FEMS microbiology reviews最新文献_第7页

Crosstalk between gut microbiota and RNA N6-methyladenosine modification in cancer. 癌症中肠道微生物群与RNA n6 -甲基腺苷修饰之间的串扰。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad036

Hao Su, Henley Cheung, Harry Cheuk-Hay Lau, Hongyan Chen, Xiaoting Zhang, Na Qin, Yifei Wang, Matthew Tak Vai Chan, William Ka Kei Wu, Huarong Chen

引用次数: 0

Editorial 14th international symposium on lactic acid bacteria (LAB14). 第十四届乳酸菌国际学术研讨会(LAB14)。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad043

Eddy J Smid, Sarah Lebeer, Egon B Hansen

引用次数: 0

From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry. 从基因型到表型：推断与食品工业相关的微生物特征的计算方法。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad030

Signe T Karlsen, Martin H Rau, Benjamín J Sánchez, Kristian Jensen, Ahmad A Zeidan

{"title":"From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry.","authors":"Signe T Karlsen, Martin H Rau, Benjamín J Sánchez, Kristian Jensen, Ahmad A Zeidan","doi":"10.1093/femsre/fuad030","DOIUrl":"10.1093/femsre/fuad030","url":null,"abstract":"When selecting microbial strains for the production of fermented foods, various microbial phenotypes need to be taken into account to achieve target product characteristics, such as biosafety, flavor, texture, and health-promoting effects. Through continuous advances in sequencing technologies, microbial whole-genome sequences of increasing quality can now be obtained both cheaper and faster, which increases the relevance of genome-based characterization of microbial phenotypes. Prediction of microbial phenotypes from genome sequences makes it possible to quickly screen large strain collections in silico to identify candidates with desirable traits. Several microbial phenotypes relevant to the production of fermented foods can be predicted using knowledge-based approaches, leveraging our existing understanding of the genetic and molecular mechanisms underlying those phenotypes. In the absence of this knowledge, data-driven approaches can be applied to estimate genotype-phenotype relationships based on large experimental datasets. Here, we review computational methods that implement knowledge- and data-driven approaches for phenotype prediction, as well as methods that combine elements from both approaches. Furthermore, we provide examples of how these methods have been applied in industrial biotechnology, with special focus on the fermented food industry.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":11.3,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/69/bd/fuad030.PMC10337747.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9799218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet? 粪便污染诊断和源头追踪的基因目标是否已经彻底改变了水质分析?

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad028

Katalin Demeter, Rita Linke, Elisenda Ballesté, Georg Reischer, René E Mayer, Julia Vierheilig, Claudia Kolm, Margaret E Stevenson, Julia Derx, Alexander K T Kirschner, Regina Sommer, Orin C Shanks, Anicet R Blanch, Joan B Rose, Warish Ahmed, Andreas H Farnleitner

{"title":"Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet?","authors":"Katalin Demeter, Rita Linke, Elisenda Ballesté, Georg Reischer, René E Mayer, Julia Vierheilig, Claudia Kolm, Margaret E Stevenson, Julia Derx, Alexander K T Kirschner, Regina Sommer, Orin C Shanks, Anicet R Blanch, Joan B Rose, Warish Ahmed, Andreas H Farnleitner","doi":"10.1093/femsre/fuad028","DOIUrl":"https://doi.org/10.1093/femsre/fuad028","url":null,"abstract":"The impacts of nucleic acid-based methods - such as PCR and sequencing - to detect and analyze indicators, genetic markers or molecular signatures of microbial faecal pollution in health-related water quality research were assessed by rigorous literature analysis. A wide range of application areas and study designs has been identified since the first application more than 30 years ago (>1100 publications). Given the consistency of methods and assessment types, we suggest defining this emerging part of science as a new discipline: genetic faecal pollution diagnostics (GFPD) in health-related microbial water quality analysis. Undoubtedly, GFPD has already revolutionized faecal pollution detection (i.e., traditional or alternative general faecal indicator/marker analysis) and microbial source tracking (i.e., host-associated faecal indicator/marker analysis), the current core applications. GFPD is also expanding to many other research areas, including infection and health risk assessment, evaluation of microbial water treatment, and support of wastewater surveillance. In addition, storage of DNA extracts allows for biobanking, which opens up new perspectives. The tools of GFPD can be combined with cultivation-based standardized faecal indicator enumeration, pathogen detection, and various environmental data types, in an integrated data analysis approach. This comprehensive meta-analysis provides the scientific status quo of this field, including trend analyses and literature statistics, outlining identified application areas, and discusses the benefits and challenges of nucleic acid-based analysis in GFPD.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":11.3,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10368376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9864034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 3

Correction to: RTX proteins: A highly diverse family secreted by a common mechanism. 修正:RTX蛋白:一个由共同机制分泌的高度多样化的家族。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad024

引用次数: 0

Improving the safety and efficacy of phage therapy from the perspective of phage-mammal interactions. 从噬菌体-哺乳动物相互作用的角度提高噬菌体治疗的安全性和有效性。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad042

Geng Zou, Lijun He, Jing Rao, Zhiyong Song, Hu Du, Runze Li, Wenjing Wang, Yang Zhou, Lu Liang, Huanchun Chen, Jinquan Li

{"title":"Improving the safety and efficacy of phage therapy from the perspective of phage-mammal interactions.","authors":"Geng Zou, Lijun He, Jing Rao, Zhiyong Song, Hu Du, Runze Li, Wenjing Wang, Yang Zhou, Lu Liang, Huanchun Chen, Jinquan Li","doi":"10.1093/femsre/fuad042","DOIUrl":"https://doi.org/10.1093/femsre/fuad042","url":null,"abstract":"Phage therapy has re-emerged as a promising solution for combating antimicrobial-resistant bacterial infections. Increasingly, studies have revealed that phages possess therapeutic potential beyond their antimicrobial properties, including regulating the gut microbiome and maintain intestinal homeostasis, as a novel nanocarrier for targeted drug delivery. However, the complexity and unpredictability of phage behavior during treatment pose a significant challenge in clinical practice. The intricate interactions established between phages, humans, and bacteria throughout their long coexistence in the natural ecosystem contribute to the complexity of phage behavior in therapy, raising concerns about their efficacy and safety as therapeutic agents. Revealing the mechanisms by which phages interact with the human body will provide a theoretical basis for increased application of promising phage therapy. In this review, we provide a comprehensive summary of phage-mammal interactions, including signaling pathways, adaptive immunity responses, and phage-mediated anti-inflammatory responses. Then, from the perspective of phage-mammalian immune system interactions, we present the first systematic overview of the factors affecting phage therapy, such as the mode of administration, the physiological status of the patient, and the biological properties of the phage, to offer new insights into phage therapy for various human diseases.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":11.3,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10025229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 1

Illuminating the oral microbiome: cellular microbiology. 阐明口腔微生物组：细胞微生物学。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad045

Richard J Lamont, Daniel P Miller, Juhi Bagaitkar

引用次数: 0

Bacteria and microalgae associations in periphyton-mechanisms and biotechnological opportunities. 细菌和微藻在周边植物中的关联——机制和生物技术机遇。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad047

Francisca Vale, Cátia A Sousa, Henrique Sousa, Lúcia C Simões, Andrew J McBain, Manuel Simões

引用次数: 0

Physicochemical homeostasis in bacteria. 细菌的物理化学平衡。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad033

Bert Poolman

{"title":"Physicochemical homeostasis in bacteria.","authors":"Bert Poolman","doi":"10.1093/femsre/fuad033","DOIUrl":"https://doi.org/10.1093/femsre/fuad033","url":null,"abstract":"In living cells, the biochemical processes such as energy provision, molecule synthesis, gene expression, and cell division take place in a confined space where the internal chemical and physical conditions are different from those in dilute solutions. The concentrations of specific molecules and the specific reactions and interactions vary for different types of cells, but a number of factors are universal and kept within limits, which we refer to as physicochemical homeostasis. For instance, the internal pH of many cell types is kept within the range of 7.0 to 7.5, the fraction of macromolecules occupies 15%-20% of the cell volume (also known as macromolecular crowding) and the ionic strength is kept within limits to prevent salting-in or salting-out effects. In this article we summarize the generic physicochemical properties of the cytoplasm of bacteria, how they are connected to the energy status of the cell, and how they affect biological processes (Fig. 1). We describe how the internal pH and proton motive force are regulated, how the internal ionic strength is kept within limits, what the impact of macromolecular crowding is on the function of enzymes and the interaction between molecules, how cells regulate their volume (and turgor), and how the cytoplasm is structured. Physicochemical homeostasis is best understood in Escherichia coli, but pioneering studies have also been performed in lactic acid bacteria.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":11.3,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/61/0b/fuad033.PMC10368375.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10231890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 1

Protozoan predation as a driver of diversity and virulence in bacterial biofilms. 原生动物捕食作为细菌生物膜多样性和毒力的驱动因素。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-07-05 DOI: 10.1093/femsre/fuad040

M Mozammel Hoque, Gustavo Espinoza-Vergara, Diane McDougald

{"title":"Protozoan predation as a driver of diversity and virulence in bacterial biofilms.","authors":"M Mozammel Hoque, Gustavo Espinoza-Vergara, Diane McDougald","doi":"10.1093/femsre/fuad040","DOIUrl":"https://doi.org/10.1093/femsre/fuad040","url":null,"abstract":"Protozoa are eukaryotic organisms that play a crucial role in nutrient cycling and maintaining balance in the food web. Predation, symbiosis and parasitism are three types of interactions between protozoa and bacteria. However, not all bacterial species are equally susceptible to protozoan predation as many are capable of defending against predation in numerous ways and may even establish either a symbiotic or parasitic life-style. Biofilm formation is one such mechanism by which bacteria can survive predation. Structural and chemical components of biofilms enhance resistance to predation compared to their planktonic counterparts. Predation on biofilms gives rise to phenotypic and genetic heterogeneity in prey that leads to trade-offs in virulence in other eukaryotes. Recent advances, using molecular and genomics techniques, allow us to generate new information about the interactions of protozoa and biofilms of prey bacteria. This review presents the current state of the field on impacts of protozoan predation on biofilms. We provide an overview of newly gathered insights into (i) molecular mechanisms of predation resistance in biofilms, (ii) phenotypic and genetic diversification of prey bacteria, and (iii) evolution of virulence as a consequence of protozoan predation on biofilms.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":11.3,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10250661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 1