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Annual review of microbiology最新文献

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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
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
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
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 : 2025-08-19 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":""},"PeriodicalIF":9.9,"publicationDate":"2025-08-19","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
Marine Bacterial Biofilms: Shaping Surface Communities. 海洋细菌生物膜：塑造表面群落。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-08-19 DOI: 10.1146/annurev-micro-051524-024455
Michael G Hadfield, Marnie Freckelton, Brian T Nedved
{"title":"Marine Bacterial Biofilms: Shaping Surface Communities.","authors":"Michael G Hadfield, Marnie Freckelton, Brian T Nedved","doi":"10.1146/annurev-micro-051524-024455","DOIUrl":"10.1146/annurev-micro-051524-024455","url":null,"abstract":"<p><p>The assembly of marine benthic communities has become a focal point in marine ecology. We address how the bottom layers of benthic communities (i.e., the microbes inhabiting the basal biofilm) influence the complex accumulation of eukaryotes that grow on top of them. Specifically, we discuss (<i>a</i>) what organisms make up benthic biofilms, what brings about their attachment to surfaces, and how they vary in space and time; (<i>b</i>) what eukaryotic organisms are in marine benthic communities, how they vary in space and time, and the nature of microbial cues that bring about their recruitment to particular benthic sites; (<i>c</i>) the roles of bacterial-animal symbiosis in the composition of benthic communities; (<i>d</i>) what is happening to biofilms and their roles as habitat engineers in the rapidly changing world; and (<i>e</i>) how the geological history of bacteria and microbial mats on the ocean floor powerfully influenced the evolution of larval-bacterial interactions.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144881915","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
Roles of Marine Microbial Natural Products. 海洋微生物天然产物的作用。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-08-05 DOI: 10.1146/annurev-micro-040824-022431
Peter Bing Svendsen, Lauge Alfastsen, Lone Gram, Nathalie N S E Henriksen, Mikkel Bentzon-Tilia, Sheng-Da Zhang
{"title":"Roles of Marine Microbial Natural Products.","authors":"Peter Bing Svendsen, Lauge Alfastsen, Lone Gram, Nathalie N S E Henriksen, Mikkel Bentzon-Tilia, Sheng-Da Zhang","doi":"10.1146/annurev-micro-040824-022431","DOIUrl":"https://doi.org/10.1146/annurev-micro-040824-022431","url":null,"abstract":"<p><p>Over billions of years, marine microorganisms evolved a vast genetic potential to produce the molecules we denote as natural products or secondary metabolites. While these molecules show promise as therapeutics, their ecological roles, beyond those as antimicrobials, are receiving increasing attention. This review examines recent advances in our understanding of the ecological functions of marine microbial natural products and highlights both known and emerging roles. We summarize the involvement of these natural products in biological, ecological, and biogeochemical processes in the oceans; outline how their production may profoundly affect the producing organism; and discuss how the presence of natural product-producing microorganisms may affect microbiome composition and function. Despite progress, knowledge about the ecological roles of marine microbial natural products remains limited, and we also discuss challenges and opportunities in this field, including promising new technologies that could provide novel insights.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144788093","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 Invisible Extinction. 无形的灭绝。
IF 9.9 1区 生物学
Annual review of microbiology Pub Date : 2025-08-04 DOI: 10.1146/annurev-micro-051024-092416
Martin J Blaser, Maria Gloria Dominguez-Bello
{"title":"The Invisible Extinction.","authors":"Martin J Blaser, Maria Gloria Dominguez-Bello","doi":"10.1146/annurev-micro-051024-092416","DOIUrl":"https://doi.org/10.1146/annurev-micro-051024-092416","url":null,"abstract":"<p><p>The characterization of the human microbiome has opened a new chapter in understanding human biology and its relationship to health and disease. Yet we also have learned that our ancient coevolved microbiome has been changing across recent human generations; we have been losing a substantial amount of its diversity. This is especially concerning because the microbiota that we acquire early in life has important bearing on our developmental trajectory, especially with regard to metabolism, immunity, and cognition. Collectively, the early-life microbiota is a partner in our human developmental biology. We detail the medical, public health, and dietary phenomena bearing on the acquisition, maintenance, and loss of members of the microbiota and then consider the linkages between the altered microbiome and the diseases that have been emerging in recent years. Finally, we highlight ways to address and solve these problems associated with modernization.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":" ","pages":""},"PeriodicalIF":9.9,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783303","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 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 : 2025-07-31 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":"https://doi.org/10.1146/annurev-micro-051524-032131","url":null,"abstract":"<p><p>Members of the genus <i>Akkermansia</i> are the only known 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":""},"PeriodicalIF":9.9,"publicationDate":"2025-07-31","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
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