPCR and 16S amplicon sequencing were used to detect and identify the composition of the bacterial community <i>in situ</i>. The bacteria in the inoculant were able to successfully colonize on polyethylene, and application to individual polyethylene calf housing <i>in situ</i> influenced microbial diversity and reduced the presence of some undesirable bacteria on high-contact interior surfaces.IMPORTANCEDue to its multifactorial nature, neonatal calf diarrhea can be difficult to manage on farms. Clean housing environments are a critical disease control point, especially for calves less than one month of age. Application of a beneficial biofilm-forming bacterial product after cleaning of neonatal calf housing may influence the microbial communities present on the surface, particularly those that may present disease risk to calves in early life.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0330224"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of Illumina and Oxford Nanopore Technology systems for the genomic characterization of <i>Streptococcus pneumoniae</i>.","authors":"Fatima Dakroub, Fata Akl, Alissar Zaghlout, Jose Rita Gerges, Nancy Hourani, Celina F Boutros, George F Araj, Ghassan M Matar, Antoine Abou Fayad, Ghassan S Dbaibo","doi":"10.1128/spectrum.01294-24","DOIUrl":"https://doi.org/10.1128/spectrum.01294-24","url":null,"abstract":"<p><p>Whole-genome sequencing (WGS) is an invaluable tool that enables high-resolution genotyping to precisely identify bacterial strains. It is particularly significant for highly pathogenic bacteria such as <i>Streptococcus pneumoniae</i>, a worldwide leading cause of mortality and morbidity. Illumina sequencing is highly established for <i>S. pneumoniae</i>, while Oxford Nanopore Technologies (ONT) data are limited. Hence, evaluating ONT-only data is needed. We aimed to compare the Illumina and ONT systems for <i>S. pneumoniae</i> sequencing. Moreover, we aimed to explore whether the newer chemistry from ONT with R10.4.1 flow cells improves the data outputs from long-read sequencing. <i>S. pneumoniae</i> bacteria were isolated from hospitalized patients with invasive pneumococcal disease (IPD) and serotyped by multiplex PCR. Resistance profiles were determined with anti-microbial susceptibility testing. A total of 27 isolates were sequenced using ONT Mk1c with R9.4.1 flow cells and Kit10 chemistry (ONT_V10) and the Illumina Miseq system. Illumina and ONT data were compared, and hybrid assembly was assessed. ONT sequencing was additionally performed with R10.4.1 flow cells and Kit14 chemistry (ONT_V14) in 12 isolates. <i>S. pneumoniae</i> identification, serotyping, AMR, and GPSC prediction were successfully achieved using ONT sequencing. The ONT_V14 chemistry significantly improved both MLST and pbp prediction in long-read sequencing. Overall, the hybrid assembly produced circular and contiguous genomes with high N50 parameters. Moreover, long-read assembly followed by short-read polishing is a fast and reliable approach for hybrid assembly at ONT sequencing depth >100×. For ONT sequencing depth <50×, tools that perform short-read-first assembly, such as Unicycler are recommended.IMPORTANCEThis study provides a detailed evaluation of whole-genome sequencing technologies and bioinformatics pipelines for the characterization of <i>Streptococcus pneumoniae</i>. It represents an in-depth investigation of Illumina and Oxford Nanopore technologies (ONT) systems for bacterial sequencing. It sheds light on the performance of each platform in various aspects of sequencing, including raw and assembly statistics, capsular typing, pbp typing, GPSC, AMR, and MLST prediction. This study offers a comprehensive overview of <i>S. pneumoniae</i> genomics and a guide for clinical and research laboratories seeking to adopt bacterial sequencing by providing important considerations when choosing sequencing platforms and analysis pipelines. We report a strong case for the implementation of WGS in the clinical setting, based on its high concordance with conventional molecular and phenotypic methods. Furthermore, the flexibility and portability of the investigated pipelines facilitate their use in clinical applications.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0129424"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aircraft lavatory wastewater surveillance for movement of antimicrobial resistance genes: a proof-of-concept study.","authors":"Yawen Liu, Wendy J M Smith, Metasebia Gebrewold, Nicholas J Ashbolt, Ishi Keenum, Stuart L Simpson, Xinhong Wang, Warish Ahmed","doi":"10.1128/spectrum.00569-25","DOIUrl":"https://doi.org/10.1128/spectrum.00569-25","url":null,"abstract":"<p><p>Long-haul flight aircraft wastewater may serve as a representative microbial footprint, often of mixed country origin, offering valuable insight into the movement of pathogens and antimicrobial resistance (AMR) on a global scale. Herein, we present a proof-of-concept for aircraft-based surveillance of AMR by investigating lavatory wastewater samples from 44 repatriation flights to Australia departing from nine countries. Profiles of pathogens including ESKAPE pathogens (<i>Salmonella</i> spp., <i>Mycobacterium</i> spp., <i>Enterococcus faecium</i>, <i>Staphylococcus aureus, Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, and <i>Pseudomonas aeruginosa</i>) and antibiotic resistance genes (ARGs) (<i>aph(3')-IIIa</i>, <i>bla_NDM-1, bla_{CTX_M-1}, bla_KPC, ermB, qnrS, sul1, tetM,</i> and <i>vanA</i>) were investigated along with traditional fecal indicator bacteria (<i>Escherichia coli</i> and <i>Enterococcus</i> spp.) and fecal/urine marker genes (<i>Bacteroides</i> HF183, <i>Carjivirus</i>, human polyomavirus, and a cryptic plasmid pBI143) using quantitative PCR (qPCR). Two fecal indicator bacteria (FIB) and four human fecal/urine marker genes were detected in all aircraft wastewater samples. Detection rates for ESKAPE pathogens ranged from 6.8% (<i>S. aureus</i>) to 84.1% (<i>K. pneumoniae</i>). Of all ARG targets, <i>aph(3')-IIIa</i>, <i>ermB</i>, <i>qnrS</i>, <i>sul1,</i> and <i>tetM</i> were detected in all wastewater samples, whereas <i>bla_KPC</i> and <i>vanA</i> were not detected in any of the samples. Results reflected geographic differences in ARG abundance originating from departure countries/continents and suggested a potential risk of importing ARGs that might be rare in local wastewater systems. The loss of nucleic acid targets was less than 10% over a 24 h incubation in the presence of disinfectants, suggesting that nucleic acids are resilient enough to persist in aircraft wastewater over the maximum duration of a flight.IMPORTANCEIn the context of international connectedness, aircraft-based wastewater surveillance should be viewed as a beyond-national tool to enhance global AMR management and foster international cooperation.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0056925"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are you my mother? When host genetics and gut microbiota tell different phylogenetic stories in the Africanized honey bee hybrid (<i>Apis mellifera scutellata</i> × sspp.).","authors":"Kilmer Oliveira Soares, Celso José Bruno de Oliveira, Luis Eduardo Martínez Villegas, Priscylla Carvalho Vasconcelos, Adriana Evangelista Rodrigues, Christopher Madden, Vanessa L Hale","doi":"10.1128/spectrum.02475-24","DOIUrl":"https://doi.org/10.1128/spectrum.02475-24","url":null,"abstract":"<p><p>Africanized honey bees (<i>Apis mellifera scutellata</i> × sspp.) originated in Brazil through the crossbreeding of African (<i>A. mellifera scutellata</i>) and European (<i>A. mellifera</i> sspp.) honey bee subspecies. African genes came to dominate in these hybrid honey bees over time. Gut microbiota co-evolve with their hosts and generally reflect host phylogeny. To examine if this was true in Africanized honey bee hybrids (also known as <i>scutellata</i>-European hybrids), we compared the gut microbiota (16S rRNA) of three honey bee subspecies: African, European, and Africanized bees. Publicly available sequencing data from five honey bee studies were downloaded from the National Center for Biotechnology Information (NCBI). European bee samples (<i>n</i> = 42) came from the United Kingdom, Switzerland, and the United States. African bee samples (<i>n</i> = 82) came from Kenya. Africanized bee samples (<i>n</i> = 10) came from Brazil. Unexpectedly, Africanized honey bee gut microbiota was far more similar to European bees than to African bees despite the closer host genetic relationship between African and Africanized bees. All three subspecies shared similar relative abundances of core taxa. We posit that the similarity in gut microbiota between Africanized and European honey bees arose from the nature of the crossbreeding and the social/environmental transmission of gut microbiota within hives. Namely, African queens took over European hives. However, the hybrid offspring acquired their gut microbiota from European nurse bees and European hive materials, resulting in the stable transmission of European gut microbiota across generations. Our results provide an intriguing insight into the potential ecological, social, and environmental factors that shape the gut microbiota of the Africanized honey bee hybrid.IMPORTANCEAfricanized honey bee hybrids originated in Brazil through the crossbreeding of African and European honey bee subspecies. In this study, we examined the gut microbiota of all three honey bee subspecies (African, European, Africanized). A few core microbiota were shared across all subspecies. Interestingly, while African honey bee genes dominated in the Africanized honey bee hybrids, their gut microbial composition was most similar to European bees. This is likely related to the way these bees were crossbred-with African queens taking over European hives, while gut microbial inoculation of hybrids came from European nurse bees and European hive materials. Gut microbiota are critical to honey bee health, and studying the gut microbiota of closely related honey bee subspecies helps understand the factors that influence gut microbial composition. This is important for our broader understanding of honey bee health, conservation, and evolution.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0247524"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soil microorganism distributions depend on habitat partitioning of topography in a temperate mountain forest.","authors":"Jianyou Li, Xueying Li, Shengqian Guo, Jingjing Xi, Yizhen Shao, Yun Chen, Zhiliang Yuan","doi":"10.1128/spectrum.02056-24","DOIUrl":"https://doi.org/10.1128/spectrum.02056-24","url":null,"abstract":"<p><p>As the main decomposers in forest ecosystems, soil microorganisms are crucial in maintaining ecosystem functions and services. Topographic factors are essential for soil formation and can influence the community structure of soil microorganisms by modifying the soil environment. However, a systematic understanding of the distribution mechanisms of soil microorganisms across different terrain habitats is still lacking. This study characterized soil bacteria and fungi in the valleys, mid-slopes, and ridges of the temperate deciduous broadleaf forest in Baiyun Mountain, Luoyang, to analyze the effect of topographic habitat on the distribution patterns of soil microbial communities. Results showed that the distribution of most soil microorganisms in different terrain habitats follows the principle of ecological specialization. The distribution patterns of soil bacteria and fungi are related to the terrain habitat, and the fungal community (60.48%) exhibits a stronger habitat specificity than the bacterial community (31.78%). Soil moisture has a greater influence on fungal communities than bacterial communities, whereas soil physical and chemical properties more significantly explain variations in bacterial community distribution. These findings indicate that topographic habitat significantly influences soil microbial community distribution, and bacteria show stronger habitat adaptability than fungi.</p><p><strong>Importance: </strong>This study provides an in-depth examination of the impact of topographic habitat on the structural composition and spatial distribution characteristics of bacterial and fungal communities. The research focused on three distinct terrain habitats: valley, midslope, and ridge. Our results indicate that soil bacterial and fungal networks, along with major environmental factors, shape the composition and distribution of soil microbial communities across different terrain habitats. We found that fungi exhibit stronger habitat specificity than bacteria and are more likely to thrive in valleys with higher water content. Furthermore, major environmental factors significantly influence the distribution of soil microbial communities. These findings could inform the development of more effective forest soil management and conservation strategies tailored to different topographic habitats.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0205624"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Depalmitoylase ABHD16A negatively regulates the anti-hepatitis B virus activity of IFITM1.","authors":"Xin Wen, Mingyang Liu, Yali Fan, Junfei Xu, Zhaoyan Wang, Lin Mao, Weizhen Gu, Xuemeng Shi, Jun Xu","doi":"10.1128/spectrum.03095-24","DOIUrl":"https://doi.org/10.1128/spectrum.03095-24","url":null,"abstract":"<p><p>Interferon-inducible transmembrane (IFITM) proteins have been widely reported as antiviral factors against various viral pathogens. However, the mechanisms of IFITM regulation on hepatitis B virus (HBV), which induces chronic infection resulting in cirrhosis as well as liver cancer, remain poorly characterized. In the present study, we identified that HBV infection significantly increased the expression of IFITM1. To dissect the role of IFITM1 in HBV infection, we overexpressed IFITM1 in HepG2.215 cells and revealed that the replication of HBV was restricted by IFITM1. Recently, we demonstrated that the anti-RNA virus activity of IFITM proteins depends on palmitoylation modification, and the depalmitoylase α/β-hydrolase domain-containing 16A (ABHD16A) negatively regulates IFITM1 against RNA virus infection in human and porcine cells. However, whether ABHD16A-IFITM1 regulates DNA virus infection has not been researched. Here, by using co-immunoprecipitation (Co-IP) and acyl-PEGyl exchange gel-shift assay, ABHD16A-catalyzed depalmitoylation of IFITM1 was verified in HepG2.215 cells. In addition, we respectively knocked out IFITM1 and ABHD16A via CRISPR/Cas9 and showed that the anti-HBV activity of IFITM1 was negatively regulated by ABHD16A through depalmitoylation. Collectively, our findings demonstrated for the first time that ABHD16A catalyzes the depalmitoylation of IFITM1 to regulate its antiviral activity against HBV, which expands the biological functions of ABHD16A in immune regulation and provides potential targets for HBV infection-related disease therapy.IMPORTANCENowadays, hepatitis B virus (HBV) infection remains a major global public health problem, with over 375 million people worldwide having been infected. Chronic HBV infection leads to serious liver diseases, such as liver cirrhosis and hepatocellular carcinoma. Therefore, it is urgent to reveal the mechanism of HBV infection and uncover novel drug targets. Interferon and interferon-stimulated genes are responsible for the inhibition of HBV infection. Interferon-inducible transmembrane (IFITM) is distributed on plasma membrane, restricting various virus invasions. Nevertheless, whether and how IFITM regulates HBV infection remains unclear. Here, we show that IFITM1 inhibited the replication of HBV, which depended on palmitoylation modification. In addition, the depalmitoylase α/β-hydrolase domain-containing 16A (ABHD16A) negatively regulates the anti-HBV activity of IFITM1. Overall, our findings provided ABHD16A as a potential target for interfering with HBV replication.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0309524"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome characterization and antibiotic resistance phenotype of <i>Escherichia marmotae</i> first isolated from <i>Berylmys bowersi</i>.","authors":"Ying Liu, Jian Zhou, Tao Gu, Weiwei Ai, Jingzhu Zhou, Qing Ma, Yong Hu, Shijun Li","doi":"10.1128/spectrum.02946-24","DOIUrl":"https://doi.org/10.1128/spectrum.02946-24","url":null,"abstract":"<p><p><i>Escherichia marmotae</i> was first described in 2015 as a bacterium isolated from Himalayan marmots, with recent evidence suggesting its potential to cause human diseases. This study presents the first report of <i>E. marmotae</i> isolation from <i>Berylmys bowersi</i> in Guizhou province. We conducted genetic, biochemical, and antibiotic resistance analyses on four isolates, designated as S2-2, S2-4, S2-5, and S2-6. Phylogenetic analysis based on 16S rRNA sequences revealed over 99.5% homology with <i>E. marmotae</i>, while pulsed-field gel electrophoresis and whole-genome sequencing confirmed genetic similarity. Gene annotation highlighted the presence of 137 virulence factors and five antibiotic resistance mechanisms, including resistance to fluoroquinolones and tetracyclines. Resistance phenotypes of 35 antibiotics showed resistance to penicillin, erythromycin, rifampin, and co-trimoxazole. The strains exhibited significant biochemical diversity, with positive results for several fermentation pathways and negative motility assays. This study underscores the emerging zoonotic potential of <i>E. marmotae</i> and its associated health risks in wildlife and humans.IMPORTANCEThe isolation of <i>Escherichia marmotae</i> from <i>Berylmys bowersi</i> represents a novel discovery, expanding the known host range of this bacterium. Our comprehensive analysis of its genetic, biochemical, and antibiotic resistance profiles provides critical insights into its potential as a zoonotic pathogen. The findings highlight the need for ongoing surveillance of <i>E. marmotae</i>, especially in wildlife populations, to assess its pathogenicity and potential threats to both animal and human health. Given its antibiotic resistance and virulence factor repertoire, <i>E. marmotae</i> may pose a significant public health concern in the future, warranting further investigation into its ecological and clinical relevance.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0294624"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The diversity of prokaryotes and fungi hosted in crude oils.","authors":"Xiaoxue Qi, Shijie Bai, Suyang Cai, Xuegong Li, Qilin Xiao","doi":"10.1128/spectrum.01689-24","DOIUrl":"https://doi.org/10.1128/spectrum.01689-24","url":null,"abstract":"<p><p>The diversity of prokaryotes and fungi in crude oils has not been understood clearly, though unique microbial communities may be hosted in crude oil. This study investigated the chemical compositions and microbial communities of crude oils from Henan, Bamianhe, and Jianghan oilfields of China. Statistical analysis revealed significant variations of both prokaryotic and fungal communities (<i>P</i> < 0.05) within different oilfields and oils with different biodegradation levels. Diversity analysis showed little difference in prokaryotic, but a significant difference in fungal (<i>P</i> < 0.05). Prokaryotic diversity was higher in heavily biodegraded oils than those in unaltered and slightly biodegraded oils; the opposite was true for fungal diversity (<i>P</i> < 0.05). Moreover, thermophilic prokaryotes were detected mainly in biodegraded heavy oils produced by the practice of thermal recovery from Henan and Bamianhe oilfields, and halophilic prokaryotes were detected mainly in oils from sandstone reservoirs containing hypersaline formation water from Jianghan Oilfield. Accordingly, microbial communities in oils are affected by oil biodegradation, extraction practices, and natural environments of native inhabitants in subsurface petroleum reservoirs.IMPORTANCEThe biological activities of endogenous microorganisms in crude oil play an important role in the production and development of crude oil. Although there have been many microbiological investigations of crude oil-contaminated sites, our understanding of the phylogenetic diversity, metabolic capabilities, and community dynamics of microbial communities within crude oil is far from complete. In this paper, the prokaryotic and fungal communities of three oil fields in different regions of China were analyzed, and several factors affecting microbial degradation were further identified. This study provides a new direction for the subsequent investigation of microbial activities inside crude oil.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0168924"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanistic divergence between SOS response activation and antibiotic-induced plasmid conjugation in <i>Escherichia coli</i>.","authors":"Ruoxuan Zhao, Arkadiusz Nawrocki, Jakob Møller-Jensen, Gang Liu, John Elmerdahl Olsen, Line Elnif Thomsen","doi":"10.1128/spectrum.00090-25","DOIUrl":"https://doi.org/10.1128/spectrum.00090-25","url":null,"abstract":"<p><p>The SOS response is a critical DNA damage repair mechanism in bacteria, designed to counteract genotoxic stress and ensure survival. This system can be activated by different classes of antimicrobial agents, each inducing the SOS response through different mechanisms. Moreover, it has been observed that certain antibiotics can enhance conjugative plasmid transfer frequencies. However, while previous studies have suggested that the SOS response contributes to horizontal transfer of certain genes, its role in plasmid conjugation remains unclear. In this study, we investigated the relationship between the SOS response and conjugation of IncI1 and IncFII plasmids harboring various <i>bla_CTX-M</i> resistance genes. Results showed that cefotaxime and mitomycin C induced both the SOS response and conjugation, while ciprofloxacin induced the SOS response without affecting conjugation frequencies. Further analysis of SOS mutants, ranging from constitutively inactive to hyper-induced states, revealed no correlation between SOS levels and conjugation frequencies, despite upregulation of <i>tra</i> gene expression in a SOS hyper-induced strain. Proteomic analysis revealed that cefotaxime-induced conjugation was associated with increased transfer and pilus protein expression. In contrast, the SOS hyper-induced strain displayed limited upregulation of plasmid-encoded proteins, suggesting post-transcriptional regulation. Additionally, putative LexA binding sites on the IncI1 plasmid revealed potential SOS-mediated regulation of plasmid genes, highlighting the interaction between the SOS response and plasmid, although it did not significantly affect conjugation.IMPORTANCEPlasmids play a critical role in the dissemination of antibiotic resistance through conjugation. Recent research suggests that the use of antibiotics not only selects for already resistant variants but further increases the rate of plasmid-encoded conjugative transmission by increasing expression of the conjugative system. At the same time, these antibiotics are known to induce the stress-related SOS response in bacteria. To be able to counteract an antibiotic-induced increase in conjugative transfer of resistance plasmid, there is a need for a fundamental understanding of the regulation of transmission, including whether this happens through activation of the SOS response. In this research, we show that antibiotic-induced conjugation and induction of the SOS response happen through different mechanisms, and thus that future strategies to control the spread of antibiotics cannot interfere with the SOS response as its target.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0009025"},"PeriodicalIF":3.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}