FEMS microbiology reviews最新文献

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 : 2024-11-05 DOI: 10.1093/femsre/fuae027

Ethan Gates, Nathan Crook

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 : 2024-11-04 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":"https://doi.org/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. Firstly, 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 (cDBTL) procedure including function specification, chassis selection, interaction design, system build, performance test, modelling 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":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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 : 2024-10-10 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":"https://doi.org/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 26363 genomes labeled as Pseudomonas in 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 analyzed 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 77000 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":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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

Fungal primary and opportunistic pathogens: an ecological perspective. 真菌原生病原体和机会病原体：生态学视角。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae022

Sybren de Hoog, Chao Tang, Xin Zhou, Bruna Jacomel, Bruno Lustosa, Yinggai Song, Hazal Kandemir, Sarah A Ahmed, Shaoqin Zhou, Ricardo Belmonte-Lopes, Yu Quan, Peiying Feng, Vania A Vicente, Yingqian Kang

{"title":"Fungal primary and opportunistic pathogens: an ecological perspective.","authors":"Sybren de Hoog, Chao Tang, Xin Zhou, Bruna Jacomel, Bruno Lustosa, Yinggai Song, Hazal Kandemir, Sarah A Ahmed, Shaoqin Zhou, Ricardo Belmonte-Lopes, Yu Quan, Peiying Feng, Vania A Vicente, Yingqian Kang","doi":"10.1093/femsre/fuae022","DOIUrl":"10.1093/femsre/fuae022","url":null,"abstract":"Fungal primary pathogenicity on vertebrates is here described as a deliberate strategy where the host plays a role in increasing the species' fitness. Opportunism is defined as the coincidental survival of an individual strain in host tissue using properties that are designed for life in an entirely different habitat. In that case, the host's infection control is largely based on innate immunity, and the etiologic agent is not transmitted after infection, and thus fungal evolution is not possible. Primary pathogens encompass two types, depending on their mode of transmission. Environmental pathogens have a double life cycle, and tend to become enzootic, adapted to a preferred host in a particular habitat. In contrast, pathogens that have a host-to-host transmission pattern are prone to shift to a neighboring, immunologically naive host, potentially leading to epidemics. Beyond these prototypical life cycles, some environmental fungi are able to make large leaps between dissimilar hosts/habitats, probably due to the similarity of key factors enabling survival in an entirely different niche, and thus allowing a change from opportunistic to primary pathogenicity. Mostly, such factors seem to be associated with extremotolerance.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11409879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906370","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

Methods for studying microbial acid stress responses: from molecules to populations. 研究微生物酸应激反应的方法：从分子到群体。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae015

Merve Atasoy, Simona Bartkova, Zeynep Çetecioğlu-Gürol, Nuno P Mira, Conor O'Byrne, Fernando Pérez-Rodríguez, Aricia Possas, Ott Scheler, Jana Sedláková-Kaduková, Mirka Sinčák, Matthias Steiger, Carmit Ziv, Peter A Lund

{"title":"Methods for studying microbial acid stress responses: from molecules to populations.","authors":"Merve Atasoy, Simona Bartkova, Zeynep Çetecioğlu-Gürol, Nuno P Mira, Conor O'Byrne, Fernando Pérez-Rodríguez, Aricia Possas, Ott Scheler, Jana Sedláková-Kaduková, Mirka Sinčák, Matthias Steiger, Carmit Ziv, Peter A Lund","doi":"10.1093/femsre/fuae015","DOIUrl":"10.1093/femsre/fuae015","url":null,"abstract":"The study of how micro-organisms detect and respond to different stresses has a long history of producing fundamental biological insights while being simultaneously of significance in many applied microbiological fields including infection, food and drink manufacture, and industrial and environmental biotechnology. This is well-illustrated by the large body of work on acid stress. Numerous different methods have been used to understand the impacts of low pH on growth and survival of micro-organisms, ranging from studies of single cells to large and heterogeneous populations, from the molecular or biophysical to the computational, and from well-understood model organisms to poorly defined and complex microbial consortia. Much is to be gained from an increased general awareness of these methods, and so the present review looks at examples of the different methods that have been used to study acid resistance, acid tolerance, and acid stress responses, and the insights they can lead to, as well as some of the problems involved in using them. We hope this will be of interest both within and well beyond the acid stress research community.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140956970","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

Mechanisms of host adaptation by bacterial pathogens. 细菌病原体适应宿主的机制。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae019

Matthew F Barber, J Ross Fitzgerald

引用次数: 0

Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria. 揭示环境细菌中抗生素和重金属抗药性共同选择的机制。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae017

Brodie F Gillieatt, Nicholas V Coleman

{"title":"Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria.","authors":"Brodie F Gillieatt, Nicholas V Coleman","doi":"10.1093/femsre/fuae017","DOIUrl":"10.1093/femsre/fuae017","url":null,"abstract":"The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11253441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426620","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