npj Biofilms and Microbiomes最新文献_第2页

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

Hypermutability bypasses genetic constraints in SCV phenotypic switching in Pseudomonas aeruginosa biofilms. 铜绿假单胞菌生物膜中SCV表型转换的超易变性绕过遗传限制。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-13 DOI: 10.1038/s41522-024-00644-z

Romina A Tobares, Román A Martino, Claudia A Colque, Gaston L Castillo Moro, Alejandro J Moyano, Andrea G Albarracín Orio, Andrea M Smania

{"title":"Hypermutability bypasses genetic constraints in SCV phenotypic switching in Pseudomonas aeruginosa biofilms.","authors":"Romina A Tobares, Román A Martino, Claudia A Colque, Gaston L Castillo Moro, Alejandro J Moyano, Andrea G Albarracín Orio, Andrea M Smania","doi":"10.1038/s41522-024-00644-z","DOIUrl":"10.1038/s41522-024-00644-z","url":null,"abstract":"Biofilms are critical in the persistence of Pseudomonas aeruginosa infections, particularly in cystic fibrosis patients. This study explores the adaptive mechanisms behind the phenotypic switching between Small Colony Variants (SCVs) and revertant states in P. aeruginosa biofilms, emphasizing hypermutability due to Mismatch Repair System (MRS) deficiencies. Through experimental evolution and whole-genome sequencing, we show that both wild-type and mutator strains undergo parallel evolution by accumulating compensatory mutations in factors regulating intracellular c-di-GMP levels, particularly in the Wsp and Yfi systems. While wild-type strains face genetic constraints, mutator strains bypass these by accessing alternative genetic pathways regulating c-di-GMP and biofilm formation. This increased genetic accessibility, driven by higher mutation rates and specific mutational biases, supports sustained cycles of SCV conversion and reversion. Our findings underscore the crucial role of hypermutability in P. aeruginosa adaptation, with significant implications for managing persistent infections in clinical settings.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"14"},"PeriodicalIF":7.8,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979451","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

High interindividual variability of indoxyl sulfate production identified by an oral tryptophan challenge test. 通过口服色氨酸激发试验确定的硫酸吲哚酚生产的高个体间变异性。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-13 DOI: 10.1038/s41522-025-00651-8

Ting-Yun Lin, Wei-Kai Wu, Szu-Chun Hung

{"title":"High interindividual variability of indoxyl sulfate production identified by an oral tryptophan challenge test.","authors":"Ting-Yun Lin, Wei-Kai Wu, Szu-Chun Hung","doi":"10.1038/s41522-025-00651-8","DOIUrl":"10.1038/s41522-025-00651-8","url":null,"abstract":"Indoxyl sulfate (IS) has been implicated in the pathogenesis of cardiovascular diseases. IS is converted from indole, a metabolite of dietary tryptophan through the action of gut microbial tryptophanase, by two hepatic enzymes: CYP2E1 and SULT1A1. We hypothesized that the effect of tryptophan intake on IS production might differ from person to person. We enrolled 72 healthy persons (33 ± 7 years; 54.2% women) to undergo an oral tryptophan challenge test (OTCT), in which 7 blood samples were collected at 0, 4, 8, 12, 24, 36, and 48 h following oral administration of L-tryptophan 2000 mg. We observed high interindividual variability of IS production in the response to an OTCT. Twenty-four subjects in the lowest tertile of the baseline-adjusted area under the curve of IS were defined as low-IS producers, whereas 24 subjects in the highest tertile were defined as high-IS producers. There was no significant difference in baseline characteristics or CYP2E1 and SULT1A1-SNP genotyping distributions between the two IS-producing phenotypes. However, distinct differences in gut microbial composition were identified. In addition, the abundance of tryptophanase was significantly higher in the high-IS producers than in the low-IS producers (P = 0.01). The OTCT may serve as personalized dietary guidance. High-IS producers are more likely to be at greater risk of cardiovascular diseases and may benefit from consuming foods low in tryptophan. Potential clinical applications of the OTCT in precision nutrition warrant further investigation.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"15"},"PeriodicalIF":7.8,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979448","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 oral-gut microbiota axis: a link in cardiometabolic diseases. 口腔-肠道微生物群轴：心脏代谢疾病的一个环节。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-10 DOI: 10.1038/s41522-025-00646-5

Qian Xu, Wenting Wang, Yiwen Li, Jing Cui, Mengmeng Zhu, Yanfei Liu, Yue Liu

引用次数: 0

Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis. 肠道微生物调节类黄酮槲皮素对动脉粥样硬化的影响。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-10 DOI: 10.1038/s41522-024-00626-1

Kazuyuki Kasahara, Robert L Kerby, Ruben Aquino-Martinez, Abigail H Evered, Tzu-Wen L Cross, Jessica Everhart, Tyler K Ulland, Colin D Kay, Bradley W Bolling, Fredrik Bäckhed, Federico E Rey

{"title":"Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis.","authors":"Kazuyuki Kasahara, Robert L Kerby, Ruben Aquino-Martinez, Abigail H Evered, Tzu-Wen L Cross, Jessica Everhart, Tyler K Ulland, Colin D Kay, Bradley W Bolling, Fredrik Bäckhed, Federico E Rey","doi":"10.1038/s41522-024-00626-1","DOIUrl":"10.1038/s41522-024-00626-1","url":null,"abstract":"Gut bacterial metabolism of dietary flavonoids results in the production of a variety of phenolic acids, whose contributions to health remain poorly understood. Here, we show that supplementation with the commonly consumed flavonoid quercetin impacted gut microbiome composition and resulted in a significant reduction in atherosclerosis burden in conventionally raised (ConvR) Apolipoprotein E (ApoE) knockout (KO) mice but not in germ-free (GF) ApoE KO mice. Metabolomic analysis revealed that consumption of quercetin significantly increased plasma levels of benzoylglutamic acid, 3,4 dihydroxybenzoic acid (3,4-DHBA) and its sulfate-conjugated form in ConvR mice, but not in GF mice supplemented with the flavonoid. Levels of these metabolites were negatively associated with atherosclerosis burden. Furthermore, we show that 3,4-DHBA prevented lipopolysaccharide (LPS)-induced decrease in transendothelial electrical resistance (TEER). These results suggest that the effects of quercetin on atherosclerosis are influenced by gut microbes and are potentially mediated by bacterial metabolites derived from the flavonoid.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"12"},"PeriodicalIF":7.8,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11723976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142966150","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