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Quantifying microbial interactions: concepts, caveats, and applications 量化微生物相互作用：概念、注意事项和应用。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-07-13 DOI: 10.1016/j.mib.2024.102511
Nittay Meroz , Tal Livny , Jonathan Friedman
{"title":"Quantifying microbial interactions: concepts, caveats, and applications","authors":"Nittay Meroz ,&nbsp;Tal Livny ,&nbsp;Jonathan Friedman","doi":"10.1016/j.mib.2024.102511","DOIUrl":"10.1016/j.mib.2024.102511","url":null,"abstract":"<div><p>Microbial communities are fundamental to every ecosystem on Earth and hold great potential for biotechnological applications. However, their complex nature hampers our ability to study and understand them. A common strategy to tackle this complexity is to abstract the community into a network of interactions between its members — a phenomenological description that captures the overall effects of various chemical and physical mechanisms that underpin these relationships. This approach has proven useful for numerous applications in microbial ecology, including predicting community dynamics and stability and understanding community assembly and evolution. However, care is required in quantifying and interpreting interactions. Here, we clarify the concept of an interaction and discuss when interaction measurements are useful despite their context-dependent nature. Furthermore, we categorize different approaches for quantifying interactions, highlighting the research objectives each approach is best suited for<em>.</em></p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102511"},"PeriodicalIF":5.9,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603405","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: 0
Are microbes colimited by multiple resources? 微生物是否受到多种资源的限制？
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-07-10 DOI: 10.1016/j.mib.2024.102509
Noelle A Held , Michael Manhart
{"title":"Are microbes colimited by multiple resources?","authors":"Noelle A Held ,&nbsp;Michael Manhart","doi":"10.1016/j.mib.2024.102509","DOIUrl":"10.1016/j.mib.2024.102509","url":null,"abstract":"<div><p>Resource colimitation — the dependence of growth on multiple resources simultaneously — has become an important topic in microbiology due both to the development of systems approaches to cell physiology and ecology and to the relevance of colimitation to environmental science, biotechnology, and human health. Empirical tests of colimitation in microbes suggest that it may be common in nature. However, recent theoretical and empirical work has demonstrated the need for systematic measurements across resource conditions, in contrast to the factorial supplementation experiments used in most previous studies. The mechanistic causes of colimitation remain unclear in most cases and are an important challenge for future work, but we identify the alignment of resource consumption with the environment, interactions between resources, and biological and environmental heterogeneity as major factors. On the other hand, the consequences of colimitation are widespread for microbial physiology and ecology, especially the prediction and control of microbial growth, motivating continued consideration of this state in microbiology.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102509"},"PeriodicalIF":5.9,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1369527424000857/pdfft?md5=53d76f47d4a4ad9f4badcb17e9aee781&pid=1-s2.0-S1369527424000857-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589855","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
Epithelial responses to fungal pathogens 上皮细胞对真菌病原体的反应。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-07-10 DOI: 10.1016/j.mib.2024.102508
Kathleen A M Mills , Mariano A Aufiero , Tobias M Hohl
{"title":"Epithelial responses to fungal pathogens","authors":"Kathleen A M Mills ,&nbsp;Mariano A Aufiero ,&nbsp;Tobias M Hohl","doi":"10.1016/j.mib.2024.102508","DOIUrl":"10.1016/j.mib.2024.102508","url":null,"abstract":"<div><p>Epithelial cells orchestrate immune responses against fungal pathogens. This review highlights advances in integrating epithelial cells in immune responses against inhaled molds and dimorphic fungi, and against <em>Candida</em> species that colonize mucosal surfaces. In the lung, epithelial cells respond to interleukin-1 (IL-1) and interferon signaling to regulate effector cell influx and fungal killing. In the alimentary and vulvovaginal tracts, epithelial cells modulate fungal commensalism, invasive growth, and local immune tone, in part by responding to damage caused by candidalysin, a <em>C. albicans</em> peptide toxin, and through IL-17-dependent release of antimicrobial peptides that contribute to <em>Candida</em> colonization resistance. Understanding fungal–epithelial interactions in mammalian models of disease is critical to predict vulnerabilities and to identify opportunities for immune-based strategies to treat fungal infections.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102508"},"PeriodicalIF":5.9,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579233","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: 0
Innate immune response to Candida auris 对白色念珠菌的先天免疫反应
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-07-03 DOI: 10.1016/j.mib.2024.102510
Ashley M Holt , Jeniel E Nett
{"title":"Innate immune response to Candida auris","authors":"Ashley M Holt ,&nbsp;Jeniel E Nett","doi":"10.1016/j.mib.2024.102510","DOIUrl":"10.1016/j.mib.2024.102510","url":null,"abstract":"<div><p><em>Candida auris</em>, a newly emergent fungal species, has been spreading in health care systems and causing life-threatening infections. Intact innate immunity is essential for protection against many invasive fungal infections, including candidiasis. Here, we highlight recent studies exploring immune interactions with <em>C. auris</em>, including investigations using animal models and <em>ex vivo</em> immune cells. We summarize innate immune studies comparing <em>C. auris</em> and the common fungal pathogen <em>Candida albicans</em>. We also discuss how structures of the <em>C. auris</em> cell wall influence immune recognition, the role of soluble host factors in immune recognition, and areas of future study.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102510"},"PeriodicalIF":5.9,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533923","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: 0
The impact of the host microbiota on Candida albicans infection 宿主微生物群对白色念珠菌感染的影响
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-07-01 DOI: 10.1016/j.mib.2024.102507
Eve WL Chow , Li M Pang , Yue Wang
{"title":"The impact of the host microbiota on Candida albicans infection","authors":"Eve WL Chow ,&nbsp;Li M Pang ,&nbsp;Yue Wang","doi":"10.1016/j.mib.2024.102507","DOIUrl":"https://doi.org/10.1016/j.mib.2024.102507","url":null,"abstract":"<div><p>The human microbiota is a complex microbial ecosystem populated by bacteria, fungi, viruses, protists, and archaea. The coexistence of fungi alongside with many billions of bacteria, especially in the gut, involves complex interactions, ranging from antagonistic to beneficial, between the members of these two kingdoms. Bacteria can impact fungi through various means, such as physical interactions, secretion of metabolites, or alteration of the host immune response, thereby affecting fungal growth and virulence. This review summarizes recent progress in this field, delving into the latest understandings of bacterial–fungal–immune interactions and innovative therapeutic approaches addressing the challenges of treating fungal infections associated with microbiota imbalances.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102507"},"PeriodicalIF":5.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141485962","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: 0
Advances in regulation of homeostasis through chromatin modifications by airway commensals 气道共生动物通过染色质修饰调节体内平衡的研究进展。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-06-26 DOI: 10.1016/j.mib.2024.102505
Michael G Connor, Melanie A Hamon
{"title":"Advances in regulation of homeostasis through chromatin modifications by airway commensals","authors":"Michael G Connor,&nbsp;Melanie A Hamon","doi":"10.1016/j.mib.2024.102505","DOIUrl":"10.1016/j.mib.2024.102505","url":null,"abstract":"<div><p>Commensal bacteria are residents of the human airway where they interact with both colonizing pathogens and host respiratory epithelial cells of this mucosal surface. It is here that commensals exert their influence through host signaling cascades, host transcriptional responses and host immunity, all of which are rooted in chromatin remodeling and histone modifications. Recent studies show that airway commensals impact host chromatin, but compared the what is known for gut commensals, the field remains in its infancy. The mechanisms by which airway commensals regulate respiratory health and homeostasis through chromatin modifications is of increasing interest, specifically since their displacement precedes the increased potential for respiratory disease. Herein we will discuss recent advances and intriguing avenues of future work aimed at deciphering how airway commensals protect and influence respiratory health.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102505"},"PeriodicalIF":5.9,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S136952742400081X/pdfft?md5=21f8e19529e4ee6eb61a86b91b898acb&pid=1-s2.0-S136952742400081X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466800","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
Vertebrate and invertebrate animal infection models of Candida auris pathogenicity 念珠菌致病性的脊椎动物和无脊椎动物感染模型。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-06-25 DOI: 10.1016/j.mib.2024.102506
Melissa Martinez, Danielle A Garsin, Michael C Lorenz
{"title":"Vertebrate and invertebrate animal infection models of Candida auris pathogenicity","authors":"Melissa Martinez,&nbsp;Danielle A Garsin,&nbsp;Michael C Lorenz","doi":"10.1016/j.mib.2024.102506","DOIUrl":"10.1016/j.mib.2024.102506","url":null,"abstract":"<div><p><em>Candida auris</em> is an emerging fungal pathogen with several concerning qualities. First recognized in 2009, it has arisen in multiple geographically distinct genomic clades nearly simultaneously. <em>C. auris</em> strains are typically multidrug resistant and colonize the skin much better than most other pathogenic fungi; it also persists on abiotic surfaces, enabling outbreaks due to transmission in health care facilities. All these suggest a biology substantially different from the ‘model’ fungal pathogen, <em>Candida albicans</em> and support intensive investigation of <em>C. auris</em> biology directly. To uncover novel virulence mechanisms in this species requires the development of appropriate animal infection models. Various studies using mice, the definitive model, are inconsistent due to differences in mouse and fungal strains, immunosuppressive regimes, doses, and outcome metrics. At the same time, developing models of skin colonization present a route to new insights into an aspect of fungal pathogenesis that has not been well studied in other species. We also discuss the growing use of nonmammalian model systems, including both vertebrates and invertebrates, such as zebrafish, <em>C. elegans, Drosophila</em>, and <em>Galleria mellonella</em>, that have been productively employed in virulence studies with other fungal species. This review will discuss progress in developing appropriate animal models, outline current challenges, and highlight opportunities in demystifying this curious species.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102506"},"PeriodicalIF":5.9,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141455779","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: 0
Innate immune responses and monocyte-derived phagocyte recruitment in protective immunity to pathogenic bacteria: insights from Legionella pneumophila 致病菌保护性免疫中的先天性免疫反应和单核细胞源性吞噬细胞招募：嗜肺军团菌的启示
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-06-21 DOI: 10.1016/j.mib.2024.102495
Danielle PA Mascarenhas, Dario S Zamboni
{"title":"Innate immune responses and monocyte-derived phagocyte recruitment in protective immunity to pathogenic bacteria: insights from Legionella pneumophila","authors":"Danielle PA Mascarenhas,&nbsp;Dario S Zamboni","doi":"10.1016/j.mib.2024.102495","DOIUrl":"https://doi.org/10.1016/j.mib.2024.102495","url":null,"abstract":"<div><p><em>Legionella</em> species are Gram-negative intracellular bacteria that evolved in soil and freshwater environments, where they infect and replicate within various unicellular protozoa. The primary virulence factor of <em>Legionella</em> is the expression of a type IV secretion system (T4SS), which contributes to the translocation of effector proteins that subvert biological processes of the host cells. Because of its evolution in unicellular organisms, T4SS effector proteins are not adapted to subvert specific mammalian signaling pathways and immunity. Consequently, <em>Legionella pneumophila</em> has emerged as an interesting infection model for investigating immune responses against pathogenic bacteria in multicellular organisms. This review highlights recent advances in our understanding of mammalian innate immunity derived from studies involving <em>L. pneumophila</em>. This includes recent insights into inflammasome-mediated mechanisms restricting bacterial replication in macrophages, mechanisms inducing cell death in response to infection, induction of effector-triggered immunity, activation of specific pulmonary cell types in mammalian lungs, and the protective role of recruiting monocyte-derived cells to infected lungs.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102495"},"PeriodicalIF":5.9,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141438699","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: 0
Dynamic structural determinants in bacterial microcompartment shells 细菌微室外壳的动态结构决定因素
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-06-21 DOI: 10.1016/j.mib.2024.102497
Daniel S Trettel , Cheryl A Kerfeld , Cesar R Gonzalez-Esquer
{"title":"Dynamic structural determinants in bacterial microcompartment shells","authors":"Daniel S Trettel ,&nbsp;Cheryl A Kerfeld ,&nbsp;Cesar R Gonzalez-Esquer","doi":"10.1016/j.mib.2024.102497","DOIUrl":"https://doi.org/10.1016/j.mib.2024.102497","url":null,"abstract":"<div><p>Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO<sub>2</sub> fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein–protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102497"},"PeriodicalIF":5.9,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1369527424000730/pdfft?md5=2e910502ba77b4682b331f3fa92fcb86&pid=1-s2.0-S1369527424000730-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141438700","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
Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity 真菌与细菌共生：从机制到对生物多样性的影响
IF 5.4 2区 生物学
Current opinion in microbiology Pub Date : 2024-06-13 DOI: 10.1016/j.mib.2024.102496
Teresa E Pawlowska
{"title":"Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity","authors":"Teresa E Pawlowska","doi":"10.1016/j.mib.2024.102496","DOIUrl":"https://doi.org/10.1016/j.mib.2024.102496","url":null,"abstract":"<div><p>Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal–bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal–bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal–bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"80 ","pages":"Article 102496"},"PeriodicalIF":5.4,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1369527424000729/pdfft?md5=24e0b032b3b712dbea8582e2ff01c98c&pid=1-s2.0-S1369527424000729-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141314917","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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