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Phages to the rescue: in situ editing of the gut microbiota 噬菌体的拯救：肠道微生物群的原位编辑
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-09-13 DOI: 10.1016/j.tim.2024.09.001
Charlotte Kamm, Chase L. Beisel
{"title":"Phages to the rescue: in situ editing of the gut microbiota","authors":"Charlotte Kamm, Chase L. Beisel","doi":"10.1016/j.tim.2024.09.001","DOIUrl":"https://doi.org/10.1016/j.tim.2024.09.001","url":null,"abstract":"<p>The gut microbiome contains numerous bacteria tied to our health. However, genetically modifying this community remains a major challenge. <span><span>Brödel <em>et al</em>.</span><svg aria-label=\"Opens in new window\" focusable=\"false\" height=\"20\" viewbox=\"0 0 8 8\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\"></path></svg></span> take a critical step by engineering bacteriophages to efficiently deliver gene editors without propagation of the genetic cargo, efficiently introducing edits to bacteria residing in the mouse gut.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":"88 1","pages":""},"PeriodicalIF":15.9,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142261519","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
Akkermansia muciniphila Akkermansia muciniphila
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-09-12 DOI: 10.1016/j.tim.2024.08.010
Cindy Menjivar, Emma Pagella, Indranil Biswas
{"title":"Akkermansia muciniphila","authors":"Cindy Menjivar, Emma Pagella, Indranil Biswas","doi":"10.1016/j.tim.2024.08.010","DOIUrl":"https://doi.org/10.1016/j.tim.2024.08.010","url":null,"abstract":"No Abstract","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":"49 1","pages":""},"PeriodicalIF":15.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182253","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
Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities 绘制癌症微生物组图谱的生物信息学挑战：陷阱与机遇
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-09-12 DOI: 10.1016/j.tim.2024.08.011
Nicholas A. Bokulich, Michael S. Robeson
{"title":"Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities","authors":"Nicholas A. Bokulich, Michael S. Robeson","doi":"10.1016/j.tim.2024.08.011","DOIUrl":"https://doi.org/10.1016/j.tim.2024.08.011","url":null,"abstract":"<p>Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted ‘omics’ techniques have accelerated research into microbiome–cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":"58 1","pages":""},"PeriodicalIF":15.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182254","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 bases of herbivory in beetles. 甲虫食草的微生物基础
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-12 DOI: 10.1016/j.tim.2024.08.004
Marleny García-Lozano, Hassan Salem
{"title":"Microbial bases of herbivory in beetles.","authors":"Marleny García-Lozano, Hassan Salem","doi":"10.1016/j.tim.2024.08.004","DOIUrl":"https://doi.org/10.1016/j.tim.2024.08.004","url":null,"abstract":"<p><p>The ecological radiation of herbivorous beetles is among the most successful in the animal kingdom. It coincided with the rise and diversification of flowering plants, requiring beetles to adapt to a nutritionally imbalanced diet enriched in complex polysaccharides and toxic secondary metabolites. In this review, we explore how beetles overcame these challenges by coopting microbial genes, enzymes, and metabolites, through both horizontal gene transfer (HGT) and symbiosis. Recent efforts revealed the functional convergence governing both processes and the unique ways in which microbes continue to shape beetle digestion, development, and defense. The development of genetic and experimental tools across a diverse set of study systems has provided valuable mechanistic insights into how microbes spurred metabolic innovation and facilitated an herbivorous transition in beetles.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142354529","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 role of cyclic nucleotides in bacterial antimicrobial resistance and tolerance. 环状核苷酸在细菌抗菌性和耐受性中的作用。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-05 DOI: 10.1016/j.tim.2024.08.006
Yi Liu, Claudia Blanco-Toral, Gerald Larrouy-Maumus
{"title":"The role of cyclic nucleotides in bacterial antimicrobial resistance and tolerance.","authors":"Yi Liu, Claudia Blanco-Toral, Gerald Larrouy-Maumus","doi":"10.1016/j.tim.2024.08.006","DOIUrl":"https://doi.org/10.1016/j.tim.2024.08.006","url":null,"abstract":"<p><p>Nucleotide signalling molecules - mainly cyclic 3',5'-adenosine phosphate (cAMP), bis-(3',5')-cyclic diguanosine monophosphate (c-di-GMP), and bis-(3',5')-cyclic diadenosine monophosphate (c-di-AMP) - contribute to the regulation of cellular pathways. Numerous recent works have focused on the involvement of these cyclic nucleotide phosphates (cNPs) in bacterial resistance and tolerance to antimicrobial treatment. Indeed, the rise of antimicrobial resistance (AMR) is a rising global threat to human health, while the rise of antimicrobial tolerance underlies the development of AMR and long-term infections, placing an additional burden on this problem. Here, we summarise the current understanding of cNP signalling in bacterial physiology with a focus on our understanding of how cNP signalling affects AMR and antimicrobial tolerance in different bacterial species. We also discuss additional cNP-related drug targets in bacterial pathogens that may have therapeutic potential.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146320","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
A mechanistic framework for complex microbe-host symbioses. 复杂微生物与宿主共生的机理框架。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-05 DOI: 10.1016/j.tim.2024.08.002
Gui Araujo, José M Montoya, Torsten Thomas, Nicole S Webster, Miguel Lurgi
{"title":"A mechanistic framework for complex microbe-host symbioses.","authors":"Gui Araujo, José M Montoya, Torsten Thomas, Nicole S Webster, Miguel Lurgi","doi":"10.1016/j.tim.2024.08.002","DOIUrl":"https://doi.org/10.1016/j.tim.2024.08.002","url":null,"abstract":"<p><p>Virtually all multicellular organisms on Earth live in symbiotic associations with complex microbial communities: the microbiome. This ancient relationship is of fundamental importance for both the host and the microbiome. Recently, the analyses of numerous microbiomes have revealed an incredible diversity and complexity of symbionts, with different mechanisms identified as potential drivers of this diversity. However, the interplay of ecological and evolutionary forces generating these complex associations is still poorly understood. Here we explore and summarise the suite of ecological and evolutionary mechanisms identified as relevant to different aspects of microbiome complexity and diversity. We argue that microbiome assembly is a dynamic product of ecology and evolution at various spatio-temporal scales. We propose a theoretical framework to classify mechanisms and build mechanistic host-microbiome models to link them to empirical patterns. We develop a cohesive foundation for the theoretical understanding of the combined effects of ecology and evolution on the assembly of complex symbioses.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146319","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
Advisory Board and Contents 咨询委员会和内容
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-09-03 DOI: 10.1016/s0966-842x(24)00200-2
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/s0966-842x(24)00200-2","DOIUrl":"https://doi.org/10.1016/s0966-842x(24)00200-2","url":null,"abstract":"No Abstract","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":"61 1","pages":""},"PeriodicalIF":15.9,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182255","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
Subscription and Copyright Information 订阅和版权信息
IF 15.9 1区 生物学
Trends in Microbiology Pub Date : 2024-09-03 DOI: 10.1016/s0966-842x(24)00203-8
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/s0966-842x(24)00203-8","DOIUrl":"https://doi.org/10.1016/s0966-842x(24)00203-8","url":null,"abstract":"No Abstract","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":"10 1","pages":""},"PeriodicalIF":15.9,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182256","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
Recent advances in modelling Shigella infection. 志贺氏杆菌感染建模的最新进展。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-02-28 DOI: 10.1016/j.tim.2024.02.004
Sydney L Miles, Kathryn E Holt, Serge Mostowy
{"title":"Recent advances in modelling Shigella infection.","authors":"Sydney L Miles, Kathryn E Holt, Serge Mostowy","doi":"10.1016/j.tim.2024.02.004","DOIUrl":"10.1016/j.tim.2024.02.004","url":null,"abstract":"<p><p>Shigella is an important human-adapted pathogen which contributes to a large global burden of diarrhoeal disease. Together with the increasing threat of antimicrobial resistance and lack of an effective vaccine, there is great urgency to identify novel therapeutics and preventatives to combat Shigella infection. In this review, we discuss the development of innovative technologies and animal models to study mechanisms underlying Shigella infection of humans. We examine recent literature introducing (i) the organ-on-chip model, and its substantial contribution towards understanding the biomechanics of Shigella infection, (ii) the zebrafish infection model, which has delivered transformative insights into the epidemiological success of clinical isolates and the innate immune response to Shigella, (iii) a pioneering oral mouse model of shigellosis, which has helped to discover new inflammasome biology and protective mechanisms against shigellosis, and (iv) the controlled human infection model, which has been effective in translating basic research into human health impact and assessing suitability of novel vaccine candidates. We consider the recent contributions of each model and discuss where the future of modelling Shigella infection lies.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"917-924"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139997532","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
Engineering agricultural soil microbiomes and predicting plant phenotypes. 农业土壤微生物组工程和植物表型预测。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-02-29 DOI: 10.1016/j.tim.2024.02.003
Chiara A Berruto, Gozde S Demirer
{"title":"Engineering agricultural soil microbiomes and predicting plant phenotypes.","authors":"Chiara A Berruto, Gozde S Demirer","doi":"10.1016/j.tim.2024.02.003","DOIUrl":"10.1016/j.tim.2024.02.003","url":null,"abstract":"<p><p>Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"858-873"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140013273","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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