FEMS microbiology reviews最新文献_第6页

Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals. 共生的起源：动植物微生物致病、共生和互生的共同机制。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-11-01 DOI: 10.1093/femsre/fuac048

Christina L Wiesmann, Nicole R Wang, Yue Zhang, Zhexian Liu, Cara H Haney

{"title":"Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals.","authors":"Christina L Wiesmann, Nicole R Wang, Yue Zhang, Zhexian Liu, Cara H Haney","doi":"10.1093/femsre/fuac048","DOIUrl":"10.1093/femsre/fuac048","url":null,"abstract":"Regardless of the outcome of symbiosis, whether it is pathogenic, mutualistic or commensal, bacteria must first colonize their hosts. Intriguingly, closely related bacteria that colonize diverse hosts with diverse outcomes of symbiosis have conserved host-association and virulence factors. This review describes commonalities in the process of becoming host associated amongst bacteria with diverse lifestyles. Whether a pathogen, commensal or mutualist, bacteria must sense the presence of and migrate towards a host, compete for space and nutrients with other microbes, evade the host immune system, and change their physiology to enable long-term host association. We primarily focus on well-studied taxa, such as Pseudomonas, that associate with diverse model plant and animal hosts, with far-ranging symbiotic outcomes. Given the importance of opportunistic pathogens and chronic infections in both human health and agriculture, understanding the mechanisms that facilitate symbiotic relationships between bacteria and their hosts will help inform the development of disease treatments for both humans, and the plants we eat.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10719066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10724260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

What's in a name? Characteristics of clinical biofilms. 名字里有什么？临床生物膜的特征。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad050

Mads Lichtenberg, Tom Coenye, Matthew R Parsek, Thomas Bjarnsholt, Tim Holm Jakobsen

{"title":"What's in a name? Characteristics of clinical biofilms.","authors":"Mads Lichtenberg, Tom Coenye, Matthew R Parsek, Thomas Bjarnsholt, Tim Holm Jakobsen","doi":"10.1093/femsre/fuad050","DOIUrl":"10.1093/femsre/fuad050","url":null,"abstract":"In vitro biofilms are communities of microbes with unique features compared to individual cells. Biofilms are commonly characterized by physical traits like size, adhesion, and a matrix made of extracellular substances. They display distinct phenotypic features, such as metabolic activity and antibiotic tolerance. However, the relative importance of these traits depends on the environment and bacterial species. Various mechanisms enable biofilm-associated bacteria to withstand antibiotics, including physical barriers, physiological adaptations, and changes in gene expression. Gene expression profiles in biofilms differ from individual cells but, there is little consensus among studies and so far, a 'biofilm signature transcriptome' has not been recognized. Additionally, the spatial and temporal variability within biofilms varies greatly depending on the system or environment. Despite all these variable conditions, which produce very diverse structures, they are all noted as biofilms. We discuss that clinical biofilms may differ from those grown in laboratories and found in the environment and discuss whether the characteristics that are commonly used to define and characterize biofilms have been shown in infectious biofilms. We emphasize that there is a need for a comprehensive understanding of the specific traits that are used to define bacteria in infections as clinical biofilms.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 5","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10305362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Exploring probiotic effector molecules and their mode of action in gut-immune interactions. 更正：探索益生菌效应分子及其在肠道免疫相互作用中的作用模式。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad055

引用次数: 0

Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. 具有异化硫酸盐/亚硫酸盐还原潜力的微生物的全球多样性和推断生态生理学。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad058

Muhe Diao, Stefan Dyksma, Elif Koeksoy, David Kamanda Ngugi, Karthik Anantharaman, Alexander Loy, Michael Pester

{"title":"Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction.","authors":"Muhe Diao, Stefan Dyksma, Elif Koeksoy, David Kamanda Ngugi, Karthik Anantharaman, Alexander Loy, Michael Pester","doi":"10.1093/femsre/fuad058","DOIUrl":"10.1093/femsre/fuad058","url":null,"abstract":"Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10591310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41114890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Type II bacterial toxin-antitoxins: hypotheses, facts, and the newfound plethora of the PezAT system. II型细菌毒素抗毒素：假说、事实和新发现的过量PezAT系统。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad052

Wai Ting Chan, Maria Pilar Garcillán-Barcia, Chew Chieng Yeo, Manuel Espinosa

{"title":"Type II bacterial toxin-antitoxins: hypotheses, facts, and the newfound plethora of the PezAT system.","authors":"Wai Ting Chan, Maria Pilar Garcillán-Barcia, Chew Chieng Yeo, Manuel Espinosa","doi":"10.1093/femsre/fuad052","DOIUrl":"10.1093/femsre/fuad052","url":null,"abstract":"Toxin-antitoxin (TA) systems are entities found in the prokaryotic genomes, with eight reported types. Type II, the best characterized, is comprised of two genes organized as an operon. Whereas toxins impair growth, the cognate antitoxin neutralizes its activity. TAs appeared to be involved in plasmid maintenance, persistence, virulence, and defence against bacteriophages. Most Type II toxins target the bacterial translational machinery. They seem to be antecessors of Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) RNases, minimal nucleotidyltransferase domains, or CRISPR-Cas systems. A total of four TAs encoded by Streptococcus pneumoniae, RelBE, YefMYoeB, Phd-Doc, and HicAB, belong to HEPN-RNases. The fifth is represented by PezAT/Epsilon-Zeta. PezT/Zeta toxins phosphorylate the peptidoglycan precursors, thereby blocking cell wall synthesis. We explore the body of knowledge (facts) and hypotheses procured for Type II TAs and analyse the data accumulated on the PezAT family. Bioinformatics analyses showed that homologues of PezT/Zeta toxin are abundantly distributed among 14 bacterial phyla mostly in Proteobacteria (48%), Firmicutes (27%), and Actinobacteria (18%), showing the widespread distribution of this TA. The pezAT locus was found to be mainly chromosomally encoded whereas its homologue, the tripartite omega-epsilon-zeta locus, was found mostly on plasmids. We found several orphan pezT/zeta toxins, unaccompanied by a cognate antitoxin.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f6/74/fuad052.PMC10532202.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10254229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Methodologies for bacterial ribonuclease characterization using RNA-seq. 使用RNA-seq鉴定细菌核糖核酸酶的方法。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad049

Laura Broglia, Anaïs Le Rhun, Emmanuelle Charpentier

引用次数: 0

Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research. 阐明口腔微生物组及其与宿主的相互作用：在口腔微生物组研究方面，omics 和生物信息学技术的最新进展。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad051

Jonathon L Baker

{"title":"Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.","authors":"Jonathon L Baker","doi":"10.1093/femsre/fuad051","DOIUrl":"10.1093/femsre/fuad051","url":null,"abstract":"The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 5","pages":""},"PeriodicalIF":10.1,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c0/95/fuad051.PMC10503653.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10297396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural analysis of novel drug targets for mitigation of Pseudomonas aeruginosa biofilms. 缓解铜绿假单胞菌生物膜的新药物靶点的结构分析。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad054

Moumita Ghosh, Shikha Raghav, Puja Ghosh, Swagatam Maity, Kavery Mohela, Deepti Jain

{"title":"Structural analysis of novel drug targets for mitigation of Pseudomonas aeruginosa biofilms.","authors":"Moumita Ghosh, Shikha Raghav, Puja Ghosh, Swagatam Maity, Kavery Mohela, Deepti Jain","doi":"10.1093/femsre/fuad054","DOIUrl":"10.1093/femsre/fuad054","url":null,"abstract":"Pseudomonas aeruginosa is an opportunistic human pathogen responsible for acute and chronic, hard to treat infections. Persistence of P. aeruginosa is due to its ability to develop into biofilms, which are sessile bacterial communities adhered to substratum and encapsulated in layers of self-produced exopolysaccharides. These biofilms provide enhanced protection from the host immune system and resilience towards antibiotics, which poses a challenge for treatment. Various strategies have been expended for combating biofilms, which involve inhibiting biofilm formation or promoting their dispersal. The current remediation approaches offer some hope for clinical usage, however, treatment and eradication of preformed biofilms is still a challenge. Thus, identifying novel targets and understanding the detailed mechanism of biofilm regulation becomes imperative. Structure-based drug discovery (SBDD) provides a powerful tool that exploits the knowledge of atomic resolution details of the targets to search for high affinity ligands. This review describes the available structural information on the putative target protein structures that can be utilized for high throughput in silico drug discovery against P. aeruginosa biofilms. Integrating available structural information on the target proteins in readily accessible format will accelerate the process of drug discovery.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41114972","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}

引用次数: 1

Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks? Praemonitus praemunitus：我们能预测和准备未来的病毒性疾病爆发吗？

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad048

Zoe Sessions, Tesia Bobrowski, Holli-Joi Martin, Jon-Michael T Beasley, Aneri Kothari, Trevor Phares, Michael Li, Vinicius M Alves, Marcus T Scotti, Nathaniel J Moorman, Ralph Baric, Alexander Tropsha, Eugene N Muratov

{"title":"Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks?","authors":"Zoe Sessions, Tesia Bobrowski, Holli-Joi Martin, Jon-Michael T Beasley, Aneri Kothari, Trevor Phares, Michael Li, Vinicius M Alves, Marcus T Scotti, Nathaniel J Moorman, Ralph Baric, Alexander Tropsha, Eugene N Muratov","doi":"10.1093/femsre/fuad048","DOIUrl":"10.1093/femsre/fuad048","url":null,"abstract":"Understanding the origins of past and present viral epidemics is critical in preparing for future outbreaks. Many viruses, including SARS-CoV-2, have led to significant consequences not only due to their virulence, but also because we were unprepared for their emergence. We need to learn from large amounts of data accumulated from well-studied, past pandemics and employ modern informatics and therapeutic development technologies to forecast future pandemics and help minimize their potential impacts. While acknowledging the complexity and difficulties associated with establishing reliable outbreak predictions, herein we provide a perspective on the regions of the world that are most likely to be impacted by future outbreaks. We specifically focus on viruses with epidemic potential, namely SARS-CoV-2, MERS-CoV, DENV, ZIKV, MAYV, LASV, noroviruses, influenza, Nipah virus, hantaviruses, Oropouche virus, MARV, and Ebola virus, which all require attention from both the public and scientific community to avoid societal catastrophes like COVID-19. Based on our literature review, data analysis, and outbreak simulations, we posit that these future viral epidemics are unavoidable, but that their societal impacts can be minimized by strategic investment into basic virology research, epidemiological studies of neglected viral diseases, and antiviral drug discovery.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10532129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10026311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbiologically influenced corrosion-more than just microorganisms. 微生物影响腐蚀——不仅仅是微生物。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad041

J Knisz, R Eckert, L M Gieg, A Koerdt, J S Lee, E R Silva, T L Skovhus, B A An Stepec, S A Wade

{"title":"Microbiologically influenced corrosion-more than just microorganisms.","authors":"J Knisz, R Eckert, L M Gieg, A Koerdt, J S Lee, E R Silva, T L Skovhus, B A An Stepec, S A Wade","doi":"10.1093/femsre/fuad041","DOIUrl":"https://doi.org/10.1093/femsre/fuad041","url":null,"abstract":"Microbiologically influenced corrosion (MIC) is a phenomenon of increasing concern that affects various materials and sectors of society. MIC describes the effects, often negative, that a material can experience due to the presence of microorganisms. Unfortunately, although several research groups and industrial actors worldwide have already addressed MIC, discussions are fragmented, while information sharing and willingness to reach out to other disciplines are limited. A truly interdisciplinary approach, which would be logical for this material/biology/chemistry-related challenge, is rarely taken. In this review, we highlight critical non-biological aspects of MIC that can sometimes be overlooked by microbiologists working on MIC but are highly relevant for an overall understanding of this phenomenon. Here, we identify gaps, methods, and approaches to help solve MIC-related challenges, with an emphasis on the MIC of metals. We also discuss the application of existing tools and approaches for managing MIC and propose ideas to promote an improved understanding of MIC. Furthermore, we highlight areas where the insights and expertise of microbiologists are needed to help progress this field.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 5","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10479746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10225655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3