Microbiology and Molecular Biology Reviews最新文献

A roadmap to understanding and anticipating microbial gene transfer in soil communities.

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-04-08 DOI: 10.1128/mmbr.00225-24

David L Gillett, Malyn Selinidis, Travis Seamons, Dalton George, Alexandria N Igwe, Ilenne Del Valle, Robert G Egbert, Kirsten S Hofmockel, Alicia L Johnson, Kirstin R W Matthews, Caroline A Masiello, Lauren B Stadler, James Chappell, Jonathan J Silberg

{"title":"A roadmap to understanding and anticipating microbial gene transfer in soil communities.","authors":"David L Gillett, Malyn Selinidis, Travis Seamons, Dalton George, Alexandria N Igwe, Ilenne Del Valle, Robert G Egbert, Kirsten S Hofmockel, Alicia L Johnson, Kirstin R W Matthews, Caroline A Masiello, Lauren B Stadler, James Chappell, Jonathan J Silberg","doi":"10.1128/mmbr.00225-24","DOIUrl":"https://doi.org/10.1128/mmbr.00225-24","url":null,"abstract":"SUMMARYEngineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. We propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.","PeriodicalId":18520,"journal":{"name":"Microbiology and Molecular Biology Reviews","volume":" ","pages":"e0022524"},"PeriodicalIF":8.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803663","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

Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-04-02 DOI: 10.1128/mmbr.00184-23

Chiara Tarracchini, Cathy Lordan, Christian Milani, Luiza P D Moreira, Qusai M Alabedallat, Alejandra de Moreno de LeBlanc, Francesca Turroni, Gabriele Andrea Lugli, Leonardo Mancabelli, Giulia Longhi, Lorraine Brennan, Jennifer Mahony, Jean Guy LeBlanc, Kanishka N Nilaweera, Paul D Cotter, Douwe van Sinderen, Marco Ventura

{"title":"Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.","authors":"Chiara Tarracchini, Cathy Lordan, Christian Milani, Luiza P D Moreira, Qusai M Alabedallat, Alejandra de Moreno de LeBlanc, Francesca Turroni, Gabriele Andrea Lugli, Leonardo Mancabelli, Giulia Longhi, Lorraine Brennan, Jennifer Mahony, Jean Guy LeBlanc, Kanishka N Nilaweera, Paul D Cotter, Douwe van Sinderen, Marco Ventura","doi":"10.1128/mmbr.00184-23","DOIUrl":"https://doi.org/10.1128/mmbr.00184-23","url":null,"abstract":"SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.","PeriodicalId":18520,"journal":{"name":"Microbiology and Molecular Biology Reviews","volume":" ","pages":"e0018423"},"PeriodicalIF":8.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764477","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

A call for healing and unity.

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-03-27 Epub Date: 2025-02-27 DOI: 10.1128/mmbr.00063-25

Patrick D Schloss

引用次数: 0

Recent developments in Aspergillus fumigatus research: diversity, drugs, and disease.

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-03-27 Epub Date: 2025-02-10 DOI: 10.1128/mmbr.00011-23

Nicole Kordana, Angus Johnson, Katherine Quinn, Joshua J Obar, Robert A Cramer

{"title":"Recent developments in Aspergillus fumigatus research: diversity, drugs, and disease.","authors":"Nicole Kordana, Angus Johnson, Katherine Quinn, Joshua J Obar, Robert A Cramer","doi":"10.1128/mmbr.00011-23","DOIUrl":"10.1128/mmbr.00011-23","url":null,"abstract":"SUMMARYAdvances in modern medical therapies for many previously intractable human diseases have improved patient outcomes. However, successful disease treatment outcomes are often prevented due to invasive fungal infections caused by the environmental mold Aspergillus fumigatus. As contemporary antifungal therapies have not experienced the same robust advances as other medical therapies, defining mechanisms of A. fumigatus disease initiation and progression remains a critical research priority. To this end, the World Health Organization recently identified A. fumigatus as a research priority human fungal pathogen and the Centers for Disease Control has highlighted the emergence of triazole-resistant A. fumigatus isolates. The expansion in the diversity of host populations susceptible to aspergillosis and the complex and dynamic A. fumigatus genotypic and phenotypic diversity call for a reinvigorated assessment of aspergillosis pathobiological and drug-susceptibility mechanisms. Here, we summarize recent advancements in the field and discuss challenges in our understanding of A. fumigatus heterogeneity and its pathogenesis in diverse host populations.","PeriodicalId":18520,"journal":{"name":"Microbiology and Molecular Biology Reviews","volume":" ","pages":"e0001123"},"PeriodicalIF":8.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges.

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-03-27 Epub Date: 2025-01-24 DOI: 10.1128/mmbr.00138-24

Suyen Solange Espinoza Miranda, Gorkhmaz Abbaszade, Wolfgang R Hess, Knut Drescher, Antoine-Emmanuel Saliba, Vasily Zaburdaev, Liraz Chai, Klaus Dreisewerd, Alexander Grünberger, Christian Westendorf, Susann Müller, Thorsten Mascher

{"title":"Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges.","authors":"Suyen Solange Espinoza Miranda, Gorkhmaz Abbaszade, Wolfgang R Hess, Knut Drescher, Antoine-Emmanuel Saliba, Vasily Zaburdaev, Liraz Chai, Klaus Dreisewerd, Alexander Grünberger, Christian Westendorf, Susann Müller, Thorsten Mascher","doi":"10.1128/mmbr.00138-24","DOIUrl":"10.1128/mmbr.00138-24","url":null,"abstract":"SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in eukaryotes, it originates in prokaryotes. Coordinated aggregation of individual cells within the confines of a colony results in emerging, higher-level functions that benefit the population as a whole. During colony differentiation, an almost infinite number of ecological and physiological population-forming forces are at work, creating complex, intricate colony structures with divergent functions. Understanding the assembly and dynamics of such populations requires resolving individual cells or cell groups within such macroscopic structures. Addressing how each cell contributes to the collective action requires pushing the resolution boundaries of key technologies that will be presented in this review. In particular, single-cell techniques provide powerful tools for studying bacterial multicellularity with unprecedented spatial and temporal resolution. These advancements include novel microscopic techniques, mass spectrometry imaging, flow cytometry, spatial transcriptomics, single-bacteria RNA sequencing, and the integration of spatiotemporal transcriptomics with microscopy, alongside advanced microfluidic cultivation systems. This review encourages exploring the synergistic potential of the new technologies in the study of bacterial multicellularity, with a particular focus on individuals in differentiated bacterial biofilms (colonies). It highlights how resolving population structures at the single-cell level and understanding their respective functions can elucidate the overarching functions of bacterial multicellular populations.","PeriodicalId":18520,"journal":{"name":"Microbiology and Molecular Biology Reviews","volume":" ","pages":"e0013824"},"PeriodicalIF":8.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143033530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Insights into ecology, pathogenesis, and biofilm formation of Enterococcus faecalis from functional genomics. 从功能基因组学深入了解粪肠球菌的生态学、发病机制和生物膜形成。

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-03-27 Epub Date: 2024-12-23 DOI: 10.1128/mmbr.00081-23

Julia L E Willett, Gary M Dunny

{"title":"Insights into ecology, pathogenesis, and biofilm formation of Enterococcus faecalis from functional genomics.","authors":"Julia L E Willett, Gary M Dunny","doi":"10.1128/mmbr.00081-23","DOIUrl":"10.1128/mmbr.00081-23","url":null,"abstract":"SUMMARYEnterococcus faecalis is a significant resident of the gastrointestinal tract of most animals, including humans. Although generally non-pathogenic in healthy hosts, this microbe is adept at the exploitation of compromises in host immune functions, resulting in life-threatening opportunistic infections whose treatments are complicated by a high degree of intrinsic and acquired resistance to antimicrobial chemotherapy. Historically, progress in enterococcal research was limited by a lack of experimental models that replicate natural infection pathways and the relevance of in vitro studies to the natural biology of the organism. In this review, we summarize the history of enterococcal research during the 20th and early 21st centuries and describe more recent genetic and genomic tools and screens developed to address challenges in the field. We also describe how the results of recent studies reveal the importance of previously uncharacterized enterococcal genes, and we provide examples of interesting determinants that have emerged as important contributors to enterococcal biology. These factors may also serve as targets for future vaccines and chemotherapeutic agents to combat life-threatening hospital infections.","PeriodicalId":18520,"journal":{"name":"Microbiology and Molecular Biology Reviews","volume":" ","pages":"e0008123"},"PeriodicalIF":8.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Variable surface antigen expression, virulence, and persistent infection by Plasmodium falciparum malaria parasites. 可变表面抗原表达、毒力和恶性疟原虫的持续感染。

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-03-27 Epub Date: 2025-01-14 DOI: 10.1128/mmbr.00114-23

Evi Hadjimichael, Kirk W Deitsch

{"title":"Variable surface antigen expression, virulence, and persistent infection by Plasmodium falciparum malaria parasites.","authors":"Evi Hadjimichael, Kirk W Deitsch","doi":"10.1128/mmbr.00114-23","DOIUrl":"10.1128/mmbr.00114-23","url":null,"abstract":"SUMMARYThe human malaria parasite Plasmodium falciparum is known for its ability to maintain lengthy infections that can extend for over a year. This property is derived from the parasite's capacity to continuously alter the antigens expressed on the surface of the infected red blood cell, thereby avoiding antibody recognition and immune destruction. The primary target of the immune system is an antigen called PfEMP1 that serves as a cell surface receptor and enables infected cells to adhere to the vascular endothelium and thus avoid filtration by the spleen. The parasite's genome encodes approximately 60 antigenically distinct forms of PfEMP1, each encoded by individual members of the multicopy var gene family. This provides the parasite with a repertoire of antigenic types that it systematically cycles through over the course of an infection, thereby maintaining an infection until the repertoire is exhausted. While this model of antigenic variation based on var gene switching explains the dynamics of acute infections in individuals with limited anti-malarial immunity, it fails to explain reports of chronic, asymptomatic infections that can last over a decade. Recent field studies have led to a re-evaluation of previous conclusions regarding the prevalence of chronic infections, and the application of new technologies has provided insights into the molecular mechanisms that enable chronic infections and how these processes evolved.","PeriodicalId":18520,"journal":{"name":"Microbiology and Molecular Biology Reviews","volume":" ","pages":"e0011423"},"PeriodicalIF":8.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Human coronaviruses: activation and antagonism of innate immune responses. 人冠状病毒：先天免疫反应的激活和拮抗。

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-03-27 Epub Date: 2024-12-19 DOI: 10.1128/mmbr.00016-23

Nikhila S Tanneti, Helen A Stillwell, Susan R Weiss

引用次数: 0

Vesicular mechanisms of drug resistance in apicomplexan parasites.

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-03-27 Epub Date: 2025-01-24 DOI: 10.1128/mmbr.00010-24

Kasturi Haldar, Souvik Bhattacharjee

{"title":"Vesicular mechanisms of drug resistance in apicomplexan parasites.","authors":"Kasturi Haldar, Souvik Bhattacharjee","doi":"10.1128/mmbr.00010-24","DOIUrl":"10.1128/mmbr.00010-24","url":null,"abstract":"SUMMARYVesicular mechanisms of drug resistance are known to exist across prokaryotes and eukaryotes. Vesicles are sacs that form when a lipid bilayer 'bends' to engulf and isolate contents from the cytoplasm or extracellular environment. They have a wide range of functions, including vehicles of communication within and across cells, trafficking of protein intermediates to their rightful organellar destinations, and carriers of substrates destined for autophagy. This review will provide an in-depth understanding of vesicular mechanisms of apicomplexan parasites, Plasmodium and Toxoplasma (that respectively cause malaria and toxoplasmosis). It will integrate mechanistic and evolutionarily insights gained from these and other pathogenic eukaryotes to develop a new model for plasmodial resistance to artemisinins, a class of drugs that have been the backbone of modern campaigns to eliminate malaria worldwide. We also discuss extracellular vesicles that present major vesicular mechanisms of drug resistance in parasite protozoa (that apicomplexans are part of). Finally, we provide a broader context of clinical drug resistance mechanisms of Plasmodium, Toxoplasma, as well as Cryptosporidium and Babesia, that are prominent members of the phyla, causative agents of cryptosporidiosis and babesiosis and significant for human and animal health.","PeriodicalId":18520,"journal":{"name":"Microbiology and Molecular Biology Reviews","volume":" ","pages":"e0001024"},"PeriodicalIF":8.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143033546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

How human papillomavirus (HPV) targets DNA repair pathways for viral replication: from guardian to accomplice.

IF 8 1区生物学

Microbiology and Molecular Biology Reviews Pub Date : 2025-03-27 Epub Date: 2025-01-27 DOI: 10.1128/mmbr.00153-23

Arushi Vats, Laimonis Laimins

{"title":"How human papillomavirus (HPV) targets DNA repair pathways for viral replication: from guardian to accomplice.","authors":"Arushi Vats, Laimonis Laimins","doi":"10.1128/mmbr.00153-23","DOIUrl":"10.1128/mmbr.00153-23","url":null,"abstract":"SUMMARYHuman papillomaviruses (HPVs) are small DNA viruses that are responsible for significant disease burdens worldwide, including cancers of the cervix, anogenital tract, and oropharynx. HPVs infect stratified epithelia at a variety of body locations and link their productive life cycles to the differentiation of the host cell. These viruses have evolved sophisticated mechanisms to exploit cellular pathways, such as DNA damage repair (DDR), to regulate their life cycles. HPVs activate key DDR pathways such as ATM, ATR, and FA, which are critical for maintaining genomic integrity but are often dysregulated in cancers. Importantly, these DDR pathways are essential for HPV replication in undifferentiated cells and amplification upon differentiation. The ability to modulate these DDR pathways not only enables HPV persistence but also contributes to cellular transformation. In this review, we discuss the recent advances in understanding the mechanisms by which HPV manipulates the host DDR pathways and how these depend upon enhanced topoisomerase activity and R-loop formation. Furthermore, the strategies to manipulate DDR pathways utilized by high-risk HPVs are compared with those used by other DNA viruses that exhibit similarities and distinct differences.","PeriodicalId":18520,"journal":{"name":"Microbiology and Molecular Biology Reviews","volume":" ","pages":"e0015323"},"PeriodicalIF":8.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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