FEMS microbiology reviews最新文献

Microbial functional diversity and redundancy: moving forward.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-12-17 DOI: 10.1093/femsre/fuae031

Pierre Ramond, Pierre E Galand, Ramiro Logares

引用次数: 0

Multidisciplinary methodologies used in the study of cable bacteria.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-12-13 DOI: 10.1093/femsre/fuae030

Michaela M H Wawryk, Philip Ley, Diana Vasquez-Cardenas, Rico F Tabor, Perran L M Cook

引用次数: 0

Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms. 揭示假单胞菌群的基因组多样性：探索分类、核心庞基因组和抗生素耐药性机制。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae025

Zulema Udaondo, Juan Luis Ramos, Kaleb Abram

{"title":"Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.","authors":"Zulema Udaondo, Juan Luis Ramos, Kaleb Abram","doi":"10.1093/femsre/fuae025","DOIUrl":"10.1093/femsre/fuae025","url":null,"abstract":"The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier \"Pseudomonas putida\" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as \"Pseudomonas putida\" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399862","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

Assembly of functional microbial ecosystems: from molecular circuits to communities. 功能微生物生态系统的组装：从分子电路到群落。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae026

Shengbo Wu, Yongsheng Zhou, Lei Dai, Aidong Yang, Jianjun Qiao

{"title":"Assembly of functional microbial ecosystems: from molecular circuits to communities.","authors":"Shengbo Wu, Yongsheng Zhou, Lei Dai, Aidong Yang, Jianjun Qiao","doi":"10.1093/femsre/fuae026","DOIUrl":"10.1093/femsre/fuae026","url":null,"abstract":"Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate, or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. First, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn procedure including function specification, chassis selection, interaction design, system build, performance test, modeling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575602","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

Why HPV16? Why, now, HPV42? How the discovery of HPV42 in rare cancers provides an opportunity to challenge our understanding about the transition between health and disease for common members of the healthy microbiota. 为什么是 HPV16？为什么现在又是 HPV42？在罕见癌症中发现 HPV42 如何提供了一个机会，挑战我们对健康微生物群常见成员在健康与疾病之间转变的理解。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae029

Ignacio G Bravo, Sophia Belkhir, Philippe Paget-Bailly

{"title":"Why HPV16? Why, now, HPV42? How the discovery of HPV42 in rare cancers provides an opportunity to challenge our understanding about the transition between health and disease for common members of the healthy microbiota.","authors":"Ignacio G Bravo, Sophia Belkhir, Philippe Paget-Bailly","doi":"10.1093/femsre/fuae029","DOIUrl":"10.1093/femsre/fuae029","url":null,"abstract":"In 2022, a bioinformatic, agnostic approach identified HPV42 as causative agent of a rare cancer, later confirmed experimentally. This unexpected association offers an opportunity to reconsider our understanding about papillomavirus infections and cancers. We have expanded our knowledge about the diversity of papillomaviruses and the diseases they cause. Yet, we still lack answers to fundamental questions, such as what makes HPV16 different from the closely related HPV31 or HPV33; or why the very divergent HPV13 and HPV32 cause focal epithelial hyperplasia, while HPV6 or HPV42 do not, despite their evolutionary relatedness. Certain members of the healthy skin microbiota are associated to rare clinical conditions. We propose that a focus on cellular phenotypes, most often transient and influenced by intrinsic and extrinsic factors, may help understand the continuum between health and disease. A conceptual switch is required towards an interpretation of biology as a diversity of states connected by transition probabilities, rather than quasi-deterministic programs. Under this perspective, papillomaviruses may only trigger malignant transformation when specific viral genotypes interact with precise cellular states. Drawing on Canguilhem's concepts of normal and pathological, we suggest that understanding the transition between fluid cellular states can illuminate how commensal-like infections transition from benign to malignant.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11644485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675555","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

Key roles of two-component systems in intestinal signal sensing and virulence regulation in enterohemorrhagic Escherichia coli. 双组分系统在肠出血性大肠杆菌肠道信号传感和毒力调节中的关键作用。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae028

Hongmin Sun, Di Huang, Yu Pang, Jingnan Chen, Chenbo Kang, Mengjie Zhao, Bin Yang

{"title":"Key roles of two-component systems in intestinal signal sensing and virulence regulation in enterohemorrhagic Escherichia coli.","authors":"Hongmin Sun, Di Huang, Yu Pang, Jingnan Chen, Chenbo Kang, Mengjie Zhao, Bin Yang","doi":"10.1093/femsre/fuae028","DOIUrl":"10.1093/femsre/fuae028","url":null,"abstract":"Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that infects humans by colonizing the large intestine. Upon reaching the large intestine, EHEC mediates local signal recognition and the transcriptional regulation of virulence genes to promote adherence and colonization in a highly site-specific manner. Two-component systems (TCSs) represent an important strategy used by EHEC to couple external stimuli with the regulation of gene expression, thereby allowing EHEC to rapidly adapt to changing environmental conditions. An increasing number of studies published in recent years have shown that EHEC senses a variety of host- and microbiota-derived signals present in the human intestinal tract and coordinates the expression of virulence genes via multiple TCS-mediated signal transduction pathways to initiate the disease-causing process. Here, we summarize how EHEC detects a wide range of intestinal signals and precisely regulates virulence gene expression through multiple signal transduction pathways during the initial stages of infection, with a particular emphasis on the key roles of TCSs. This review provides valuable insights into the importance of TCSs in EHEC pathogenesis, which has relevant implications for the development of antibacterial therapies against EHEC infection.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11644481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617004","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

The biochemical mechanisms of plastic biodegradation. 塑料生物降解的生化机制。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae027

Ethan G Gates, Nathan Crook

引用次数: 0

The emerging role of SARS-CoV-2 nonstructural protein 1 (nsp1) in epigenetic regulation of host gene expression. SARS-CoV-2 非结构蛋白 1 (nsp1) 在宿主基因表达的表观遗传调控中的新作用。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae023

Konstantin I Ivanov, Haibin Yang, Ruixue Sun, Chunmei Li, Deyin Guo

{"title":"The emerging role of SARS-CoV-2 nonstructural protein 1 (nsp1) in epigenetic regulation of host gene expression.","authors":"Konstantin I Ivanov, Haibin Yang, Ruixue Sun, Chunmei Li, Deyin Guo","doi":"10.1093/femsre/fuae023","DOIUrl":"10.1093/femsre/fuae023","url":null,"abstract":"Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes widespread changes in epigenetic modifications and chromatin architecture in the host cell. Recent evidence suggests that SARS-CoV-2 nonstructural protein 1 (nsp1) plays an important role in driving these changes. Previously thought to be primarily involved in host translation shutoff and cellular mRNA degradation, nsp1 has now been shown to be a truly multifunctional protein that affects host gene expression at multiple levels. The functions of nsp1 are surprisingly diverse and include not only the downregulation of cellular mRNA translation and stability, but also the inhibition of mRNA export from the nucleus, the suppression of host immune signaling, and, most recently, the epigenetic regulation of host gene expression. In this review, we first summarize the current knowledge on SARS-CoV-2-induced changes in epigenetic modifications and chromatin structure. We then focus on the role of nsp1 in epigenetic reprogramming, with a particular emphasis on the silencing of immune-related genes. Finally, we discuss potential molecular mechanisms underlying the epigenetic functions of nsp1 based on evidence from SARS-CoV-2 interactome studies.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132261","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

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes. 波罗的海微生物的生物多样性：鉴定海洋微生物新方法的力量。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae024

Hanna Mazur-Marzec, Anders F Andersson, Agata Błaszczyk, Przemysław Dąbek, Ewa Górecka, Michał Grabski, Katarzyna Jankowska, Agata Jurczak-Kurek, Anna K Kaczorowska, Tadeusz Kaczorowski, Bengt Karlson, Marija Kataržytė, Justyna Kobos, Ewa Kotlarska, Beata Krawczyk, Aneta Łuczkiewicz, Kasia Piwosz, Bartosz Rybak, Krzysztof Rychert, Conny Sjöqvist, Waldemar Surosz, Beata Szymczycha, Anna Toruńska-Sitarz, Grzegorz Węgrzyn, Andrzej Witkowski, Alicja Węgrzyn

{"title":"Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes.","authors":"Hanna Mazur-Marzec, Anders F Andersson, Agata Błaszczyk, Przemysław Dąbek, Ewa Górecka, Michał Grabski, Katarzyna Jankowska, Agata Jurczak-Kurek, Anna K Kaczorowska, Tadeusz Kaczorowski, Bengt Karlson, Marija Kataržytė, Justyna Kobos, Ewa Kotlarska, Beata Krawczyk, Aneta Łuczkiewicz, Kasia Piwosz, Bartosz Rybak, Krzysztof Rychert, Conny Sjöqvist, Waldemar Surosz, Beata Szymczycha, Anna Toruńska-Sitarz, Grzegorz Węgrzyn, Andrzej Witkowski, Alicja Węgrzyn","doi":"10.1093/femsre/fuae024","DOIUrl":"10.1093/femsre/fuae024","url":null,"abstract":"Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375361","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

The rise and future of CRISPR-based approaches for high-throughput genomics. 基于 CRISPR 的高通量基因组学方法的兴起与未来。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae020

Silke Vercauteren, Simon Fiesack, Laetitia Maroc, Natalie Verstraeten, Liselot Dewachter, Jan Michiels, Sibylle C Vonesch

{"title":"The rise and future of CRISPR-based approaches for high-throughput genomics.","authors":"Silke Vercauteren, Simon Fiesack, Laetitia Maroc, Natalie Verstraeten, Liselot Dewachter, Jan Michiels, Sibylle C Vonesch","doi":"10.1093/femsre/fuae020","DOIUrl":"10.1093/femsre/fuae020","url":null,"abstract":"Clustered regularly interspaced short palindromic repeats (CRISPR) has revolutionized the field of genome editing. To circumvent the permanent modifications made by traditional CRISPR techniques and facilitate the study of both essential and nonessential genes, CRISPR interference (CRISPRi) was developed. This gene-silencing technique employs a deactivated Cas effector protein and a guide RNA to block transcription initiation or elongation. Continuous improvements and a better understanding of the mechanism of CRISPRi have expanded its scope, facilitating genome-wide high-throughput screens to investigate the genetic basis of phenotypes. Additionally, emerging CRISPR-based alternatives have further expanded the possibilities for genetic screening. This review delves into the mechanism of CRISPRi, compares it with other high-throughput gene-perturbation techniques, and highlights its superior capacities for studying complex microbial traits. We also explore the evolution of CRISPRi, emphasizing enhancements that have increased its capabilities, including multiplexing, inducibility, titratability, predictable knockdown efficacy, and adaptability to nonmodel microorganisms. Beyond CRISPRi, we discuss CRISPR activation, RNA-targeting CRISPR systems, and single-nucleotide resolution perturbation techniques for their potential in genome-wide high-throughput screens in microorganisms. Collectively, this review gives a comprehensive overview of the general workflow of a genome-wide CRISPRi screen, with an extensive discussion of strengths and weaknesses, future directions, and potential alternatives.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11409895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859471","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