FEMS microbiology reviews最新文献_第2页

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

Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts. 宿主与细菌之间的相互作用：从古老的专业内共生菌中获得的生态学和进化论启示。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae021

Zélia Bontemps, Kiran Paranjape, Lionel Guy

{"title":"Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts.","authors":"Zélia Bontemps, Kiran Paranjape, Lionel Guy","doi":"10.1093/femsre/fuae021","DOIUrl":"10.1093/femsre/fuae021","url":null,"abstract":"Interactions between eukaryotic hosts and their bacterial symbionts drive key ecological and evolutionary processes, from regulating ecosystems to the evolution of complex molecular machines and processes. Over time, endosymbionts generally evolve reduced genomes, and their relationship with their host tends to stabilize. However, host-bacteria relationships may be heavily influenced by environmental changes. Here, we review these effects on one of the most ancient and diverse endosymbiotic groups, formed by-among others-Legionellales, Francisellaceae, and Piscirickettsiaceae. This group is referred to as Deep-branching Intracellular Gammaproteobacteria (DIG), whose last common ancestor presumably emerged about 2 Ga ago. We show that DIGs are globally distributed, but generally at very low abundance, and are mainly identified in aquatic biomes. Most DIGs harbour a type IVB secretion system, critical for host-adaptation, but its structure and composition vary. Finally, we review the different types of microbial interactions that can occur in diverse environments, with direct or indirect effects on DIG populations. The increased use of omics technologies on environmental samples will allow a better understanding of host-bacterial interactions and help unravel the definition of DIGs as a group from an ecological, molecular, and evolutionary perspective.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855341","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 vast landscape of carbohydrate fermentation in prokaryotes. 原核生物碳水化合物发酵的广阔前景

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae016

Timothy J Hackmann

{"title":"The vast landscape of carbohydrate fermentation in prokaryotes.","authors":"Timothy J Hackmann","doi":"10.1093/femsre/fuae016","DOIUrl":"10.1093/femsre/fuae016","url":null,"abstract":"Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11187502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183896","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

Escherichia coli DNA replication: the old model organism still holds many surprises. 大肠杆菌的 DNA 复制：这一古老的模式生物仍有许多惊喜。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae018

Krystian Łazowski, Roger Woodgate, Iwona J Fijalkowska

{"title":"Escherichia coli DNA replication: the old model organism still holds many surprises.","authors":"Krystian Łazowski, Roger Woodgate, Iwona J Fijalkowska","doi":"10.1093/femsre/fuae018","DOIUrl":"10.1093/femsre/fuae018","url":null,"abstract":"Research on Escherichia coli DNA replication paved the groundwork for many breakthrough discoveries with important implications for our understanding of human molecular biology, due to the high level of conservation of key molecular processes involved. To this day, it attracts a lot of attention, partially by virtue of being an important model organism, but also because the understanding of factors influencing replication fidelity might be important for studies on the emergence of antibiotic resistance. Importantly, the wide access to high-resolution single-molecule and live-cell imaging, whole genome sequencing, and cryo-electron microscopy techniques, which were greatly popularized in the last decade, allows us to revisit certain assumptions about the replisomes and offers very detailed insight into how they work. For many parts of the replisome, step-by-step mechanisms have been reconstituted, and some new players identified. This review summarizes the latest developments in the area, focusing on (a) the structure of the replisome and mechanisms of action of its components, (b) organization of replisome transactions and repair, (c) replisome dynamics, and (d) factors influencing the base and sugar fidelity of DNA synthesis.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11253446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141563083","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

Determinants of bacterial survival and proliferation in blood. 细菌在血液中存活和增殖的决定因素。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2024-05-08 DOI: 10.1093/femsre/fuae013

Pierre Lê-Bury, Hebert Echenique-Rivera, Javier Pizarro-Cerdá, Olivier Dussurget

引用次数: 0

Epitopes in the HA and NA of H5 and H7 avian influenza viruses that are important for antigenic drift. 对抗原漂移至关重要的 H5 和 H7 禽流感病毒 HA 和 NA 表位。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-05-08 DOI: 10.1093/femsre/fuae014

Jasmina M Luczo, Erica Spackman

{"title":"Epitopes in the HA and NA of H5 and H7 avian influenza viruses that are important for antigenic drift.","authors":"Jasmina M Luczo, Erica Spackman","doi":"10.1093/femsre/fuae014","DOIUrl":"10.1093/femsre/fuae014","url":null,"abstract":"Avian influenza viruses evolve antigenically to evade host immunity. Two influenza A virus surface glycoproteins, the haemagglutinin and neuraminidase, are the major targets of host immunity and undergo antigenic drift in response to host pre-existing humoral and cellular immune responses. Specific sites have been identified as important epitopes in prominent subtypes such as H5 and H7, which are of animal and public health significance due to their panzootic and pandemic potential. The haemagglutinin is the immunodominant immunogen, it has been extensively studied, and the antigenic reactivity is closely monitored to ensure candidate vaccine viruses are protective. More recently, the neuraminidase has received increasing attention for its role as a protective immunogen. The neuraminidase is expressed at a lower abundance than the haemagglutinin on the virus surface but does elicit a robust antibody response. This review aims to compile the current information on haemagglutinin and neuraminidase epitopes and immune escape mutants of H5 and H7 highly pathogenic avian influenza viruses. Understanding the evolution of immune escape mutants and the location of epitopes is critical for identification of vaccine strains and development of broadly reactive vaccines that can be utilized in humans and animals.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140907908","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

Diving into drug-screening: Zebrafish Embryos as an in vivo Platform for Antimicrobial Drug Discovery and Assessment 潜入药物筛选：斑马鱼胚胎作为抗菌药物发现和评估的体内平台

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2024-04-30 DOI: 10.1093/femsre/fuae011

Eva Habjan, Gina K Schouten, Alexander Speer, Peter van Ulsen, Wilbert Bitter

{"title":"Diving into drug-screening: Zebrafish Embryos as an in vivo Platform for Antimicrobial Drug Discovery and Assessment","authors":"Eva Habjan, Gina K Schouten, Alexander Speer, Peter van Ulsen, Wilbert Bitter","doi":"10.1093/femsre/fuae011","DOIUrl":"https://doi.org/10.1093/femsre/fuae011","url":null,"abstract":"The rise of multidrug-resistant bacteria underlines the need for innovative treatments, yet the introduction of new drugs has stagnated despite numerous antimicrobial discoveries. A major hurdle is a poor correlation between promising in vitro data and in vivo efficacy in animal models, which is essential for clinical development. Early in vivo testing is hindered by the expense and complexity of existing animal models. Therefore, there is a pressing need for cost-effective, rapid pre-clinical models with high translational value. To overcome these challenges, zebrafish embryos have emerged as an attractive model for infectious disease studies, offering advantages such as ethical alignment, rapid development, ease of maintenance, and genetic manipulability. The zebrafish embryo infection model, involving microinjection or immersion of pathogens and potential antibiotic hit compounds, provides a promising solution for early-stage drug screening. It offers a cost-effective and rapid means of assessing the efficacy, toxicity and mechanism of action of compounds in a whole-organism context. This review discusses the experimental design of this model, but also its benefits and challenges. Additionally, it highlights recently identified compounds in the zebrafish embryo infection model and discusses the relevance of the model in predicting the compound's clinical potential.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"187 1","pages":""},"PeriodicalIF":11.3,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140833443","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