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Microbial functional diversity and redundancy: moving forward. 微生物功能多样性和冗余：向前发展。
IF 12.3 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae031
Pierre Ramond, Pierre E Galand, Ramiro Logares
{"title":"Microbial functional diversity and redundancy: moving forward.","authors":"Pierre Ramond, Pierre E Galand, Ramiro Logares","doi":"10.1093/femsre/fuae031","DOIUrl":"10.1093/femsre/fuae031","url":null,"abstract":"<p><p>Microbial functional ecology is expanding as we can now measure the traits of wild microbes that affect ecosystem functioning. Here, we review techniques and advances that could be the bedrock for a unified framework to study microbial functions. These include our newfound access to environmental microbial genomes, collections of microbial traits, but also our ability to study microbes' distribution and expression. We then explore the technical, ecological, and evolutionary processes that could explain environmental patterns of microbial functional diversity and redundancy. Next, we suggest reconciling microbiology with biodiversity-ecosystem functioning studies by experimentally testing the significance of microbial functional diversity and redundancy for the efficiency, resistance, and resilience of ecosystem processes. Such advances will aid in identifying state shifts and tipping points in microbiomes, enhancing our understanding of how and where will microbes guide Earth's biomes in the context of a changing planet.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11756291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846287","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 impact of phenotypic heterogeneity on fungal pathogenicity and drug resistance. 表型异质性对真菌致病性和耐药性的影响。
IF 12.3 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf001
Lukasz Kozubowski, Judith Berman
{"title":"The impact of phenotypic heterogeneity on fungal pathogenicity and drug resistance.","authors":"Lukasz Kozubowski, Judith Berman","doi":"10.1093/femsre/fuaf001","DOIUrl":"10.1093/femsre/fuaf001","url":null,"abstract":"<p><p>Phenotypic heterogeneity in genetically clonal populations facilitates cellular adaptation to adverse environmental conditions while enabling a return to the basal physiological state. It also plays a crucial role in pathogenicity and the acquisition of drug resistance in unicellular organisms and cancer cells, yet the exact contributing factors remain elusive. In this review, we outline the current state of understanding concerning the contribution of phenotypic heterogeneity to fungal pathogenesis and antifungal drug resistance.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11756289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983171","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
Forging new paths in bacterial motility and sensory transduction: highlights from BLAST XVIII. 细菌运动和感觉转导的新途径：来自BLAST XVIII的亮点。
IF 12.3 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf042
TuAnh N Huynh, Sima Setayeshgar, Abishek Shrivastava, Joanne Engel
{"title":"Forging new paths in bacterial motility and sensory transduction: highlights from BLAST XVIII.","authors":"TuAnh N Huynh, Sima Setayeshgar, Abishek Shrivastava, Joanne Engel","doi":"10.1093/femsre/fuaf042","DOIUrl":"10.1093/femsre/fuaf042","url":null,"abstract":"<p><p>The Bacterial Locomotion And Signal Transduction (BLAST) conference was founded in 1991 and has been held biennially thereafter. While BLAST meetings have typically covered two-component and chemotactic signaling, as well as aspects of motor and flagellum, this year's program broadened its scope and included emerging areas of research, such as microbial signal perception, cellular signal processing, downstream physiological impacts of bacterial signaling, microbe interactions and communities, integrative approaches, and technology innovations. This review summarizes the oral presentations from BLAST XVIII, held in January 2025 in Cancun, Mexico.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12422006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144948063","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
Where the microbes aren't. 微生物不存在的地方。
IF 10.1 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae034
Charles S Cockell
{"title":"Where the microbes aren't.","authors":"Charles S Cockell","doi":"10.1093/femsre/fuae034","DOIUrl":"10.1093/femsre/fuae034","url":null,"abstract":"<p><p>Although a large fraction of Earth's volume and most places beyond the planet lack life because physical and chemical conditions are too extreme, intriguing scientific questions are raised in many environments within or at the edges of life's niche space in which active life is absent. This review explores the environments in which active microorganisms do not occur. Within the known niche space for life, uninhabited, but habitable physical spaces potentially offer opportunities for hypothesis testing, such as using them as negative control environments to investigate the influence of life on planetary processes. At the physico-chemical limits of life, questions such as whether spaces devoid of actively metabolizing or reproducing life constitute uninhabitable space or space containing vacant niches that could be occupied with appropriate adaptation are raised. We do not know the extent to which evolution has allowed life to occupy all niche space within its biochemical potential. The case of habitable extraterrestrial environments and the scientific and ethical questions that they raise is discussed.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11737512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893328","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
Advances in Helicobacter pylori lipopolysaccharide structure and function. 幽门螺杆菌脂多糖结构与功能研究进展。
IF 12.3 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf034
Xiaoqiong Tang, Alfred Tay, Mohammed Benghezal, Barry J Marshall, Hong Tang, Hong Li
{"title":"Advances in Helicobacter pylori lipopolysaccharide structure and function.","authors":"Xiaoqiong Tang, Alfred Tay, Mohammed Benghezal, Barry J Marshall, Hong Tang, Hong Li","doi":"10.1093/femsre/fuaf034","DOIUrl":"10.1093/femsre/fuaf034","url":null,"abstract":"<p><p>Helicobacter pylori is a widespread pathogen responsible for chronic gastritis, peptic ulcers, and an elevated risk of gastric cancer. Lipopolysaccharide (LPS), localized exclusively in the outer leaflet of the outer membrane, is essential for maintaining bacterial integrity. Recent advances have deepened our understanding of H. pylori LPS structure, particularly lipid A modifications and the redefinition of the core oligosaccharide and O-antigen regions. The complete set of enzymes involved in LPS biosynthesis has been identified in the reference strain G27, and comparative genomics has revealed a notable regional difference (the absence of the heptan domain in East Asian strains). Here, we summarize recent insights into the structure and function of H. pylori LPS, emphasizing its role in bacterial persistence and its promise as a target for LPS-based glycoconjugate vaccine development.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12342981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144728979","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
Ex vivo study of neuroinvasive and neurotropic viruses: what is current and what is next. 神经侵入性和嗜神经性病毒的离体研究：当前和未来。
IF 12.3 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf024
Alexandre Lalande, Cyrille Mathieu
{"title":"Ex vivo study of neuroinvasive and neurotropic viruses: what is current and what is next.","authors":"Alexandre Lalande, Cyrille Mathieu","doi":"10.1093/femsre/fuaf024","DOIUrl":"10.1093/femsre/fuaf024","url":null,"abstract":"<p><p>Numerous pathogens, including viruses, enter the central nervous system and cause neurological disorders, such as encephalitis. Viruses are the main etiologic agents of such neurological diseases, and some of them cause a high death toll worldwide. Our knowledge about neuroinvasive and encephalitogenic virus infections is still limited due to the relative inaccessibility of the brain. To mitigate this shortcoming, neural ex vivo models have been developed and turned out to be of paramount importance for understanding neuroinvasive and neurotropic viruses. In this review, we describe the major ex vivo models for the central nervous system, including neural cultures, brain organoids, and organotypic brain cultures. We highlight the key findings from these models and illustrate how these models inform on viral processes, including neurotropism, neuroinvasion, and neurovirulence. We discuss the limitations of ex vivo models, highlight ongoing progress, and outline next-generation ex vivo models for virus research at the interface of neuroscience and infectious diseases.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12199766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144265792","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
Post-translational modifications of the nucleoid protein H-NS: sites, mechanisms, and regulatory cues. 类核蛋白H-NS的翻译后修饰：位点、机制和调控线索。
IF 12.3 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf045
Yabo Liu, Xiaoxue Wang
{"title":"Post-translational modifications of the nucleoid protein H-NS: sites, mechanisms, and regulatory cues.","authors":"Yabo Liu, Xiaoxue Wang","doi":"10.1093/femsre/fuaf045","DOIUrl":"10.1093/femsre/fuaf045","url":null,"abstract":"<p><p>Histone-like nucleoid structuring protein H-NS plays a pivotal role in orchestrating bacterial chromatin and regulating horizontal gene transfer (HGT) elements. In response to environmental signals, H-NS undergoes dynamic post-translational modifications (PTMs) that resemble the epigenetic codes of eukaryotic histones. This review explores how environmental cues regulate PTMs at specific sites within distinct domains of H-NS, thereby modulating its oligomerization and DNA-binding capabilities to reprogram bacterial responses. Notably, HGT elements commonly encode counter-silencing factors, including PTM-modifying enzymes, that counteract H-NS repression. We propose that combinatorial PTM patterns on H-NS form the bacterial histone-like epigenetic code, regulating the expression of HGT elements. Collectively, these interactions establish a sophisticated network of silencing and counter-silencing mechanisms that drive bacterial genome evolution.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12449154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000013","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
Genetic variability, genotyping, and genomics of Mycobacterium leprae. 麻风分枝杆菌的遗传变异、基因分型和基因组学。
IF 10.1 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf012
Afzal Ansari, Roopendra Kumar, Suman Kumar Ray, Aarti Patel, Purna Dwivedi, Arup Ghosh, Edson Machado, Philip N Suffys, Pushpendra Singh
{"title":"Genetic variability, genotyping, and genomics of Mycobacterium leprae.","authors":"Afzal Ansari, Roopendra Kumar, Suman Kumar Ray, Aarti Patel, Purna Dwivedi, Arup Ghosh, Edson Machado, Philip N Suffys, Pushpendra Singh","doi":"10.1093/femsre/fuaf012","DOIUrl":"10.1093/femsre/fuaf012","url":null,"abstract":"<p><p>Leprosy, caused by Mycobacterium leprae and Mycobacterium lepromatosis, remains a significant global health issue despite a tremendous decline in its worldwide prevalence in the last four decades. Mycobacterium leprae strains possess very limited genetic variability, making it difficult to distinguish them using traditional genotyping tools. Successful genome sequencing of a considerable number of M. leprae strains in the recent past has allowed development of improved genotyping tools for the molecular epidemiology of leprosy. Comparative genomics has identified distinct M. leprae genotypes and revealed their characteristic genomic markers. This review summarizes the progress made in M. leprae genomics, with special emphasis on the development of genotyping schemes. Further, an updated genotyping scheme is introduced that also includes the newly reported genotypes 1B_Bangladesh, 1D_Malagasy, 3K-0/3K-1, 3Q and 4N/O. Additionally, genotype-specific markers (single nucleotide polymorphisms, Insertion/Deletion) have been incorporated into the typing scheme for the first time to enable differentiation of closely related strains. This will be particularly useful for geographic regions where M. leprae strains characterized by a small number of genotypes are predominant. The detailed compilation of genomic markers will also enable accurate identification of M. leprae genotypes, using targeted analysis of variable regions. Such markers are good candidates for developing artificial intelligence-based algorithms for classifying M. leprae genomic datasets.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"49 ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143984954","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
Exploring heme and iron acquisition strategies of Porphyromonas gingivalis-current facts and hypotheses. 探讨牙龈卟啉单胞菌的血红素和铁获取策略-目前的事实和假设。
IF 10.1 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf019
Michał Śmiga, Teresa Olczak
{"title":"Exploring heme and iron acquisition strategies of Porphyromonas gingivalis-current facts and hypotheses.","authors":"Michał Śmiga, Teresa Olczak","doi":"10.1093/femsre/fuaf019","DOIUrl":"10.1093/femsre/fuaf019","url":null,"abstract":"<p><p>Iron and heme are crucial for pathogenic bacteria living in the human host but are not available in free form due to their binding by iron- and heme-sequestering proteins. Porphyromonas gingivalis causes dysbiosis in the oral microbiome and is considered a keystone pathogen in the onset and progression of periodontal diseases. Its ability to infect and multiply in host cells and its presence in distant tissues and fluids highlights its pathogenic versatility and explains the relationship between periodontal diseases and systemic or neurodegenerative diseases. Porphyromonas gingivalis has evolved specialized mechanisms that allow it to thrive in the host under adverse nutrient-limited conditions. This review presents the updated summary of the mechanisms of iron and heme acquisition by P. gingivalis, with a central role played by gingipains and the unique Hmu system. The potential role of other iron and heme acquisition systems, such as Hus and Iht, indicates the importance of the partially conserved heme biosynthesis pathway, involving homologs of the HemN, HemG, and HemH proteins. In light of increasing antibiotic resistance, difficulties with diagnosis, and drug administration, targeting the mechanisms of heme and iron acquisition of P. gingivalis represents a promising target for developing diagnostic tests, preventive or therapeutic strategies.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12094164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993801","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
Bacterial osmoprotectants-a way to survive in saline conditions and potential crop allies. 细菌渗透保护剂——在盐水条件下生存的一种方法和潜在的作物盟友。
IF 12.3 2区 生物学
FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf020
Aleksandra Goszcz, Karolina Furtak, Robert Stasiuk, Joanna Wójtowicz, Marcin Musiałowski, Michela Schiavon, Klaudia Dębiec-Andrzejewska
{"title":"Bacterial osmoprotectants-a way to survive in saline conditions and potential crop allies.","authors":"Aleksandra Goszcz, Karolina Furtak, Robert Stasiuk, Joanna Wójtowicz, Marcin Musiałowski, Michela Schiavon, Klaudia Dębiec-Andrzejewska","doi":"10.1093/femsre/fuaf020","DOIUrl":"10.1093/femsre/fuaf020","url":null,"abstract":"<p><p>Soil salinization, affecting 6.5% of arable land, deteriorates soil properties, reduces microbiota activity, hinders plant growth, and accelerates soil erosion. Excessive salt induces physiological drought and toxicity stress in plants, causing chlorosis, ion imbalances, and enzyme disruptions. This paper discusses microorganisms' resistance mechanisms, plant responses to salt stress, and summarizes current knowledge on bacterial osmoprotectants and their functions. It also reviews emerging agrobiotechnological strategies using microbial osmoprotectants to remediate salinized soils and enhance plant growth and productivity under salt stress. Osmoprotectants stabilize proteins, buffer redox potential, and retain water, thus alleviating osmotic stress and promoting bacteria and plants growth. Their application improves soil properties by enhancing aggregate formation, water permeability, moisture content, cation exchange capacity, and ion availability. Despite extensive literature on the function of osmoprotectants, the knowledge about their role in soil environments and agrobiotechnology applications remains limited. This paper indicates proposed research perspectives, including discovering new osmoprotectants, their correlation with soil fertilization, interactions with the soil microbiome, and plant responses. It also identifies significant knowledge gaps in these areas, highlighting the need for further studies to consolidate existing data and assess the potential of this approach to enhance soil health and crop productivity in saline environments.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076789","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
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