FEMS microbiology reviews最新文献_第8页

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":"47 4","pages":""},"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

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

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

Physicochemical homeostasis in bacteria. 细菌的理化平衡。

IF 10.1 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":"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":"47 4","pages":""},"PeriodicalIF":10.1,"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: 0

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":"47 4","pages":""},"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

Illuminating the oral microbiome and its host interactions: animal models of disease. 阐明口腔微生物组及其宿主相互作用:疾病的动物模型。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-05-19 DOI: 10.1093/femsre/fuad018

George Hajishengallis

{"title":"Illuminating the oral microbiome and its host interactions: animal models of disease.","authors":"George Hajishengallis","doi":"10.1093/femsre/fuad018","DOIUrl":"10.1093/femsre/fuad018","url":null,"abstract":"Periodontitis and caries are driven by complex interactions between the oral microbiome and host factors, i.e. inflammation and dietary sugars, respectively. Animal models have been instrumental in our mechanistic understanding of these oral diseases, although no single model can faithfully reproduce all aspects of a given human disease. This review discusses evidence that the utility of an animal model lies in its capacity to address a specific hypothesis and, therefore, different aspects of a disease can be investigated using distinct and complementary models. As in vitro systems cannot replicate the complexity of in vivo host-microbe interactions and human research is typically correlative, model organisms-their limitations notwithstanding-remain essential in proving causality, identifying therapeutic targets, and evaluating the safety and efficacy of novel treatments. To achieve broader and deeper insights into oral disease pathogenesis, animal model-derived findings can be synthesized with data from in vitro and clinical research. In the absence of better mechanistic alternatives, dismissal of animal models on fidelity issues would impede further progress to understand and treat oral disease.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 3","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10198557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9603830","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

Nuclear genome organization in fungi: from gene folding to Rabl chromosomes. 真菌的核基因组组织：从基因折叠到 Rabl 染色体。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2023-05-19 DOI: 10.1093/femsre/fuad021

David E Torres, Andrew T Reckard, Andrew D Klocko, Michael F Seidl

{"title":"Nuclear genome organization in fungi: from gene folding to Rabl chromosomes.","authors":"David E Torres, Andrew T Reckard, Andrew D Klocko, Michael F Seidl","doi":"10.1093/femsre/fuad021","DOIUrl":"10.1093/femsre/fuad021","url":null,"abstract":"Comparative genomics has recently provided unprecedented insights into the biology and evolution of the fungal lineage. In the postgenomics era, a major research interest focuses now on detailing the functions of fungal genomes, i.e. how genomic information manifests into complex phenotypes. Emerging evidence across diverse eukaryotes has revealed that the organization of DNA within the nucleus is critically important. Here, we discuss the current knowledge on the fungal genome organization, from the association of chromosomes within the nucleus to topological structures at individual genes and the genetic factors required for this hierarchical organization. Chromosome conformation capture followed by high-throughput sequencing (Hi-C) has elucidated how fungal genomes are globally organized in Rabl configuration, in which centromere or telomere bundles are associated with opposite faces of the nuclear envelope. Further, fungal genomes are regionally organized into topologically associated domain-like (TAD-like) chromatin structures. We discuss how chromatin organization impacts the proper function of DNA-templated processes across the fungal genome. Nevertheless, this view is limited to a few fungal taxa given the paucity of fungal Hi-C experiments. We advocate for exploring genome organization across diverse fungal lineages to ensure the future understanding of the impact of nuclear organization on fungal genome function.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 3","pages":""},"PeriodicalIF":10.1,"publicationDate":"2023-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9743069","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

The small intestine: dining table of host-microbiota meetings. 小肠:宿主-微生物群会议的餐桌。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-05-19 DOI: 10.1093/femsre/fuad022

Karen Delbaere, Inez Roegiers, Auriane Bron, Claude Durif, Tom Van de Wiele, Stephanie Blanquet-Diot, Ludovica Marinelli

{"title":"The small intestine: dining table of host-microbiota meetings.","authors":"Karen Delbaere, Inez Roegiers, Auriane Bron, Claude Durif, Tom Van de Wiele, Stephanie Blanquet-Diot, Ludovica Marinelli","doi":"10.1093/femsre/fuad022","DOIUrl":"https://doi.org/10.1093/femsre/fuad022","url":null,"abstract":"Growing evidence suggests the importance of the small intestinal bacteria in the diet-host-microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity, and how the intestinal bacteria in homeostatic conditions participate in nutrient digestion and absorption. We illustrate the importance of a controlled bacterial density and of the preservation of absorptive surface for the host's nutritional status. In particular, we discuss these aspects of the small intestinal environment in the framework of two disease conditions, namely small intestinal bacterial overgrowth (SIBO) and short bowel syndrome (SBS). We also detail in vivo, ex vivo, and in vitro models developed to simulate the small intestinal environment, some applied for (diet-)host-bacteria interaction studies. Lastly, we highlight recent technological, medical, and scientific advances applicable to investigate this complex and yet understudied body environment to broaden our knowledge in support of further progress in the medical practice, and to proceed towards the integration of the (small)intestinal bacteria in personalized therapeutic approaches.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 3","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9798351","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: 2

After a century of nisin research - where are we now? 经过一个世纪的 nisin 研究--我们现在在哪里？

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-05-19 DOI: 10.1093/femsre/fuad023

Des Field, Miguel Fernandez de Ullivarri, R Paul Ross, Colin Hill

{"title":"After a century of nisin research - where are we now?","authors":"Des Field, Miguel Fernandez de Ullivarri, R Paul Ross, Colin Hill","doi":"10.1093/femsre/fuad023","DOIUrl":"10.1093/femsre/fuad023","url":null,"abstract":"It is almost a century since nisin was discovered in fermented milk cultures, coincidentally in the same year that penicillin was first described. Over the last 100 years this small, highly modified pentacyclic peptide has not only found success in the food industry as a preservative but has also served as the paradigm for our understanding of the genetic organization, expression, and regulation of genes involved in lantibiotic biosynthesis-one of the few cases of extensive post-translation modification in prokaryotes. Recent developments in understanding the complex biosynthesis of nisin have shed light on the cellular location of the modification and transport machinery and the co-ordinated series of spatio-temporal events required to produce active nisin and provide resistance and immunity. The continued unearthing of new natural variants from within human and animal gastrointestinal tracts has sparked interest in the potential application of nisin to influence the microbiome, given the growing recognition of the role the gastrointestinal microbiota plays in health and disease. Moreover, interdisciplinary approaches have taken advantage of biotechnological advancements to bioengineer nisin to produce novel variants and expand nisin functionality for applications in the biomedical field. This review will discuss the latest progress in these aspects of nisin research.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 3","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10257480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9699418","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

Engineering lanthipeptides by introducing a large variety of RiPP modifications to obtain new-to-nature bioactive peptides. 通过引入大量的RiPP修饰来获得新的天然生物活性肽。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2023-05-19 DOI: 10.1093/femsre/fuad017

Yuxin Fu, Yanli Xu, Fleur Ruijne, Oscar P Kuipers

{"title":"Engineering lanthipeptides by introducing a large variety of RiPP modifications to obtain new-to-nature bioactive peptides.","authors":"Yuxin Fu, Yanli Xu, Fleur Ruijne, Oscar P Kuipers","doi":"10.1093/femsre/fuad017","DOIUrl":"https://doi.org/10.1093/femsre/fuad017","url":null,"abstract":"Natural bioactive peptide discovery is a challenging and time-consuming process. However, advances in synthetic biology are providing promising new avenues in peptide engineering that allow for the design and production of a large variety of new-to-nature peptides with enhanced or new bioactivities, using known peptides as templates. Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs). The modularity of post-translational modification (PTM) enzymes and ribosomal biosynthesis inherent to lanthipeptides enables their engineering and screening in a high-throughput manner. The field of RiPPs research is rapidly evolving, with many novel PTMs and their associated modification enzymes being identified and characterized. The modularity presented by these diverse and promiscuous modification enzymes has made them promising tools for further in vivo engineering of lanthipeptides, allowing for the diversification of their structures and activities. In this review, we explore the diverse modifications occurring in RiPPs and discuss the potential applications and feasibility of combining various modification enzymes for lanthipeptide engineering. We highlight the prospect of lanthipeptide- and RiPP-engineering to produce and screen novel peptides, including mimics of potent non-ribosomally produced antimicrobial peptides (NRPs) such as daptomycin, vancomycin, and teixobactin, which offer high therapeutic potential.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 3","pages":""},"PeriodicalIF":11.3,"publicationDate":"2023-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10373908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10243649","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