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Annual review of microbiology最新文献

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Mutagenesis: Insights from Single-Cell, Real-Time Approaches. 诱变：从单细胞实时方法的见解。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-09-16 DOI: 10.1146/annurev-micro-050224-093623
Marina Elez, Chiara Enrico Bena, Lydia Robert
{"title":"Mutagenesis: Insights from Single-Cell, Real-Time Approaches.","authors":"Marina Elez, Chiara Enrico Bena, Lydia Robert","doi":"10.1146/annurev-micro-050224-093623","DOIUrl":"https://doi.org/10.1146/annurev-micro-050224-093623","url":null,"abstract":"<p><p>All genetic variation fueling evolution depends on mutations. Although mutations have been extensively studied for almost a century, until a decade ago the investigation of mutations was limited to population-level analysis. This constraint has hampered the exploration of cellular heterogeneity in mutation processes and its evolutionary implications. To overcome these limitations, quantitative visualization methods for studying mutations in the bacterium <i>Escherichia coli</i> at the single-cell level have been developed. These approaches offer the possibility of accessing a major source of mutations, i.e., DNA polymerase errors, and their fate, i.e., repair versus conversion to mutation. In addition, such methods allow for quantitative characterization of the effects of mutations on cell fitness. This article discusses insights into the mutation process derived from these new single-cell mutagenesis approaches.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074377","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
Why Do Filamentous Actinomycetota Produce Such a Vast Array of Specialized Metabolites? 为什么丝状放线菌会产生如此大量的特殊代谢物？
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-09-12 DOI: 10.1146/annurev-micro-060424-051257
Luis M Cantu Morin, Kilian Dekoninck, Varun Sridhar, Saoirse Disney-McKeethen, Theresa Proctor, Ashley Y Eng, Matthew F Traxler
{"title":"Why Do Filamentous <i>Actinomycetota</i> Produce Such a Vast Array of Specialized Metabolites?","authors":"Luis M Cantu Morin, Kilian Dekoninck, Varun Sridhar, Saoirse Disney-McKeethen, Theresa Proctor, Ashley Y Eng, Matthew F Traxler","doi":"10.1146/annurev-micro-060424-051257","DOIUrl":"https://doi.org/10.1146/annurev-micro-060424-051257","url":null,"abstract":"<p><p>Bacteria of the phylum <i>Actinomycetota</i> are extremely diverse: They inhabit niches ranging from soils and ocean sediments to the normal human microbiota, and they cause tuberculosis, one of the most prevalent chronic bacterial infections. They display an accordingly wide range of adaptive traits that enable their persistence, including, in some clades, a vast repertoire of biologically active small molecules. While humans have capitalized on this trove of useful natural products (also called secondary or specialized metabolites), the utility of these molecules for their producers has been challenging to directly assess. In this review, we consider adaptations that may have paved the way for the evolution of the expansive specialized metabolisms present in certain clades of <i>Actinomycetota</i>. We also consider the evolutionary pressures that may have driven diversification of these metabolisms and document how these organisms use these molecules in microbial interactions.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145051409","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
Horizontal Gene Transfer and Recombination in Cyanobacteriota. 蓝藻的水平基因转移与重组。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-09-10 DOI: 10.1146/annurev-micro-041522-100420
Devaki Bhaya, Gabriel Birzu, Eduardo P C Rocha
{"title":"Horizontal Gene Transfer and Recombination in Cyanobacteriota.","authors":"Devaki Bhaya, Gabriel Birzu, Eduardo P C Rocha","doi":"10.1146/annurev-micro-041522-100420","DOIUrl":"https://doi.org/10.1146/annurev-micro-041522-100420","url":null,"abstract":"<p><p>Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032576","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
Microbial Enzymes for Biomass Conversion. 生物质转化微生物酶。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-09-09 DOI: 10.1146/annurev-micro-051524-025214
Alex Graça Contato, Thiago Machado Pasin, Maria de Lourdes Teixeira de Moraes Polizeli
{"title":"Microbial Enzymes for Biomass Conversion.","authors":"Alex Graça Contato, Thiago Machado Pasin, Maria de Lourdes Teixeira de Moraes Polizeli","doi":"10.1146/annurev-micro-051524-025214","DOIUrl":"https://doi.org/10.1146/annurev-micro-051524-025214","url":null,"abstract":"<p><p>Plant biomass has emerged as a cornerstone of the global bioenergy landscape because of its abundance and cost-effectiveness. The cell wall of plant biomass is an intricate network of cellulose, hemicellulose, and lignin. The hydrolysis of cellulose and hemicellulose by holoenzymes converts these polymers into monosaccharides and paves the way for the production of bioethanol and other bio-based products. This enzymatic and fermentative process is crucial for the sustainable use of agro-industrial residues as renewable energy sources, reducing reliance on fossil fuels and lowering greenhouse gas emissions. This review explores critical aspects of lignocellulolytic enzyme systems, all of which derive from microorganisms. Furthermore, it underscores the advantages of microbial sources and their potential for enhancing enzyme properties through genetic engineering and enzyme immobilization.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028712","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
Making Fungal-Photobiont Symbioses in the Lab: Past, Present, and Future of the Elusive In Vitro Lichen. 在实验室中制造真菌-光生共生：难以捉摸的体外地衣的过去，现在和未来。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-09-09 DOI: 10.1146/annurev-micro-051524-031834
Arseniy Belosokhov, Toby Spribille
{"title":"Making Fungal-Photobiont Symbioses in the Lab: Past, Present, and Future of the Elusive In Vitro Lichen.","authors":"Arseniy Belosokhov, Toby Spribille","doi":"10.1146/annurev-micro-051524-031834","DOIUrl":"https://doi.org/10.1146/annurev-micro-051524-031834","url":null,"abstract":"<p><p>The ability to synthesize lichen symbioses in vitro from pure cultures of transformable symbionts would be a game changer for experiments to identify the metabolic interplay that underpins the success of lichens. However, despite multiple reports of successful lichen resynthesis, no lichen lab model system exists today. We reviewed 150 years of in vitro lichen studies and found that the term resynthesis is applied to many types of fungal-photobiont cocultures that do not resemble lichens. Some of the most lichen-like results, for their part, were obtained from nonaxenic tissue culture. Only a few studies reported obtaining natural-looking lichens from axenic input cultures, but all appear to have been isolated successes obtained against the background of extensive contamination. We suggest revisiting resynthesis experiments in light of recent advances in our understanding of lichen microbial composition to test whether in vitro lichen morphogenesis requires microbial inputs beyond those of the canonical fungal and algal symbionts.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028742","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
Cyanophages: Billions of Years of Coevolution with Cyanobacteria. 噬藻：与蓝藻共同进化的数十亿年。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-09-05 DOI: 10.1146/annurev-micro-042924-095145
Qiong Li, Feng Yang, Cong-Zhao Zhou
{"title":"Cyanophages: Billions of Years of Coevolution with Cyanobacteria.","authors":"Qiong Li, Feng Yang, Cong-Zhao Zhou","doi":"10.1146/annurev-micro-042924-095145","DOIUrl":"https://doi.org/10.1146/annurev-micro-042924-095145","url":null,"abstract":"<p><p>Prevalent in marine and freshwater ecosystems, cyanophages compose a class of double-stranded DNA viruses that specifically infect cyanobacteria. During billions of years of coevolution, cyanophages and cyanobacteria have significantly contributed to the biogeochemical cycling and genetic diversity of aquatic ecosystems. As natural predators of cyanobacteria, cyanophages hold promise as eco-friendly agents against harmful cyanobacterial blooms. Recent technical advances in omics and cryo-electron microscopy have revealed the remarkable diversity of cyanophages in genome sequence and tail morphology. In this review, we summarize the genomic and metagenomic data, phylogenetic analyses, and diverse three-dimensional structures of cyanophages, in addition to their interplays with hosts. We also discuss the in vivo assembly processes of cyanophages, the exploration of uncultured cyanophages and host pairing, and the synthetic engineering and potential applications of cyanophages.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005794","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 Central Role of Gut Microbes in Host Purine Homeostasis. 肠道微生物在宿主嘌呤稳态中的核心作用。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-09-03 DOI: 10.1146/annurev-micro-041522-100126
Heather L Emery, Robert L Kerby, Federico E Rey
{"title":"The Central Role of Gut Microbes in Host Purine Homeostasis.","authors":"Heather L Emery, Robert L Kerby, Federico E Rey","doi":"10.1146/annurev-micro-041522-100126","DOIUrl":"https://doi.org/10.1146/annurev-micro-041522-100126","url":null,"abstract":"<p><p>Purines are ubiquitous metabolites that play evolutionarily conserved roles, including as precursors to molecules central to life. Purine synthesis is metabolically and energetically expensive; thus, under physiological conditions, intermediates of purine degradation are efficiently reused through salvage pathways. Excess purines are oxidized and eliminated via the kidneys and intestine. The efficient elimination of excess purines in humans is critical because the primary waste product of purine metabolism, uric acid, is proinflammatory and has been linked to multiple health conditions. Recent studies suggest that gut bacteria influence the purine pool locally and systemically. Bacteria can break down uric acid and other purines aerobically and anaerobically and may regulate their homeostasis. In this article, we provide an overview of purines and their metabolism, and we discuss our current understanding of the complex purine-dependent cross talk and cross-feeding between the host and the gut microbiome.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144991187","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
Carbon Metabolism of Intracellular Parasitic Protists. 细胞内寄生原生生物的碳代谢。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-08-28 DOI: 10.1146/annurev-micro-032421-120925
Malcolm J McConville, Eleanor C Saunders, Julie E Ralton
{"title":"Carbon Metabolism of Intracellular Parasitic Protists.","authors":"Malcolm J McConville, Eleanor C Saunders, Julie E Ralton","doi":"10.1146/annurev-micro-032421-120925","DOIUrl":"https://doi.org/10.1146/annurev-micro-032421-120925","url":null,"abstract":"<p><p>Apicomplexan and trypanosomatid parasites cause important human diseases, including malaria, toxoplasmosis, Chagas disease, and human leishmaniasis. The mammalian-infective stages of these parasites colonize nutrient-rich, intracellular niches in a range of different host cells. These niches include specialized vacuoles (<i>Plasmodium</i> spp., <i>Toxoplasma gondii</i>), the mature lysosome of phagocytic cells (<i>Leishmania</i>), and the cytoplasm of nucleated host cells (<i>Trypanosoma cruzi</i>). Here, we review the different growth and metabolic strategies utilized by each of these protists to survive in these niches. Although all stages utilize sugars as preferred carbon sources, different species or developmental stages vary markedly in their dependence on aerobic fermentation versus respiratory metabolism and their co-utilization of other carbon sources. Stage-specific differences in glycolytic and mitochondrial respiratory capacity may be a hardwired feature of each stage and reflect the trade-off of achieving high growth rates at the expense of host range adaptability and establishing long-lived persistent infections.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939522","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
Non-Conventional Yeasts as a Source of Genetic Diversity and Biotechnological Potential. 作为遗传多样性和生物技术潜力来源的非常规酵母。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-08-26 DOI: 10.1146/annurev-micro-052324-091517
Pablo Villarreal, Jennifer Molinet, Stephanie Braun-Galleani, Francisco A Cubillos
{"title":"Non-Conventional Yeasts as a Source of Genetic Diversity and Biotechnological Potential.","authors":"Pablo Villarreal, Jennifer Molinet, Stephanie Braun-Galleani, Francisco A Cubillos","doi":"10.1146/annurev-micro-052324-091517","DOIUrl":"https://doi.org/10.1146/annurev-micro-052324-091517","url":null,"abstract":"<p><p>Most of our current knowledge about yeast is based on the workhorse <i>Saccharomyces cerevisiae</i>. However, can this yeast represent the vast array of natural yeast life-forms? This review discusses significant recent advances in the study of non-<i>Saccharomyces</i> yeasts, also known as non-conventional yeasts (NCYs). We (<i>a</i>) review recent literature on bioprospecting methodologies and on population genomics that have expanded our understanding of NCY diversity, (<i>b</i>) highlight critical species with industrial applications, and (<i>c</i>) offer insights into how NCYs' genetic diversity translates into phenotypic plasticity and adaptation to extreme environments. We assess the limitations that are delaying the widespread use of NCYs in biotechnology, including the need for ambitious bioprospecting efforts and robust genetic tools in the scaling up of NCY-based processes for industry. NCYs could offer novel sustainable solutions in the food, beverage, pharmaceutical, and bioenergy sectors and could open a new frontier of commercial opportunities.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939578","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
Prokaryotic Circadian Systems: Cyanobacteria and Beyond. 原核生物昼夜系统：蓝藻及其他。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-08-26 DOI: 10.1146/annurev-micro-041222-022934
Mingxu Fang, Carrie L Partch, Andy LiWang, Susan S Golden
{"title":"Prokaryotic Circadian Systems: Cyanobacteria and Beyond.","authors":"Mingxu Fang, Carrie L Partch, Andy LiWang, Susan S Golden","doi":"10.1146/annurev-micro-041222-022934","DOIUrl":"https://doi.org/10.1146/annurev-micro-041222-022934","url":null,"abstract":"<p><p>Circadian clocks are biological timekeeping mechanisms that synchronize physiology with the 24-h day-night cycle and provide temporal order to cellular events that recur daily as circadian rhythms. The cyanobacterium <i>Synechococcus elongatus</i> displays robust circadian rhythms and for more than 30 years has served as a model organism for uncovering the principles of prokaryotic timekeeping. The fundamental driving force behind these rhythms is a three-protein oscillator composed of KaiA, KaiB, and KaiC. In this review, we summarize current knowledge of the molecular mechanism of the Kai oscillator and focus on the dynamic conformational changes of these proteins over the period of a day. We also discuss how timing information is relayed from the oscillator to regulate downstream gene expression, thereby influencing cellular physiology. Furthermore, we explore circadian or circadian-like timing systems identified in other prokaryotes. We hope this review can inspire the discovery of new clock mechanisms in the microbial world and beyond.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939544","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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