npj Biofilms and Microbiomes最新文献_第4页

Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China. 中国西南地区人群肠道微生物组及其与环境因素和代谢紊乱的关系。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-02-04 DOI: 10.1038/s41522-025-00661-6

Qianyu Qu, Qingyu Dou, Zhejun Xiang, Bin Yu, Lili Chen, Zhenxin Fan, Xing Zhao, Shujuan Yang, Peibin Zeng

引用次数: 0

Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-02-02 DOI: 10.1038/s41522-025-00659-0

Anthoula Chatzimpinou, Anne Diehl, A Tobias Harhoff, Kristina Driller, Bieke Vanslembrouck, Jian-Hua Chen, Kristaps Kairišs, Valentina Loconte, Mark A Le Gros, Carolyn Larabell, Kürşad Turgay, Hartmut Oschkinat, Venera Weinhardt

{"title":"Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion.","authors":"Anthoula Chatzimpinou, Anne Diehl, A Tobias Harhoff, Kristina Driller, Bieke Vanslembrouck, Jian-Hua Chen, Kristaps Kairišs, Valentina Loconte, Mark A Le Gros, Carolyn Larabell, Kürşad Turgay, Hartmut Oschkinat, Venera Weinhardt","doi":"10.1038/s41522-025-00659-0","DOIUrl":"10.1038/s41522-025-00659-0","url":null,"abstract":"Bacterial biofilms are complex cell communities within a self-produced extracellular matrix, crucial in various fields but challenging to analyze in 3D. We developed a \"biofilm-in-capillary\" growth method compatible with full-rotation soft X-ray tomography, enabling high-resolution 3D imaging of bacterial cells and their matrix during biofilm formation. This approach offers 50 nm isotropic spatial resolution, rapid imaging, and quantitative native analysis of biofilm structure. Using Bacillus subtilis biofilms, we detected coherent alignment and chaining of wild-type cells towards the oxygen-rich capillary tip. In contrast, the ΔtasA genetic knock-out showed a loss of cellular orientation and changes in the extracellular matrix. Adding TasA protein to the ΔtasA strain restored matrix density and led to cell assembly compaction, but without the chaining observed in wild-type biofilms. This scalable and transferable approach opens new avenues for examining biofilm structure and function across various species, including mixed biofilms, and response to genetic and environmental factors.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"23"},"PeriodicalIF":7.8,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11788442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080839","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

Author Correction: Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-30 DOI: 10.1038/s41522-025-00656-3

Zeng Zhang, Yajing Fang, Yangli He, Mohamed A Farag, Min Zeng, Yukai Sun, Siqi Peng, Shuaiming Jiang, Xian Zhang, Kaining Chen, Meng Xu, Zhe Han, Jiachao Zhang

引用次数: 0

Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-29 DOI: 10.1038/s41522-025-00655-4

Yi Xue, Xue Kang

{"title":"Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy.","authors":"Yi Xue, Xue Kang","doi":"10.1038/s41522-025-00655-4","DOIUrl":"10.1038/s41522-025-00655-4","url":null,"abstract":"Dispersal plays a crucial role in the development and ecology of biofilms. While extensive studies focused on elucidating the molecular mechanisms governing this process, few have characterized the associated temporal changes in composition and structure. Here, we employed solid-state nuclear magnetic resonance (NMR) techniques to achieve time-resolved characterization of Bacillus subtilis biofilms over a 5-day period. The mature biofilm, established within 48 h, undergoes significant degradation in following 72 h. The steepest decline of proteins precedes that of exopolysaccharides, likely reflecting their distinct spatial distribution. Exopolysaccharide sugar units display clustered temporal patterns, suggesting the presence of distinct polysaccharide types. A sharp rise in aliphatic carbon signals on day 4 probably corresponds to a surge in biosurfactant production. Different dynamic regimes respond differently to dispersal: the mobile domain exhibits increased rigidity, while the rigid domain remains stable. These findings provide novel insights and perspectives on the complex process of biofilm dispersal.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"21"},"PeriodicalIF":7.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11779841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067027","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

Pharmacodynamics of interspecies interactions in polymicrobial infections. 多种微生物感染中种间相互作用的药效学研究。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-21 DOI: 10.1038/s41522-024-00621-6

C Herzberg, J G C van Hasselt

{"title":"Pharmacodynamics of interspecies interactions in polymicrobial infections.","authors":"C Herzberg, J G C van Hasselt","doi":"10.1038/s41522-024-00621-6","DOIUrl":"10.1038/s41522-024-00621-6","url":null,"abstract":"The pharmacodynamic response of bacterial pathogens to antibiotics can be influenced by interactions with other bacterial species in polymicrobial infections (PMIs). Understanding the complex eco-evolutionary dynamics of PMIs and their impact on antimicrobial treatment response represents a step towards developing improved treatment strategies for PMIs. Here, we investigated how interspecies interactions in a multi-species bacterial community affect the pharmacodynamic response to antimicrobial treatment. To this end, we developed an in silico model which combined agent-based modeling with ordinary differential equations. Our analyses suggest that both interspecies interactions, modifying either drug sensitivity or bacterial growth rate, and drug-specific pharmacological properties drive the bacterial pharmacodynamic response. Furthermore, lifestyle of the bacterial population and the range of interactions can influence the impact of species interactions. In conclusion, this study provides a foundation for the design of antimicrobial treatment strategies for PMIs which leverage the effects of interspecies interactions.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"20"},"PeriodicalIF":7.8,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143009045","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

Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences. 人类和非人类灵长类动物的链球菌丰度和口腔向性反映了宿主和生活方式的差异。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-17 DOI: 10.1038/s41522-024-00642-1

Irina M Velsko, Christina Warinner

引用次数: 0

A human oral commensal-mediated protection against Sjögren's syndrome with maintenance of T cell immune homeostasis and improved oral microbiota. 通过维持T细胞免疫稳态和改善口腔微生物群，人类口腔共通介导的对Sjögren综合征的保护作用。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-16 DOI: 10.1038/s41522-025-00654-5

Yu-Chao Tseng, Kai-Sheng Liao, Wei-Ting Lin, Chin Li, Chia-Bin Chang, Jie-Wei Hsu, Chin-Pui Chan, Chun-Ming Chen, Hon-Pin Wang, Hsiu-Chuan Chien, Jann-Tay Wang, Song-Chou Hsieh, Shu-Fen Wu

{"title":"A human oral commensal-mediated protection against Sjögren's syndrome with maintenance of T cell immune homeostasis and improved oral microbiota.","authors":"Yu-Chao Tseng, Kai-Sheng Liao, Wei-Ting Lin, Chin Li, Chia-Bin Chang, Jie-Wei Hsu, Chin-Pui Chan, Chun-Ming Chen, Hon-Pin Wang, Hsiu-Chuan Chien, Jann-Tay Wang, Song-Chou Hsieh, Shu-Fen Wu","doi":"10.1038/s41522-025-00654-5","DOIUrl":"10.1038/s41522-025-00654-5","url":null,"abstract":"Sjögren's syndrome (SS) is a prevalent systemic autoimmune disease with substantial impacts on women's health worldwide. Although oral Haemophilus parainfluenzae is reduced in SS, its significance remains unclear. This study aimed to elucidate the pathophysiological role of H. parainfluenzae in SS. Reduced salivary H. parainfluenzae levels in SS patients were confirmed through quantitative PCR. Oral H. parainfluenzae inoculation in NOD mice alleviated focal sialadenitis, improved salivary function, and reduced IFN-γ+CD3+ and IFN-γ+CD8+ T cells in salivary gland-draining lymph nodes, maintaining immune homeostasis against a biased type 1 response. Inoculation also enhanced salivary microbiota diversity, balanced the Firmicutes-to-Proteobacteria ratio, and reduced the overwhelming presence of Pseudomonas mendocina. In vitro, H. parainfluenzae-preconditioned A253 cells limited CD8 T cell expansion with reduced IFN-γ production. These findings suggest that H. parainfluenzae improves oral microbial diversity, promotes homeostatic T-cell immunity, and protects against SS, supporting its potential as a next-generation probiotic.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"18"},"PeriodicalIF":7.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143009042","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 role of fluid friction in streamer formation and biofilm growth. 流体摩擦在流线形成和生物膜生长中的作用。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-15 DOI: 10.1038/s41522-024-00633-2

Cornelius Wittig, Michael Wagner, Romain Vallon, Thomas Crouzier, Wouter van der Wijngaart, Harald Horn, Shervin Bagheri

{"title":"The role of fluid friction in streamer formation and biofilm growth.","authors":"Cornelius Wittig, Michael Wagner, Romain Vallon, Thomas Crouzier, Wouter van der Wijngaart, Harald Horn, Shervin Bagheri","doi":"10.1038/s41522-024-00633-2","DOIUrl":"10.1038/s41522-024-00633-2","url":null,"abstract":"Biofilms constitute one of the most common forms of living matter, playing an increasingly important role in technology, health, and ecology. While it is well established that biofilm growth and morphology are highly dependent on the external flow environment, the precise role of fluid friction has remained elusive. We grew Bacillus subtilis biofilms on flat surfaces of a channel in a laminar flow at wall shear stresses spanning one order of magnitude (τw = 0.068 Pa to τw = 0.67 Pa). By monitoring the three-dimensional distribution of biofilm over seven days, we found that the biofilms consist of smaller microcolonies, shaped like leaning pillars, many of which feature a streamer in the form of a thin filament that originates near the tip of the pillar. While the shape, size, and distribution of these microcolonies depend on the imposed shear stress, the same structural features appear consistently for all shear stress values. The formation of streamers occurs after the development of a base structure, suggesting that the latter induces a secondary flow that triggers streamer formation. Moreover, we observed that the biofilm volume grows approximately linearly over seven days for all shear stress values, with a growth rate inversely proportional to the wall shear stress. We develop a scaling model, providing insight into the mechanisms by which friction limits biofilm growth.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"17"},"PeriodicalIF":7.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008970","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

Deep generative modeling of annotated bacterial biofilm images. 对有注释的细菌生物膜图像进行深度生成建模。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-14 DOI: 10.1038/s41522-025-00647-4

Angelina A Holicheva, Konstantin S Kozlov, Daniil A Boiko, Maxim S Kamanin, Daria V Provotorova, Nikita I Kolomoets, Valentine P Ananikov

{"title":"Deep generative modeling of annotated bacterial biofilm images.","authors":"Angelina A Holicheva, Konstantin S Kozlov, Daniil A Boiko, Maxim S Kamanin, Daria V Provotorova, Nikita I Kolomoets, Valentine P Ananikov","doi":"10.1038/s41522-025-00647-4","DOIUrl":"10.1038/s41522-025-00647-4","url":null,"abstract":"Biofilms are critical for understanding environmental processes, developing biotechnology applications, and progressing in medical treatments of various infections. Nowadays, a key limiting factor for biofilm analysis is the difficulty in obtaining large datasets with fully annotated images. This study introduces a versatile approach for creating synthetic datasets of annotated biofilm images with employing deep generative modeling techniques, including VAEs, GANs, diffusion models, and CycleGAN. Synthetic datasets can significantly improve the training of computer vision models for automated biofilm analysis, as demonstrated with the application of Mask R-CNN detection model. The approach represents a key advance in the field of biofilm research, offering a scalable solution for generating high-quality training data and working with different strains of microorganisms at different stages of formation. Terabyte-scale datasets can be easily generated on personal computers. A web application is provided for the on-demand generation of biofilm images.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"16"},"PeriodicalIF":7.8,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11733122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984303","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

Life stage impact on the human skin ecosystem: lipids and the microbial community. 生命阶段对人体皮肤生态系统的影响：脂质和微生物群落。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-13 DOI: 10.1038/s41522-025-00652-7

Martin P Pagac, Bala Davient, Luca Antonio Plado, Hilbert Yuen In Lam, Shi Mun Lee, Aarthi Ravikrishnan, Wee Ling Esther Chua, Sneha Muralidharan, Aishwarya Sridharan, Antony S Irudayaswamy, Ramasamy Srinivas, Stephen Wearne, Ahmad Nazri Mohamed Naim, Eliza Xin Pei Ho, H Q Amanda Ng, Junmei Samantha Kwah, Eileen Png, Anne K Bendt, Markus R Wenk, Federico Torta, Niranjan Nagarajan, John Common, Yap Seng Chong, Elizabeth Huiwen Tham, Lynette Pei-Chi Shek, Evelyn Xiu Ling Loo, John Chambers, Yik Weng Yew, Marie Loh, Thomas L Dawson

{"title":"Life stage impact on the human skin ecosystem: lipids and the microbial community.","authors":"Martin P Pagac, Bala Davient, Luca Antonio Plado, Hilbert Yuen In Lam, Shi Mun Lee, Aarthi Ravikrishnan, Wee Ling Esther Chua, Sneha Muralidharan, Aishwarya Sridharan, Antony S Irudayaswamy, Ramasamy Srinivas, Stephen Wearne, Ahmad Nazri Mohamed Naim, Eliza Xin Pei Ho, H Q Amanda Ng, Junmei Samantha Kwah, Eileen Png, Anne K Bendt, Markus R Wenk, Federico Torta, Niranjan Nagarajan, John Common, Yap Seng Chong, Elizabeth Huiwen Tham, Lynette Pei-Chi Shek, Evelyn Xiu Ling Loo, John Chambers, Yik Weng Yew, Marie Loh, Thomas L Dawson","doi":"10.1038/s41522-025-00652-7","DOIUrl":"10.1038/s41522-025-00652-7","url":null,"abstract":"Sebaceous free fatty acids are metabolized by multiple skin microbes into bioactive lipid mediators termed oxylipins. This study investigated correlations between skin oxylipins and microbes on the superficial skin of pre-pubescent children (N = 36) and adults (N = 100), including pre- (N = 25) and post-menopausal females (N = 25). Lipidomics and metagenomics revealed that Malassezia restricta positively correlated with the oxylipin 9,10-DiHOME on adult skin and negatively correlated with its precursor, 9,10-EpOME, on pre-pubescent skin. Co-culturing Malassezia with keratinocytes demonstrated a link between 9,10-DiHOME and pro-inflammatory cytokines IL-1β and IL-6 production. We also observed strong correlations between other skin oxylipins and microbial taxa, highlighting life stage differences in sebum production and microbial community composition. Our findings imply a complex host-microbe communication system mediated by lipid metabolism occurring on human skin, warranting further research into its role in skin health and disease and paving the way towards novel therapeutic targets and treatments.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"13"},"PeriodicalIF":7.8,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971676","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