FEMS microbes最新文献_第2页

Exploring near-infrared spectroscopy and hyperspectral imaging as novel characterization methods for anaerobic gut fungi. 探索近红外光谱和高光谱成像作为厌氧肠道真菌的新型表征方法。

FEMS microbes Pub Date : 2024-09-10 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae025

Markus Neurauter, Julia M Vinzelj, Sophia F A Strobl, Christoph Kappacher, Tobias Schlappack, Jovan Badzoka, Matthias Rainer, Christian W Huck, Sabine M Podmirseg

{"title":"Exploring near-infrared spectroscopy and hyperspectral imaging as novel characterization methods for anaerobic gut fungi.","authors":"Markus Neurauter, Julia M Vinzelj, Sophia F A Strobl, Christoph Kappacher, Tobias Schlappack, Jovan Badzoka, Matthias Rainer, Christian W Huck, Sabine M Podmirseg","doi":"10.1093/femsmc/xtae025","DOIUrl":"10.1093/femsmc/xtae025","url":null,"abstract":"Neocallimastigomycota are a phylum of anaerobic gut fungi (AGF) that inhabit the gastrointestinal tract of herbivores and play a pivotal role in plant matter degradation. Their identification and characterization with marker gene regions has long been hampered due to the high inter- and intraspecies length variability in the commonly used fungal marker gene region internal transcribed spacer (ITS). While recent research has improved methodology (i.e. switch to LSU D2 as marker region), molecular methods will always introduce bias through nucleic acid extraction or PCR amplification. Here, near-infrared spectroscopy (NIRS) and hyperspectral imaging (HSI) are introduced as two nucleic acid sequence-independent tools for the characterization and identification of AGF strains. We present a proof-of-concept for both, achieving an independent prediction accuracy of above 95% for models based on discriminant analysis trained with samples of three different genera. We further demonstrated the robustness of the NIRS model by testing it on cultures of different growth times. Overall, NIRS provides a simple, reliable, and nondestructive approach for AGF classification, independent of molecular approaches. The HSI method provides further advantages by requiring less biomass and adding spatial information, a valuable feature if this method is extended to mixed cultures or environmental samples in the future.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae025"},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11412074/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enterococcal-host interactions in the gastrointestinal tract and beyond. 肠道内外肠球菌与宿主的相互作用

FEMS microbes Pub Date : 2024-09-09 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae027

Wiam Abdalla Mo Madani, Yusibeska Ramos, Juan R Cubillos-Ruiz, Diana K Morales

{"title":"Enterococcal-host interactions in the gastrointestinal tract and beyond.","authors":"Wiam Abdalla Mo Madani, Yusibeska Ramos, Juan R Cubillos-Ruiz, Diana K Morales","doi":"10.1093/femsmc/xtae027","DOIUrl":"10.1093/femsmc/xtae027","url":null,"abstract":"The gastrointestinal tract (GIT) is typically considered the natural niche of enterococci. However, these bacteria also inhabit extraintestinal tissues, where they can disrupt organ physiology and cause life-threatening infections. Here, we discuss how enterococci, primarily Enterococcus faecalis, interact with the intestine and other host anatomical locations such as the oral cavity, heart, liver, kidney, and vaginal tract. The metabolic flexibility of these bacteria allows them to quickly adapt to new environments, promoting their persistence in diverse tissues. In transitioning from commensals to pathogens, enterococci must overcome harsh conditions such as nutrient competition, exposure to antimicrobials, and immune pressure. Therefore, enterococci have evolved multiple mechanisms to adhere, colonize, persist, and endure these challenges in the host. This review provides a comprehensive overview of how enterococci interact with diverse host cells and tissues across multiple organ systems, highlighting the key molecular pathways that mediate enterococcal adaptation, persistence, and pathogenic behavior.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae027"},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11466040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean. 北太平洋东部热带地区微生物群落组成和相互作用的粒度分馏信息。

FEMS microbes Pub Date : 2024-09-06 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae028

Madeleine A Thompson, David L Valentine, Xuefeng Peng

{"title":"Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean.","authors":"Madeleine A Thompson, David L Valentine, Xuefeng Peng","doi":"10.1093/femsmc/xtae028","DOIUrl":"10.1093/femsmc/xtae028","url":null,"abstract":"Marine microorganisms are drivers of biogeochemical cycles in the world's oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae028"},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11873797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of the metabolism of the yeast Yarrowia lipolytica growing as a biofilm. 以生物膜形式生长的脂溶性亚罗酵母的新陈代谢特征。

FEMS microbes Pub Date : 2024-08-24 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae026

Akarawit Jenjitwanich, Hans Marx, Michael Sauer

{"title":"Characterization of the metabolism of the yeast Yarrowia lipolytica growing as a biofilm.","authors":"Akarawit Jenjitwanich, Hans Marx, Michael Sauer","doi":"10.1093/femsmc/xtae026","DOIUrl":"https://doi.org/10.1093/femsmc/xtae026","url":null,"abstract":"Yarrowia lipolytica is a well-characterized yeast with remarkable metabolic adaptability. It is capable of producing various products from different carbon sources and easily switching between planktonic and biofilm states. A biofilm represents a natural means of cell immobilization that could support continuous cultivation and production processes, such as perfusion cultivation. However, the metabolic activities of Y. lipolytica in biofilms have not yet been studied in detail. Therefore, this study aimed to compare the metabolic activities of Y. lipolytica in biofilm and planktonic states. Conventionally, a stirred tank bioreactor was used to cultivate Y. lipolytica in a planktonic state. On the other hand, a trickle bed bioreactor system was used for biofilm cultivation. The low pH at 3 was maintained to favor polyol production. The accumulation of citric acid was observed over time only in the biofilm state, which significantly differed from the planktonic state. Although the biofilm cultivation process has lower productivity, it has been observed that the production rate remains constant and the total product yield is comparable to the planktonic state when supplied with 42% oxygen-enriched air. This finding indicates that the biofilm state has the potential for continuous bioprocessing applications and is possibly a feasible option.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae026"},"PeriodicalIF":0.0,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11552517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142634115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization. 城市海洋沉积物中的大肠埃希氏菌：通过解释毒性、生物膜形成、耐卤性和抗生素耐药性来推断污染或归化。

FEMS microbes Pub Date : 2024-08-14 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae024

Isabel K Erb, Carolina Suarez, Ellinor M Frank, Johan Bengtsson-Palme, Elisabet Lindberg, Catherine J Paul

{"title":"Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization.","authors":"Isabel K Erb, Carolina Suarez, Ellinor M Frank, Johan Bengtsson-Palme, Elisabet Lindberg, Catherine J Paul","doi":"10.1093/femsmc/xtae024","DOIUrl":"10.1093/femsmc/xtae024","url":null,"abstract":"Marine sediments have been suggested as a reservoir for pathogenic bacteria, including Escherichia coli. The origins, and properties promoting survival of E. coli in marine sediments (including osmotolerance, biofilm formation capacity, and antibiotic resistance), have not been well-characterized. Phenotypes and genotypes of 37 E. coli isolates from coastal marine sediments were characterized. The isolates were diverse: 30 sequence types were identified that have been previously documented in humans, livestock, and other animals. Virulence genes were found in all isolates, with more virulence genes found in isolates sampled from sediment closer to the effluent discharge point of a wastewater treatment plant. Antibiotic resistance was demonstrated phenotypically for one isolate, which also carried tetracycline resistance genes on a plasmid. Biofilm formation capacity varied for the different isolates, with most biofilm formed by phylogroup B1 isolates. All isolates were halotolerant, growing at 3.5% NaCl. This suggests that the properties of some isolates may facilitate survival in marine environments and can explain in part how marine sediments can be a reservoir for pathogenic E. coli. As disturbance of sediment could resuspend bacteria, this should be considered as a potential contributor to compromised bathing water quality at nearby beaches.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae024"},"PeriodicalIF":0.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11378635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142156840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Editorial: thematic issue on modulating the environment with microbes. 编辑："用微生物调节环境 "专题。

FEMS microbes Pub Date : 2024-07-27 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae021

Utkarsh Sood, Gauri Garg, Rup Lal

引用次数: 0

Community context influences the conjugation efficiency of Escherichia coli. 群落环境影响大肠埃希菌的连接效率。

FEMS microbes Pub Date : 2024-07-27 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae023

Misshelle Bustamante, Floor Koopman, Jesper Martens, Jolanda K Brons, Javier DelaFuente, Thomas Hackl, Oscar P Kuipers, G Sander van Doorn, Marjon G J de Vos

{"title":"Community context influences the conjugation efficiency of Escherichia coli.","authors":"Misshelle Bustamante, Floor Koopman, Jesper Martens, Jolanda K Brons, Javier DelaFuente, Thomas Hackl, Oscar P Kuipers, G Sander van Doorn, Marjon G J de Vos","doi":"10.1093/femsmc/xtae023","DOIUrl":"10.1093/femsmc/xtae023","url":null,"abstract":"In urinary tract infections (UTIs), different bacteria can live in a polymicrobial community consisting of different species. It is unknown how community members affect the conjugation efficiency of uropathogenic Escherichia coli. We investigated the influence of individual species often coisolated from urinary infections (UTI) on the conjugation efficiency of E. coli isolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donor E. coli strain containing the pOXA-48 plasmid and six uropathogenic E. coli isolates, in the presence and absence of five different species commonly coisolated in polymicrobial UTIs to elucidate their effect on the conjugation efficiency of E. coli. We found that the basal conjugation rates of pOXA-48, in the absence of other species, are dependent on the bacterial host genetic background. Additionally, we found that bacterial interactions have an overall positive effect on the conjugation rate of pOXA-48. Particularly, Gram-positive enterococcal species were found to enhance the conjugation rates towards uropathogenic E. coli isolates. We hypothesize that the nature of the coculture and physical interactions are important for these increased conjugation rates in an artificial urine medium environment.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae023"},"PeriodicalIF":0.0,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142019772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enterococcal quorum-controlled protease alters phage infection. 肠球菌法定人数控制蛋白酶改变了噬菌体感染。

FEMS microbes Pub Date : 2024-07-26 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae022

Emma K Sheriff, Fernanda Salvato, Shelby E Andersen, Anushila Chatterjee, Manuel Kleiner, Breck A Duerkop

{"title":"Enterococcal quorum-controlled protease alters phage infection.","authors":"Emma K Sheriff, Fernanda Salvato, Shelby E Andersen, Anushila Chatterjee, Manuel Kleiner, Breck A Duerkop","doi":"10.1093/femsmc/xtae022","DOIUrl":"10.1093/femsmc/xtae022","url":null,"abstract":"Increased prevalence of multidrug-resistant bacterial infections has sparked interest in alternative antimicrobials, including bacteriophages (phages). Limited understanding of the phage infection process hampers our ability to utilize phages to their full therapeutic potential. To understand phage infection dynamics, we performed proteomics on Enterococcus faecalis infected with the phage VPE25. We discovered that numerous uncharacterized phage proteins are produced during phage infection of E. faecalis. Additionally, we identified hundreds of changes in bacterial protein abundances during infection. One such protein, enterococcal gelatinase (GelE), an fsr quorum-sensing-regulated protease involved in biofilm formation and virulence, was reduced during VPE25 infection. Plaque assays showed that mutation of either the quorum-sensing regulator fsrA or gelE resulted in plaques with a \"halo\" morphology and significantly larger diameters, suggesting decreased protection from phage infection. GelE-associated protection during phage infection is dependent on the putative murein hydrolase regulator LrgA and antiholin-like protein LrgB, whose expression have been shown to be regulated by GelE. Our work may be leveraged in the development of phage therapies that can modulate the production of GelE thereby altering biofilm formation and decreasing E. faecalis virulence.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae022"},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11328733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142001475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The role of the universal sugar transport system components PtsI (EI) and PtsH (HPr) in Enterococcus faecium 通用糖转运系统成分 PtsI (EI) 和 PtsH (HPr) 在粪肠球菌中的作用

FEMS microbes Pub Date : 2024-06-03 DOI: 10.1093/femsmc/xtae018

Michelle Hallenbeck, Michelle J. Chua, James Collins

引用次数: 0

Activity-based protein profiling of serine hydrolases and penicillin-binding proteins in Enterococcus faecium 基于活性的粪肠球菌丝氨酸水解酶和青霉素结合蛋白特征分析

FEMS microbes Pub Date : 2024-05-15 DOI: 10.1093/femsmc/xtae015

J. S. Grunnvåg, K. Hegstad, Christian S. Lentz

{"title":"Activity-based protein profiling of serine hydrolases and penicillin-binding proteins in Enterococcus faecium","authors":"J. S. Grunnvåg, K. Hegstad, Christian S. Lentz","doi":"10.1093/femsmc/xtae015","DOIUrl":"https://doi.org/10.1093/femsmc/xtae015","url":null,"abstract":"\u0000 Enterococcus faecium is a gut commensal bacterium that is gaining increasing relevance as an opportunistic, nosocomial pathogen. Its high level of intrinsic and acquired antimicrobial resistance is causing a lack of treatment options, particularly for infections with vancomycin-resistant strains, and prioritizes the identification and functional validation of novel druggable targets. Here, we use activity-based protein profiling (ABPP), a chemoproteomics approach using functionalized covalent inhibitors, to detect active serine hydrolases across 11 E. faecium and Enterococcus lactis strains. Serine hydrolases are a big and diverse enzyme family, that includes known drug targets such as penicillin-binding proteins (PBPs), whereas other subfamilies are underexplored. Comparative gel-based ABPP using Bocillin-FL revealed strain- and growth condition dependent variations in PBP activities. Profiling with the broadly serine hydrolase-reactive fluorescent probe fluorophosphonate-TMR showed a high similarity across E. faecium clade A1 strains, but higher variation across A2 and E. lactis strains. To identify these serine hydrolases, we used a biotinylated probe analog allowing for enrichment and identification via liquid chromatography-mass spectrometry. We identified 11 largely uncharacterized targets (α,β-hydrolases, SGNH-hydrolases, phospholipases, amidases, peptidases) that are druggable and accessible in live vancomycin-resistant E. faecium E745 and may possess vital functions that are to be characterized in future studies.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"60 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140972500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0