FEMS microbiology reviews最新文献_第2页

Microbial adaptive pathogenicity strategies to the host inflammatory environment. 微生物对宿主炎症环境的适应性致病策略。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae032

Sophia U J Hitzler, Candela Fernández-Fernández, Dolly E Montaño, Axel Dietschmann, Mark S Gresnigt

{"title":"Microbial adaptive pathogenicity strategies to the host inflammatory environment.","authors":"Sophia U J Hitzler, Candela Fernández-Fernández, Dolly E Montaño, Axel Dietschmann, Mark S Gresnigt","doi":"10.1093/femsre/fuae032","DOIUrl":"10.1093/femsre/fuae032","url":null,"abstract":"Pathogenic microorganisms can infect a variety of niches in the human body. During infection, these microbes can only persist if they adapt adequately to the dynamic host environment and the stresses imposed by the immune system. While viruses entirely rely on host cells to replicate, bacteria and fungi use their pathogenicity mechanisms for the acquisition of essential nutrients that lie under host restriction. An inappropriate deployment of pathogenicity mechanisms will alert host defence mechanisms that aim to eradicate the pathogen. Thus, these adaptations require tight regulation to guarantee nutritional access without eliciting strong immune activation. To work efficiently, the immune system relies on a complex signalling network, involving a myriad of immune mediators, some of which are quite directly associated with imminent danger for the pathogen. To manipulate the host immune system, viruses have evolved cytokine receptors and viral cytokines. However, among bacteria and fungi, selected pathogens have evolved the capacity to use these inflammatory response-specific signals to regulate their pathogenicity. In this review, we explore how bacterial and fungal pathogens can sense the immune system and use adaptive pathogenicity strategies to evade and escape host defence to ensure their persistence in the host.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11737513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893312","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

Extreme smells-microbial production of volatile organic compounds at the limits of life.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf004

Miguel Ángel Salinas-García, Jonas Fernbach, Riikka Rinnan, Anders Priemé

引用次数: 0

Charting the microbial frontier: a comprehensive guidebook for advancing microbiome research. 绘制微生物前沿：推进微生物组研究的综合指南。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae033

Hui Wu

引用次数: 0

Standardizing experimental approaches to investigate interactions between bacteria and ectomycorrhizal fungi. 规范研究细菌与外生菌根真菌相互作用的实验方法。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae035

Louis Berrios, T Bertie Ansell, Peter D Dahlberg, Kabir G Peay

引用次数: 0

Microbial engineering for monocyclic aromatic compounds production.

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf003

Guipeng Hu, Cong Gao, Xiaomin Li, Wei Song, Jing Wu

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