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Annual review of microbiology最新文献

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Introduction. 介绍。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 DOI: 10.1146/annurev-mi-77-072723-100001
Susan Gottesman
{"title":"Introduction.","authors":"Susan Gottesman","doi":"10.1146/annurev-mi-77-072723-100001","DOIUrl":"https://doi.org/10.1146/annurev-mi-77-072723-100001","url":null,"abstract":"","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"v"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10650410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Microbiome Assembly in Fermented Foods. 发酵食品中的微生物组组装。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 DOI: 10.1146/annurev-micro-032521-041956
Nicolas L Louw, Kasturi Lele, Ruby Ye, Collin B Edwards, Benjamin E Wolfe
{"title":"Microbiome Assembly in Fermented Foods.","authors":"Nicolas L Louw,&nbsp;Kasturi Lele,&nbsp;Ruby Ye,&nbsp;Collin B Edwards,&nbsp;Benjamin E Wolfe","doi":"10.1146/annurev-micro-032521-041956","DOIUrl":"10.1146/annurev-micro-032521-041956","url":null,"abstract":"<p><p>For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"381-402"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10285345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria. RNA-DNA杂交对细菌基因组完整性的影响。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2022-09-08 DOI: 10.1146/annurev-micro-102521-014450
Emma K McLean, Taylor M Nye, Frances C Lowder, Lyle A Simmons
{"title":"The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria.","authors":"Emma K McLean,&nbsp;Taylor M Nye,&nbsp;Frances C Lowder,&nbsp;Lyle A Simmons","doi":"10.1146/annurev-micro-102521-014450","DOIUrl":"https://doi.org/10.1146/annurev-micro-102521-014450","url":null,"abstract":"<p><p>During the essential processes of DNA replication and transcription, RNA-DNA hybrid intermediates are formed that pose significant risks to genome integrity when left unresolved. To manage RNA-DNA hybrids, all cells rely on RNase H family enzymes that specifically cleave the RNA portion of the many different types of hybrids that form in vivo. Recent experimental advances have provided new insight into how RNA-DNA hybrids form and the consequences to genome integrity that ensue when persistent hybrids remain unresolved. Here we review the types of RNA-DNA hybrids, including R-loops, RNA primers, and ribonucleotide misincorporations, that form during DNA replication and transcription and discuss how each type of hybrid can contribute to genome instability in bacteria. Further, we discuss how bacterial RNase HI, HII, and HIII and bacterial FEN enzymes contribute to genome maintenance through the resolution of hybrids.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"76 ","pages":"461-480"},"PeriodicalIF":10.5,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9527769/pdf/nihms-1836951.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10181226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 1
Harnessing the Immune Response to Fungal Pathogens for Vaccine Development. 利用对真菌病原体的免疫反应开发疫苗。
IF 8.5 1区 生物学
Annual review of microbiology Pub Date : 2022-09-08 Epub Date: 2022-06-27 DOI: 10.1146/annurev-micro-041020-111511
Amariliz Rivera, Jennifer Lodge, Chaoyang Xue
{"title":"Harnessing the Immune Response to Fungal Pathogens for Vaccine Development.","authors":"Amariliz Rivera, Jennifer Lodge, Chaoyang Xue","doi":"10.1146/annurev-micro-041020-111511","DOIUrl":"10.1146/annurev-micro-041020-111511","url":null,"abstract":"<p><p>Invasive fungal infections are emerging diseases that kill over 1.5 million people per year worldwide. With the increase of immunocompromised populations, the incidence of invasive fungal infections is expected to continue to rise. Vaccines for viral and bacterial infectious diseases have had a transformative impact on human health worldwide. However, no fungal vaccines are currently in clinical use. Recently, interest in fungal vaccines has grown significantly. One <i>Candida</i> vaccine has completed phase 2 clinical trials, and research on vaccines against coccidioidomycosis continues to advance. Additionally, multiple groups have discovered various <i>Cryptococcus</i> mutant strains that promote protective responses to subsequent challenge in mouse models. There has also been progress in antibody-mediated fungal vaccines. In this review, we highlight recent fungal vaccine research progress, outline the wealth of data generated, and summarize current research for both fungal biology and immunology studies relevant to fungal vaccine development. We also review technological advancements in vaccine development and highlight the future prospects of a human vaccine against invasive fungal infections.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"76 ","pages":"703-726"},"PeriodicalIF":8.5,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11926770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10546034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Emerging Concepts in Cholera Vaccine Design. 霍乱疫苗设计中的新概念。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2022-09-08 Epub Date: 2022-06-27 DOI: 10.1146/annurev-micro-041320-033201
Brandon Sit, Bolutife Fakoya, Matthew K Waldor
{"title":"Emerging Concepts in Cholera Vaccine Design.","authors":"Brandon Sit,&nbsp;Bolutife Fakoya,&nbsp;Matthew K Waldor","doi":"10.1146/annurev-micro-041320-033201","DOIUrl":"https://doi.org/10.1146/annurev-micro-041320-033201","url":null,"abstract":"<p><p>Cholera is a severe diarrheal disease caused by the bacterium <i>Vibrio cholerae</i> and constitutes a significant public health threat in many areas of the world. <i>V. cholerae</i> infection elicits potent and long-lasting immunity, and efforts to develop cholera vaccines have been ongoing for more than a century. Currently available inactivated two-dose oral cholera vaccines are increasingly deployed to both prevent and actively curb cholera outbreaks, and they are key components of the global effort to eradicate cholera. However, these killed whole-cell vaccines have several limitations, and a variety of new oral and nonoral cholera vaccine platforms have recently been developed. Here, we review emerging concepts in cholera vaccine design and implementation that have been driven by insights from human and animal studies. As a prototypical vaccine-preventable disease, cholera continues to be an excellent target for the development and application of cutting-edge technologies and platforms that may transform vaccinology.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"681-702"},"PeriodicalIF":10.5,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40403515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 3
Mining Fatty Acid Biosynthesis for New Antimicrobials. 从脂肪酸生物合成中寻找新型抗菌剂。
IF 8.5 1区 生物学
Annual review of microbiology Pub Date : 2022-09-08 Epub Date: 2022-06-01 DOI: 10.1146/annurev-micro-041320-110408
Christopher D Radka, Charles O Rock
{"title":"Mining Fatty Acid Biosynthesis for New Antimicrobials.","authors":"Christopher D Radka, Charles O Rock","doi":"10.1146/annurev-micro-041320-110408","DOIUrl":"10.1146/annurev-micro-041320-110408","url":null,"abstract":"<p><p>Antibiotic resistance is a serious public health concern, and new drugs are needed to ensure effective treatment of many bacterial infections. Bacterial type II fatty acid synthesis (FASII) is a vital aspect of bacterial physiology, not only for the formation of membranes but also to produce intermediates used in vitamin production. Nature has evolved a repertoire of antibiotics inhibiting different aspects of FASII, validating these enzymes as potential targets for new antibiotic discovery and development. However, significant obstacles have been encountered in the development of FASII antibiotics, and few FASII drugs have advanced beyond the discovery stage. Most bacteria are capable of assimilating exogenous fatty acids. In some cases they can dispense with FASII if fatty acids are present in the environment, making the prospects for identifying broad-spectrum drugs against FASII targets unlikely. Single-target, pathogen-specific FASII drugs appear the best option, but a major drawback to this approach is the rapid acquisition of resistance via target missense mutations. This complication can be mitigated during drug development by optimizing the compound design to reduce the potential impact of on-target missense mutations at an early stage in antibiotic discovery. The lessons learned from the difficulties in FASII drug discovery that have come to light over the last decade suggest that a refocused approach to designing FASII inhibitors has the potential to add to our arsenal of weapons to combat resistance to existing antibiotics.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"76 ","pages":"281-304"},"PeriodicalIF":8.5,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9463108/pdf/nihms-1826601.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10186705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Metabolic Reprogramming and Longevity in Quiescence. 代谢重编程与静止状态下的寿命
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2022-09-08 DOI: 10.1146/annurev-micro-041320-111014
Jonathan Dworkin, Caroline S Harwood
{"title":"Metabolic Reprogramming and Longevity in Quiescence.","authors":"Jonathan Dworkin,&nbsp;Caroline S Harwood","doi":"10.1146/annurev-micro-041320-111014","DOIUrl":"https://doi.org/10.1146/annurev-micro-041320-111014","url":null,"abstract":"<p><p>Since Jacques Monod's foundational work in the 1940s, investigators studying bacterial physiology have largely (but not exclusively) focused on the exponential phase of bacterial cultures, which is characterized by rapid growth and high biosynthesis activity in the presence of excess nutrients. However, this is not the predominant state of bacterial life. In nature, most bacteria experience nutrient limitation most of the time. In fact, investigators even prior to Monod had identified other aspects of bacterial growth, including what is now known as the stationary phase, when nutrients become limiting. This review will discuss how bacteria transition to growth arrest in response to nutrient limitation through changes in transcription, translation, and metabolism. We will then examine how these changes facilitate survival during potentially extended periods of nutrient limitation, with particular attention to the metabolic strategies that underpin bacterial longevity in this state.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"76 ","pages":"91-111"},"PeriodicalIF":10.5,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10670325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 8
Regulation of Host-Pathogen Interactions via the Ubiquitin System. 泛素系统对宿主-病原体相互作用的调控。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2022-09-08 DOI: 10.1146/annurev-micro-041020-025803
Rukmini Mukherjee, Ivan Dikic
{"title":"Regulation of Host-Pathogen Interactions via the Ubiquitin System.","authors":"Rukmini Mukherjee,&nbsp;Ivan Dikic","doi":"10.1146/annurev-micro-041020-025803","DOIUrl":"https://doi.org/10.1146/annurev-micro-041020-025803","url":null,"abstract":"<p><p>Ubiquitination is a posttranslational modification that regulates a multitude of cellular functions. Pathogens, such as bacteria and viruses, have evolved sophisticated mechanisms that evade or counteract ubiquitin-dependent host responses, or even exploit the ubiquitin system to their own advantage. This is largely done by numerous pathogen virulence factors that encode E3 ligases and deubiquitinases, which are often used as weapons in pathogen-host cell interactions. Moreover, upon pathogen attack, host cellular signaling networks undergo major ubiquitin-dependent changes to protect the host cell, including coordination of innate immunity, remodeling of cellular organelles, reorganization of the cytoskeleton, and reprogramming of metabolic pathways to restrict growth of the pathogen. Here we provide mechanistic insights into ubiquitin regulation of host-pathogen interactions and how it affects bacterial and viral pathogenesis and the organization and response of the host cell.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"211-233"},"PeriodicalIF":10.5,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33449745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 9
Signal Transduction Network Principles Underlying Bacterial Collective Behaviors. 细菌集体行为背后的信号转导网络原理。
IF 8.5 1区 生物学
Annual review of microbiology Pub Date : 2022-09-08 Epub Date: 2022-05-24 DOI: 10.1146/annurev-micro-042922-122020
Andrew A Bridges, Jojo A Prentice, Ned S Wingreen, Bonnie L Bassler
{"title":"Signal Transduction Network Principles Underlying Bacterial Collective Behaviors.","authors":"Andrew A Bridges, Jojo A Prentice, Ned S Wingreen, Bonnie L Bassler","doi":"10.1146/annurev-micro-042922-122020","DOIUrl":"10.1146/annurev-micro-042922-122020","url":null,"abstract":"<p><p>Bacteria orchestrate collective behaviors and accomplish feats that would be unsuccessful if carried out by a lone bacterium. Processes undertaken by groups of bacteria include bioluminescence, biofilm formation, virulence factor production, and release of public goods that are shared by the community. Collective behaviors are controlled by signal transduction networks that integrate sensory information and transduce the information internally. Here, we discuss network features and mechanisms that, even in the face of dramatically changing environments, drive precise execution of bacterial group behaviors. We focus on representative quorum-sensing and second-messenger cyclic dimeric GMP (c-di-GMP) signal relays. We highlight ligand specificity versus sensitivity, how small-molecule ligands drive discrimination of kin versus nonkin, signal integration mechanisms, single-input sensory systems versus coincidence detectors, and tuning of input-output dynamics via feedback regulation. We summarize how different features of signal transduction systems allow groups of bacteria to successfully interpret and collectively react to dynamically changing environments.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"76 ","pages":"235-257"},"PeriodicalIF":8.5,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9463083/pdf/nihms-1790607.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10186701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Introduction. 介绍。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2022-09-08 DOI: 10.1146/annurev-mi-76-062422-100001
Susan Gottesman
{"title":"Introduction.","authors":"Susan Gottesman","doi":"10.1146/annurev-mi-76-062422-100001","DOIUrl":"https://doi.org/10.1146/annurev-mi-76-062422-100001","url":null,"abstract":"","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"v"},"PeriodicalIF":10.5,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33449742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
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