npj Biofilms and Microbiomes最新文献_第3页

Bacterial biofilm-derived H-NS protein acts as a defense against Neutrophil Extracellular Traps (NETs). 细菌生物膜衍生的H-NS蛋白作为对中性粒细胞胞外陷阱（NETs）的防御。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-04-15 DOI: 10.1038/s41522-025-00691-0

A L Hendricks, K R More, A Devaraj, J R Buzzo, F H Robledo-Avila, S Partida-Sanchez, L O Bakaletz, S D Goodman

{"title":"Bacterial biofilm-derived H-NS protein acts as a defense against Neutrophil Extracellular Traps (NETs).","authors":"A L Hendricks, K R More, A Devaraj, J R Buzzo, F H Robledo-Avila, S Partida-Sanchez, L O Bakaletz, S D Goodman","doi":"10.1038/s41522-025-00691-0","DOIUrl":"https://doi.org/10.1038/s41522-025-00691-0","url":null,"abstract":"Extracellular DNA (eDNA) is crucial for the structural integrity of bacterial biofilms as they undergo transformation from B-DNA to Z-DNA as the biofilm matures. This transition to Z-DNA increases biofilm rigidity and prevents binding by canonical B-DNA-binding proteins, including nucleases. One of the primary defenses against bacterial infections are Neutrophil Extracellular Traps (NETs), wherein neutrophils release their own eDNA to trap and kill bacteria. Here we show that H-NS, a bacterial nucleoid associated protein (NAP) that is also released during biofilm development, is able to incapacitate NETs. Indeed, when exposed to human derived neutrophils, H-NS prevented the formation of NETs and lead to NET eDNA retraction in previously formed NETs. NETs that were exposed to H-NS also lost their ability to kill free-living bacteria which made H-NS an attractive therapeutic candidate for the control of NET-related human diseases. A model of H-NS release from biofilms and NET incapacitation is discussed.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"58"},"PeriodicalIF":7.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12000423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144064309","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

Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads. 通过连接和整合双16S rRNA扩增子读取，改进微生物组多样性分析。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-04-12 DOI: 10.1038/s41522-025-00686-x

Kyoung Su Kim, Jihye Noh, Bong-Soo Kim, Hong Koh, Dong-Woo Lee

{"title":"Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.","authors":"Kyoung Su Kim, Jihye Noh, Bong-Soo Kim, Hong Koh, Dong-Woo Lee","doi":"10.1038/s41522-025-00686-x","DOIUrl":"https://doi.org/10.1038/s41522-025-00686-x","url":null,"abstract":"Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"57"},"PeriodicalIF":7.8,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11993755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036762","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

Probiotics and prebiotics: new treatment strategies for oral potentially malignant disorders and gastrointestinal precancerous lesions. 益生菌和益生元：治疗口腔潜在恶性疾病和胃肠道癌前病变的新策略。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-04-08 DOI: 10.1038/s41522-025-00688-9

Zhuwei Huang, Jiaye Zhu, Xiangwen Bu, Shulai Lu, Yixian Luo, Ting Liu, Ning Duan, Wenmei Wang, Yong Wang, Xiang Wang

引用次数: 0

Synergic interactions between Trichoderma and the soil microbiomes improve plant iron availability and growth. 木霉与土壤微生物群之间的协同作用改善了植物铁的有效性和生长。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-04-08 DOI: 10.1038/s41522-025-00684-z

Yadong Shao, Shaohua Gu, Haiying Peng, Lisheng Zhang, Sidong Li, Roeland L Berendsen, Tianjie Yang, Caixia Dong, Zhong Wei, Yangchun Xu, Qirong Shen

{"title":"Synergic interactions between Trichoderma and the soil microbiomes improve plant iron availability and growth.","authors":"Yadong Shao, Shaohua Gu, Haiying Peng, Lisheng Zhang, Sidong Li, Roeland L Berendsen, Tianjie Yang, Caixia Dong, Zhong Wei, Yangchun Xu, Qirong Shen","doi":"10.1038/s41522-025-00684-z","DOIUrl":"10.1038/s41522-025-00684-z","url":null,"abstract":"Iron bioavailability is often limited especially in calcareous soils. Trichoderma harzianum strongly improves plant iron uptake and growth in calcareous soils. However, little is known about the mechanisms by which T. harzianum mobilizes iron in calcareous soils. Here, the model strain T. harzianum NJAU4742 and a synthetic microbial community (SynCom) was used to show that the efficacy of T. harzianum in enhancing plant iron nutrition in calcareous soils depends on the soil microbiome. Enhanced iron-mobilization functions of the SynCom were observed in the presence of T. harzianum NJAU4742. Concurrently, T. harzianum NJAU4742 improved the iron-mobilization capacity of the SynCom by enriching strains that are able to do so. Finally, Chryseobacterium populi was identified as a key driver of iron mobilization, while their synergistic colonization further enhances this process. This study unveils a pivotal mechanism by which T. harzianum NJAU4742-mediated re-structuring of the soil microbiome and ameliorates plant iron nutrition.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"56"},"PeriodicalIF":7.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812021","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

Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems. 环境不稳定通过丰富具有不同双组分调节系统的专业分类群来降低抗震性。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-03-31 DOI: 10.1038/s41522-025-00679-w

Simon Mills, Umer Zeeshan Ijaz, Piet N L Lens

{"title":"Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.","authors":"Simon Mills, Umer Zeeshan Ijaz, Piet N L Lens","doi":"10.1038/s41522-025-00679-w","DOIUrl":"10.1038/s41522-025-00679-w","url":null,"abstract":"Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance1. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"54"},"PeriodicalIF":7.8,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753416","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

The regulatory framework for microbiome-based therapies: insights into European regulatory developments. 基于微生物组的疗法的监管框架：对欧洲监管发展的见解。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-03-28 DOI: 10.1038/s41522-025-00683-0

Julie Rodriguez, Magali Cordaillat-Simmons, Bruno Pot, Céline Druart

引用次数: 0

Vaginal host immune-microbiome-metabolite interactions associated with spontaneous preterm birth in a predominantly white cohort. 阴道宿主免疫-微生物-代谢物相互作用与自发性早产相关，主要是白人队列。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-03-26 DOI: 10.1038/s41522-025-00671-4

Megan Cavanagh, Emmanuel Amabebe, Neha S Kulkarni, Maria D Papageorgiou, Heather Walker, Matthew D Wyles, Dilly O Anumba

{"title":"Vaginal host immune-microbiome-metabolite interactions associated with spontaneous preterm birth in a predominantly white cohort.","authors":"Megan Cavanagh, Emmanuel Amabebe, Neha S Kulkarni, Maria D Papageorgiou, Heather Walker, Matthew D Wyles, Dilly O Anumba","doi":"10.1038/s41522-025-00671-4","DOIUrl":"10.1038/s41522-025-00671-4","url":null,"abstract":"In order to improve spontaneous preterm birth (sPTB) risk stratification in a predominantly white cohort of non-labouring pregnant women, we analysed their vaginal microbiota, metabolite, cytokine and foetal fibronectin (FFN) concentrations at two gestational time points (GTPs): GTP1 (20+0-22+6 weeks, preterm = 17; term = 32); and GTP2 (26+0-28+6 weeks, preterm = 14; term = 31). At GTP1, the preterm-delivered women showed abundant G. vaginalis (AUC = 0.77) over L. crispatus and L. iners, and upregulation of 10 metabolites. At GTP2, the same women had more lactobacilli- and mixed anaerobes-dominated microbiota, upregulation of five metabolites, and decreased TNFR1, distinguishing them from their term counterparts (AUC = 0.88). From GTP1 to GTP2, sPTB was associated with increased microbiota α-diversity, and upregulation of pantothenate and urate. CXCL10 declined in the term-delivered women by ~3-fold, but increased in the preterm-delivered women (AUC = 0.68), enhanced by FFN (AUC = 0.74). Characterising the complex dynamic interactions between cervicovaginal microbial metabolites and host immune responses could enhance sPTB risk stratification.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"52"},"PeriodicalIF":7.8,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11947164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143720595","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

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-03-25 DOI: 10.1038/s41522-025-00677-y

Yingli Jing, Qiuying Wang, Fan Bai, Zihan Li, Yan Li, Weijin Liu, Yitong Yan, Shuangyue Zhang, Chen Gao, Yan Yu

{"title":"Age-related alterations in gut homeostasis are microbiota dependent.","authors":"Yingli Jing, Qiuying Wang, Fan Bai, Zihan Li, Yan Li, Weijin Liu, Yitong Yan, Shuangyue Zhang, Chen Gao, Yan Yu","doi":"10.1038/s41522-025-00677-y","DOIUrl":"10.1038/s41522-025-00677-y","url":null,"abstract":"Accumulating data suggest that remodeling aged gut microbiota improves aging-related imbalance in intestinal homeostasis. However, evidence in favor of the beneficial effect of remodeling gut microbiota on intestinal stress and immune responses during aging is scarce. The current study revealed that old mice presented impaired gut barrier integrity. Transcriptome sequencing coupled with bioinformatics analysis revealed that aging altered gene expression profiles of the colon and mesenteric lymph nodes, which are involved mainly in stress and immune responses, respectively. Notably, gut microbiota was closely related to the differentially expressed genes. Microbiota depletion in old mice ameliorated gut barrier integrity and partially reversed the inflammatory factors upregulated in aging mice. Furthermore, fecal microbiota transplantation from young mice to old mice resulted in a significant improvement in intestinal barrier integrity and immune homeostasis. These findings highlight the potential of microbiota-targeted interventions on aging-related physiological processes and call for further investigation.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"51"},"PeriodicalIF":7.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710421","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

Population-level control of two manganese oxidases expands the niche for bacterial manganese biomineralization. 两种锰氧化酶的种群水平控制扩大了细菌锰生物矿化的生态位。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-03-24 DOI: 10.1038/s41522-025-00670-5

Gaitan Gehin, Nicolas Carraro, Jan Roelof van der Meer, Jasquelin Peña

{"title":"Population-level control of two manganese oxidases expands the niche for bacterial manganese biomineralization.","authors":"Gaitan Gehin, Nicolas Carraro, Jan Roelof van der Meer, Jasquelin Peña","doi":"10.1038/s41522-025-00670-5","DOIUrl":"10.1038/s41522-025-00670-5","url":null,"abstract":"The enzymatic oxidation of aqueous divalent manganese (Mn) is a widespread microbial trait that produces reactive Mn(III, IV) oxide minerals. These biominerals drive carbon, nutrient, and trace metal cycles, thus playing important environmental and ecological roles. However, the regulatory mechanisms and physiological functions of Mn biomineralization are unknown. This challenge arises from the common occurrence of multiple Mn oxidases within the same organism and the use of Mn oxides as indicators of combined gene activity. Through the detection of gene activation in individual cells, we discover that expression of mnxG and mcoA, two Mn oxidase-encoding genes in Pseudomonas putida GB-1, is confined to subsets of cells within the population, with each gene showing distinct spatiotemporal patterns that reflect local microenvironments. These coordinated intra-population dynamics control Mn biomineralization and illuminate the strategies used by microbial communities to dictate the extent, location, and timing of biogeochemical transformations.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"50"},"PeriodicalIF":7.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11930936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692943","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

Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics. 比较宏基因组学鉴定阴道crispatus乳杆菌和乳杆菌iners菌株水平差异。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-03-23 DOI: 10.1038/s41522-025-00682-1

Sai Ravi Chandra Nori, Calum J Walsh, Fionnuala M McAuliffe, Rebecca L Moore, Douwe Van Sinderen, Conor Feehily, Paul D Cotter

{"title":"Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.","authors":"Sai Ravi Chandra Nori, Calum J Walsh, Fionnuala M McAuliffe, Rebecca L Moore, Douwe Van Sinderen, Conor Feehily, Paul D Cotter","doi":"10.1038/s41522-025-00682-1","DOIUrl":"10.1038/s41522-025-00682-1","url":null,"abstract":"The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with Lactobacillus crispatus and Lactobacillus iners being the most dominant. We found genes, including putative mucin-binding genes, distinct to L. crispatus subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in L. crispatus related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in L. crispatus but absent in L. iners and Gardnerella vaginalis. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"49"},"PeriodicalIF":7.8,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11930926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692946","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