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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
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
How does evolution work in superabundant microbes? 超级丰富的微生物是如何进化的？
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-02-14 DOI: 10.1016/j.tim.2024.01.009
Dmitry A Filatov, Mark Kirkpatrick
{"title":"How does evolution work in superabundant microbes?","authors":"Dmitry A Filatov, Mark Kirkpatrick","doi":"10.1016/j.tim.2024.01.009","DOIUrl":"10.1016/j.tim.2024.01.009","url":null,"abstract":"<p><p>Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"836-846"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139742096","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 techniques for evolutionary engineering of microbes - exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases. 微生物进化工程的突变技术--利用 CRISPR-Cas、寡核苷酸、重组酶和聚合酶。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-03-15 DOI: 10.1016/j.tim.2024.02.006
Anna Zimmermann, Julian E Prieto-Vivas, Karin Voordeckers, Changhao Bi, Kevin J Verstrepen
{"title":"Mutagenesis techniques for evolutionary engineering of microbes - exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases.","authors":"Anna Zimmermann, Julian E Prieto-Vivas, Karin Voordeckers, Changhao Bi, Kevin J Verstrepen","doi":"10.1016/j.tim.2024.02.006","DOIUrl":"10.1016/j.tim.2024.02.006","url":null,"abstract":"<p><p>The natural process of evolutionary adaptation is often exploited as a powerful tool to obtain microbes with desirable traits. For industrial microbes, evolutionary engineering is often used to generate variants that show increased yields or resistance to stressful industrial environments, thus obtaining superior microbial cell factories. However, even in large populations, the natural supply of beneficial mutations is typically low, which implies that obtaining improved microbes is often time-consuming and inefficient. To overcome this limitation, different techniques have been developed that boost mutation rates. While some of these methods simply increase the overall mutation rate across a genome, others use recent developments in DNA synthesis, synthetic biology, and CRISPR-Cas techniques to control the type and location of mutations. This review summarizes the most important recent developments and methods in the field of evolutionary engineering in model microorganisms. It discusses how both in vitro and in vivo approaches can increase the genetic diversity of the host, with a special emphasis on in vivo techniques for the optimization of metabolic pathways for precision fermentation.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"884-901"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140787","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
Supramolecular assemblies in bacterial immunity: an emerging paradigm. 细菌免疫中的超分子组装：一种新兴范式。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-06-27 DOI: 10.1016/j.tim.2024.06.003
Leighton Payne, Simon Jackson, Rafael Pinilla-Redondo
{"title":"Supramolecular assemblies in bacterial immunity: an emerging paradigm.","authors":"Leighton Payne, Simon Jackson, Rafael Pinilla-Redondo","doi":"10.1016/j.tim.2024.06.003","DOIUrl":"10.1016/j.tim.2024.06.003","url":null,"abstract":"<p><p>The study of bacterial immune systems has recently gained momentum, revealing a fascinating trend: many systems form large supramolecular assemblies. Here, we examine the potential mechanisms underpinning the evolutionary success of these structures, draw parallels to eukaryotic immunity, and offer fresh perspectives to stimulate future research into bacterial immunity.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"828-831"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470971","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
Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. 理化压力下生境中噬菌体的适应策略和生态作用。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-03-02 DOI: 10.1016/j.tim.2024.02.002
Dan Huang, Rong Xia, Chengyi Chen, Jingqiu Liao, Linxing Chen, Dongsheng Wang, Pedro J J Alvarez, Pingfeng Yu
{"title":"Adaptive strategies and ecological roles of phages in habitats under physicochemical stress.","authors":"Dan Huang, Rong Xia, Chengyi Chen, Jingqiu Liao, Linxing Chen, Dongsheng Wang, Pedro J J Alvarez, Pingfeng Yu","doi":"10.1016/j.tim.2024.02.002","DOIUrl":"10.1016/j.tim.2024.02.002","url":null,"abstract":"<p><p>Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"902-916"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140022666","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
Cancer-associated SNPs in bacteria: lessons from Helicobacter pylori. 细菌中与癌症相关的 SNPs：幽门螺旋杆菌的启示。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-03-13 DOI: 10.1016/j.tim.2024.02.001
Bodo Linz, Heinrich Sticht, Nicole Tegtmeyer, Steffen Backert
{"title":"Cancer-associated SNPs in bacteria: lessons from Helicobacter pylori.","authors":"Bodo Linz, Heinrich Sticht, Nicole Tegtmeyer, Steffen Backert","doi":"10.1016/j.tim.2024.02.001","DOIUrl":"10.1016/j.tim.2024.02.001","url":null,"abstract":"<p><p>Several single-nucleotide polymorphisms (SNPs) in human chromosomes are known to predispose to cancer. However, cancer-associated SNPs in bacterial pathogens were unknown until discovered in the stomach pathogen Helicobacter pylori. Those include an alanine-threonine polymorphism in the EPIYA-B phosphorylation motif of the injected effector protein CagA that affects cancer risk by modifying inflammatory responses and loss of host cell polarity. A serine-to-leucine change in serine protease HtrA is associated with boosted proteolytic cleavage of epithelial junction proteins and introduction of DNA double-strand breaks (DSBs) in host chromosomes, which co-operatively elicit malignant alterations. In addition, H. pylori genome-wide association studies (GWAS) identified several other SNPs potentially associated with increased gastric cancer (GC) risk. Here we discuss the clinical importance, evolutionary origin, and functional advantage of the H. pylori SNPs. These exciting new data highlight cancer-associated SNPs in bacteria, which should be explored in more detail in future studies.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"847-857"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140132656","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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