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Annual review of microbiology最新文献

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Circadian Biology in Parasites: Beyond Known Mechanisms. 寄生虫的昼夜生物学：超越已知机制。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 DOI: 10.1146/annurev-micro-060424-051248
Mukhtar Sadykov, Filipa Rijo-Ferreira
{"title":"Circadian Biology in Parasites: Beyond Known Mechanisms.","authors":"Mukhtar Sadykov, Filipa Rijo-Ferreira","doi":"10.1146/annurev-micro-060424-051248","DOIUrl":"10.1146/annurev-micro-060424-051248","url":null,"abstract":"<p><p>Circadian rhythms play a fundamental role in regulating biological processes across the tree of life. While these 24-h cycles are well-characterized in model organisms, their role in parasitic organisms has remained largely unexplored until recently. Here, we review emerging evidence that parasites possess intrinsic timekeeping abilities, focusing particularly on the malaria parasite <i>Plasmodium</i>. We examine two principal paradigms of biological timing: transcriptional-translational feedback loops and posttranscriptional feedback loops. Despite lacking canonical clock genes found in other eukaryotes, <i>Plasmodium</i> employs sophisticated regulatory machinery, including ApiAP2 transcription factors, chromatin regulators, and noncoding RNAs, that could form novel timing circuits. We discuss how these mechanisms might enable parasites to synchronize with host rhythms and optimize their development and transmission. Understanding these temporal regulatory networks could reveal new therapeutic strategies and expand our knowledge of biological timing mechanisms across evolution.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"79 1","pages":"731-751"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12692157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353411","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
The Biology of Akkermansia. 阿克曼西亚的生物学。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-07-31 DOI: 10.1146/annurev-micro-051524-032131
Elizabeth R Hughes, Maria E Panzetta, Agastya Sharma, Raphael H Valdivia
{"title":"The Biology of <i>Akkermansia</i>.","authors":"Elizabeth R Hughes, Maria E Panzetta, Agastya Sharma, Raphael H Valdivia","doi":"10.1146/annurev-micro-051524-032131","DOIUrl":"10.1146/annurev-micro-051524-032131","url":null,"abstract":"<p><p>Members of the genus <i>Akkermansia</i> are the only cultured representatives of <i>Verrucomicrobiota</i> within the gastrointestinal tract. <i>Akkermansia muciniphila</i>, the best-characterized representative of the genus, is a mucin-degrading specialist that has emerged as a microbe of significant interest due to its influence on the health of its hosts. We describe emerging themes in the biology of <i>Akkermansia</i> species, including their diversity; cellular structures; physiology; interactions with other intestinal microbes; responses to diet; and effects on mammalian hosts, particularly their role in modulating immune responses. We also describe some of the tools available to explore the molecular biology of <i>Akkermansia</i> and discuss its increasingly complex interactions with other members of the microbiota and their implications for gastrointestinal health.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"287-310"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758906","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
Introduction. 介绍。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 DOI: 10.1146/annurev-micro-073025-050101
Susan Gottesman
{"title":"Introduction.","authors":"Susan Gottesman","doi":"10.1146/annurev-micro-073025-050101","DOIUrl":"https://doi.org/10.1146/annurev-micro-073025-050101","url":null,"abstract":"","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"79 1","pages":"v-vi"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353414","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 : 2025-10-01 Epub 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":"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":"713-730"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","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
Genetic Exchange in Leishmania: Understanding the Cryptic Sexual Cycle. 利什曼原虫的基因交换：对隐秘性周期的理解。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-06-17 DOI: 10.1146/annurev-micro-050724-091231
Carolina M C Catta-Preta, David L Sacks
{"title":"Genetic Exchange in <i>Leishmania</i>: Understanding the Cryptic Sexual Cycle.","authors":"Carolina M C Catta-Preta, David L Sacks","doi":"10.1146/annurev-micro-050724-091231","DOIUrl":"10.1146/annurev-micro-050724-091231","url":null,"abstract":"<p><p>While reproduction in <i>Leishmania</i> is primarily clonal, genomic analyses of natural isolates provide evidence for hybridization within and between species. Genetic exchange has been formally demonstrated via the generation of hybrids in the laboratory. Experimentally, genetic exchange in <i>Leishmania</i> is nonobligatory, relatively rare, and naturally confined to life cycle stages present in the sandfly midgut. Per whole genome sequencing, allele inheritance is Mendelian and involves meiosis-like recombination of the nuclear genome. Deletion of meiosis- and plasmogamy-related genes reveals their requirement for successful hybridization. Mitochondrial DNA inheritance appears uniparental for maxicircle kinetoplast DNA (kDNA) but biparental for minicircle kDNA. To account for the current absence of identified haploid gametes and for the hybridization of aneuploid genomes, alternative modes of genetic exchange have been proposed. Future studies will need to confirm the existence of gametes, explore the conditions promoting their development, and exploit the generation of sexual recombinants to map genes controlling important traits.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"105-128"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144315770","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 : 2025-10-01 Epub 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":"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":"595-614"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","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
Evolution and Ecology of Streptomyces. 链霉菌的进化与生态学。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 Epub Date: 2025-08-19 DOI: 10.1146/annurev-micro-051524-032254
David M Norte, Luis Alfredo Avitia-Dominguez, Daniel E Rozen
{"title":"Evolution and Ecology of <i>Streptomyces</i>.","authors":"David M Norte, Luis Alfredo Avitia-Dominguez, Daniel E Rozen","doi":"10.1146/annurev-micro-051524-032254","DOIUrl":"10.1146/annurev-micro-051524-032254","url":null,"abstract":"<p><p><i>Streptomyces</i> are among the most well-studied and important groups of bacteria, largely owing to their prolific production of biomedically important compounds like antibiotics and antifungals. Research over more than a half-century has elucidated the molecular and mechanistic details of <i>Streptomyces</i> multicellular development and the production of secondary metabolites. In contrast, the evolutionary and ecological mechanisms that underlie these phenotypes are comparatively understudied. Our aim in this review is to examine these aspects of <i>Streptomyces</i> biology, with a focus on the benefits associated with their complex life cycle, their multicellular architecture and development, and their production of antibiotics. In addition to highlighting existing studies, we point to clear knowledge gaps that can serve to motivate further research on these bacteria. A greater understanding of <i>Streptomyces</i> evolution and ecology is needed to improve our ability to exploit these organisms for biomedical and agricultural applications.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":"383-403"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144881914","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 : 2025-10-01 Epub 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":"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":"685-711"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","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
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 : 2025-10-01 Epub 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":"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, 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":"773-793"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","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
Decoding Microbial Community Assembly: Insights on Vectors of Infectious Diseases. 解码微生物群落组装：对传染病载体的见解。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-10-01 DOI: 10.1146/annurev-micro-082024-094943
Dasiel Obregon, Apolline Maitre, Elianne Piloto-Sardiñas, Alejandra Wu-Chuang, Lianet Abuin-Denis, Ana Laura Cano-Argüelles, Justė Aželytė, Ivan Corona-Guerrero, Lourdes Mateos-Hernández, Myriam Kratou, Štefánia Skičková, Karolína Svobodová, Alejandro Cabezas-Cruz
{"title":"Decoding Microbial Community Assembly: Insights on Vectors of Infectious Diseases.","authors":"Dasiel Obregon, Apolline Maitre, Elianne Piloto-Sardiñas, Alejandra Wu-Chuang, Lianet Abuin-Denis, Ana Laura Cano-Argüelles, Justė Aželytė, Ivan Corona-Guerrero, Lourdes Mateos-Hernández, Myriam Kratou, Štefánia Skičková, Karolína Svobodová, Alejandro Cabezas-Cruz","doi":"10.1146/annurev-micro-082024-094943","DOIUrl":"10.1146/annurev-micro-082024-094943","url":null,"abstract":"<p><p>Vector-borne diseases (VBDs), which are caused by pathogens transmitted by vectors such as mosquitoes and ticks, account for more than 17% of infectious diseases and more than 700,000 deaths annually. The complexity of VBDs arises from ecological interactions among hosts, vectors, pathogens, and the environment, with vector microbiota playing a pivotal role in the modulation of vector competence. Advances in sequencing and in microbiome analysis have deepened our understanding of microbial community assembly within vectors and revealed opportunities for novel control strategies. Network analysis has become essential for uncovering microbial interactions and identifying keystone species that affect community stability and pathogen transmission. Despite progress, key challenges remain in deciphering the drivers of vector microbiota assembly. This review highlights factors shaping microbiota assembly, the potential of network analysis, and promising interventions such as antimicrobiota vaccines and paratransgenesis to reduce pathogen transmission. Future research should focus on standardizing methodologies and leveraging emerging technologies for effective and sustainable VBD control.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"79 1","pages":"547-572"},"PeriodicalIF":9.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353380","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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