npj Biofilms and Microbiomes最新文献

Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions. 广泛获得的抗菌素耐药细菌重组后抗生素条件下的个体微生物群落。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-14 DOI: 10.1038/s41522-025-00705-x

Jae Woo Baek, Songwon Lim, Nayeon Park, Byeongsop Song, Nikhil Kirtipal, Jens Nielsen, Adil Mardinoglu, Saeed Shoaie, Jae-Il Kim, Jang Won Son, Ara Koh, Sunjae Lee

{"title":"Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.","authors":"Jae Woo Baek, Songwon Lim, Nayeon Park, Byeongsop Song, Nikhil Kirtipal, Jens Nielsen, Adil Mardinoglu, Saeed Shoaie, Jae-Il Kim, Jang Won Son, Ara Koh, Sunjae Lee","doi":"10.1038/s41522-025-00705-x","DOIUrl":"10.1038/s41522-025-00705-x","url":null,"abstract":"In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"78"},"PeriodicalIF":7.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012787","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

SadB, a mediator of AmrZ proteolysis and biofilm development in Pseudomonas aeruginosa. 铜绿假单胞菌AmrZ蛋白水解和生物膜发育的介质SadB。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-13 DOI: 10.1038/s41522-025-00710-0

Yossi Ben-David, Michael Sporny, Yigal Brochin, Bar Piscon, Shira Roth, Itzhak Zander, Michal Nisani, Sivan Shoshani, Orly Yaron, Sarit Karako-Lampert, Ilana Lebenthal-Loinger, Amos Danielli, Yarden Opatowsky, Ehud Banin

引用次数: 0

Exploring the bioactive landscape: peptides and non-peptides from the human microbiota. 探索生物活性景观：来自人类微生物群的肽和非肽。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-08 DOI: 10.1038/s41522-025-00713-x

Abdul Bari Shah, Hyeonjae Cho, Sang Hee Shim

引用次数: 0

Analysis of biofilm assembly by large area automated AFM. 生物膜组装的大面积自动AFM分析。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-08 DOI: 10.1038/s41522-025-00704-y

Ruben Millan-Solsona, Spenser R Brown, Lance Zhang, Sita Sirisha Madugula, HuanHuan Zhao, Blythe Dumerer, Amber N Bible, Nickolay V Lavrik, Rama K Vasudevan, Arpan Biswas, Jennifer L Morrell-Falvey, Scott Retterer, Martí Checa, Liam Collins

{"title":"Analysis of biofilm assembly by large area automated AFM.","authors":"Ruben Millan-Solsona, Spenser R Brown, Lance Zhang, Sita Sirisha Madugula, HuanHuan Zhao, Blythe Dumerer, Amber N Bible, Nickolay V Lavrik, Rama K Vasudevan, Arpan Biswas, Jennifer L Morrell-Falvey, Scott Retterer, Martí Checa, Liam Collins","doi":"10.1038/s41522-025-00704-y","DOIUrl":"https://doi.org/10.1038/s41522-025-00704-y","url":null,"abstract":"Biofilms are complex microbial communities critical in medical, industrial, and environmental contexts. Understanding their assembly, structure, genetic regulation, interspecies interactions, and environmental responses is key to developing effective control and mitigation strategies. While atomic force microscopy (AFM) offers critically important high-resolution insights on structural and functional properties at the cellular and even sub-cellular level, its limited scan range and labor-intensive nature restricts the ability to link these smaller scale features to the functional macroscale organization of the films. We begin to address this limitation by introducing an automated large area AFM approach capable of capturing high-resolution images over millimeter-scale areas, aided by machine learning for seamless image stitching, cell detection, and classification. Large area AFM is shown to provide a very detailed view of spatial heterogeneity and cellular morphology during the early stages of biofilm formation which were previously obscured. Using this approach, we examined the organization of Pantoea sp. YR343 on PFOTS-treated glass surfaces. Our findings reveal a preferred cellular orientation among surface-attached cells, forming a distinctive honeycomb pattern. Detailed mapping of flagella interactions suggests that flagellar coordination plays a role in biofilm assembly beyond initial attachment. Additionally, we use large-area AFM to characterize surface modifications on silicon substrates, observing a significant reduction in bacterial density. This highlights the potential of this method for studying surface modifications to better understand and control bacterial adhesion and biofilm formation.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"75"},"PeriodicalIF":7.8,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12062311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044433","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

Oral microbiome-derived biomarkers for non-invasive diagnosis of head and neck squamous cell carcinoma. 口腔微生物来源的生物标志物用于头颈部鳞状细胞癌的非侵入性诊断。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-07 DOI: 10.1038/s41522-025-00708-8

Jingtai Zhi, Yibo Liang, Wang Zhao, Jie Qiao, Yongzhe Zheng, Xin Peng, Li Li, Xianfeng Wei, Wei Wang

{"title":"Oral microbiome-derived biomarkers for non-invasive diagnosis of head and neck squamous cell carcinoma.","authors":"Jingtai Zhi, Yibo Liang, Wang Zhao, Jie Qiao, Yongzhe Zheng, Xin Peng, Li Li, Xianfeng Wei, Wei Wang","doi":"10.1038/s41522-025-00708-8","DOIUrl":"https://doi.org/10.1038/s41522-025-00708-8","url":null,"abstract":"Mounting evidence suggests that sustained microbial dysbiosis is associated with the development of multiple cancers, while the species-level bacterial taxa and metabolic dysfunction of oral microbiome in patients with head and neck squamous cell carcinoma (HNSCC) remains unclear. In this cross-sectional study, comprehensive metagenomic and 16S rRNA amplicon sequencing analyses of oral swab samples from 172 patients were performed. Unsupervised clustering algorithms of relative microbial abundance profiles revealed three distinctive microbiome clusters. Based on the metagenomic and 16S rRNA amplicon sequencing data, machine learning-based methods were used to construct the HNSCC diagnostic classifier, which exhibited high area under the curve values of 0.78-0.89. Our study provided the first exhaustive metagenomic and 16S rRNA amplicon sequencing analyses to date, revealing that microbial-metabolic dysbiosis is a potential risk factor for HNSCC progression and therefore providing a robust theoretical basis for potential diagnostic and therapeutic strategies for HNSCC patients.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"74"},"PeriodicalIF":7.8,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12059021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002958","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

Increasing drying changes the relationship between biodiversity and ecosystem multifunctionality. 干旱加剧改变了生物多样性与生态系统多功能性之间的关系。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-06 DOI: 10.1038/s41522-025-00711-z

Chaoran Li, Jun Hou, Ming Kong, Yu Yao, Tanveer M Adyel, Jun Wu, Guoxiang You, Yue Yu, Songqi Liu, Zijun Yang, Lingzhan Miao

{"title":"Increasing drying changes the relationship between biodiversity and ecosystem multifunctionality.","authors":"Chaoran Li, Jun Hou, Ming Kong, Yu Yao, Tanveer M Adyel, Jun Wu, Guoxiang You, Yue Yu, Songqi Liu, Zijun Yang, Lingzhan Miao","doi":"10.1038/s41522-025-00711-z","DOIUrl":"https://doi.org/10.1038/s41522-025-00711-z","url":null,"abstract":"Increased drying of rivers under global climate change is leading to biodiversity loss. However, it is not clear whether biodiversity loss affects river functions. In this study, we investigated the changes in biofilm community diversity and functions in an artificial stream after different drying durations. A critical drying duration of around 60 days was found in the microbial composition and functions. Therefore, different drying durations can be divided into short-term drying (~0-20 days) and long-term drying (~60-130 days) to analyse the effect of biodiversity in terms of ecosystem functions. In summary, the dominant relationship of biodiversity on community stability got uncoupled after long-term drying. Community assembly became dominant in maintaining multifunctionality with increasing drying duration rather than biodiversity as traditionally perceived. This study reveals the importance of community assembly, extending theoretical knowledge of the relationship between biodiversity and ecosystem multifunctionality.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"72"},"PeriodicalIF":7.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12056148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022639","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

EPS inhibitor treatment of Salmonella impacts evolution without selecting for resistance to biofilm inhibition. EPS抑制剂处理沙门氏菌影响进化而不选择对生物膜抑制的抗性。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-06 DOI: 10.1038/s41522-025-00693-y

Mathieu Joos, Sybren Van Ginneken, Xabier Villanueva, Marie Dijkmans, Guglielmo A Coppola, Camilo Andres Pérez-Romero, Thijs Vackier, Erik Van der Eycken, Kathleen Marchal, Bram Lories, Hans P Steenackers

{"title":"EPS inhibitor treatment of Salmonella impacts evolution without selecting for resistance to biofilm inhibition.","authors":"Mathieu Joos, Sybren Van Ginneken, Xabier Villanueva, Marie Dijkmans, Guglielmo A Coppola, Camilo Andres Pérez-Romero, Thijs Vackier, Erik Van der Eycken, Kathleen Marchal, Bram Lories, Hans P Steenackers","doi":"10.1038/s41522-025-00693-y","DOIUrl":"https://doi.org/10.1038/s41522-025-00693-y","url":null,"abstract":"Virulence factors of pathogens, such as toxin production and biofilm formation, often exhibit a public character, providing benefits to nearby non-producers. Consequently, anti-virulence drugs targeting these public traits may not select for resistance, as resistant mutants that resume production of the virulence factor share the benefits of their resistance with surrounding sensitive cells. In agreement with this, we show that even after long-term treatment with a 2-amino-imidazole (2-AI) biofilm inhibitor, Salmonella populations remained as susceptible to biofilm inhibition as the ancestral populations. Nonetheless, further genotypic and phenotypic analysis revealed that the Salmonella populations did adapt to the treatment and accumulated mutations in efflux pump regulators and alternative sigma factors. These mutations resulted in a reduced biofilm-forming capacity and increased efflux activity. Their selection was due to a growth delaying side effect of the biofilm inhibitor. Enhanced efflux activity helped overcome this growth delay, providing a fitness advantage over the ancestor. Finally, we demonstrate that chemical modification of the inhibitor enhances its specificity by partially alleviating the unintended growth delay while retaining the anti-biofilm activity, which in turn eliminated the selection pressure for increased efflux. Overall, our findings highlight that while unintended side effects can complicate anti-virulence strategies, adaptation to these effects does not necessarily restore the inhibited virulence trait. Moreover, chemical modification can mitigate these unintended side effects and enhance drug specificity.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"73"},"PeriodicalIF":7.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12056028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029664","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

Oral microbiota signature predicts the prognosis of colorectal carcinoma. 口腔微生物群特征预测结直肠癌的预后。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-05 DOI: 10.1038/s41522-025-00702-0

Shi-Hao Zhou, Yan Du, Wen-Qiong Xue, Min-Jun He, Ting Zhou, Zhi-Yang Zhao, Lu Pei, Yi-Wei Chen, Jin-Ru Xie, Chang-Ling Huang, Yong-Qiao He, Tong-Min Wang, Ying Liao, Wei-Hua Jia

{"title":"Oral microbiota signature predicts the prognosis of colorectal carcinoma.","authors":"Shi-Hao Zhou, Yan Du, Wen-Qiong Xue, Min-Jun He, Ting Zhou, Zhi-Yang Zhao, Lu Pei, Yi-Wei Chen, Jin-Ru Xie, Chang-Ling Huang, Yong-Qiao He, Tong-Min Wang, Ying Liao, Wei-Hua Jia","doi":"10.1038/s41522-025-00702-0","DOIUrl":"https://doi.org/10.1038/s41522-025-00702-0","url":null,"abstract":"Emerging evidence links oral-derived gut microbes to colorectal cancer (CRC) development, but CRC prognosis-related microbial alterations in oral remain underexplored. In a retrospective study of 312 CRC patients, we examined the oral microbiota using 16S rRNA gene full-length amplicon sequencing to identify prognostic microbial biomarkers for CRC. Neisseria oralis and Campylobacter gracilis increased CRC progression risk (HR = 2.63 with P = 0.007, HR = 2.27 with P = 0.001, respectively), while Treponema medium showed protective effects (HR = 0.41, P = 0.0002). A microbial risk score (MRS) incorporating these species effectively predicted CRC progression risk (C-index = 0.68, 95% CI = 0.61-0.76). When compared to a model constructed solely from clinical factors, including tumor stage, lymphatic metastasis, and perineural invasion, the predictive accuracy significantly improved with the addition of the MRS, resulting in a C-index rising to 0.77 (P = 2.33 × 10-5). Our findings suggest that oral microbiota biomarkers may contribute to personalized CRC monitoring strategies, their implementation in clinical surveillance necessitates confirmatory studies.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"71"},"PeriodicalIF":7.8,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144003224","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

Dynamics of gut colonization by commensal and pathogenic bacteria that attach to the intestinal epithelium. 附着在肠上皮上的共生细菌和致病菌的肠道定植动力学。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-03 DOI: 10.1038/s41522-025-00696-9

Dalaena E Rivera, Kayla Poirier, Samuel Moore, Ophélie Nicolle, Emily Morgan, Jonah Faye Longares, Anupama Singh, Grégoire Michaux, Marie-Anne Félix, Robert J Luallen

{"title":"Dynamics of gut colonization by commensal and pathogenic bacteria that attach to the intestinal epithelium.","authors":"Dalaena E Rivera, Kayla Poirier, Samuel Moore, Ophélie Nicolle, Emily Morgan, Jonah Faye Longares, Anupama Singh, Grégoire Michaux, Marie-Anne Félix, Robert J Luallen","doi":"10.1038/s41522-025-00696-9","DOIUrl":"https://doi.org/10.1038/s41522-025-00696-9","url":null,"abstract":"Bacterial adherence to the intestinal epithelium plays a role in niche establishment in the gut lumen. Through sampling natural populations of Caenorhabditis, we discovered several bacterial species that adhere to the intestinal epithelium via polar, intimate association, best described as attachment. These bacteria had varying effects on host fitness and physiology, with one species having negative effects, and the others exhibiting neutral effects. These bacteria can actively divide in the gut lumen, either replicating throughout the gut simultaneously or anteroposteriorly. In competition assays, animals pre-colonized with an attaching commensal bacteria reduced colonization by the pathogenic bacteria, but this effect was not seen when animals were colonized by both species simultaneously. Regardless of the colonization paradigm, populations exposed to both bacteria showed a near-identical mitigation of the pathogenic effects. Altogether, these strains illustrate the capacity of microbiome bacteria to attach, replicate, and establish a niche across the entire intestinal lumen.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"70"},"PeriodicalIF":7.8,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12049552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144038432","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

Nitrate supplementation affects taste by changing the oral metabolome and microbiome. 硝酸盐补充剂通过改变口腔代谢组和微生物组来影响味觉。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-02 DOI: 10.1038/s41522-025-00689-8

Shuyuan Zhang, Frederick Clasen, Haizhuang Cai, Thuy Do, Saeed Shoaie, Guy H Carpenter

{"title":"Nitrate supplementation affects taste by changing the oral metabolome and microbiome.","authors":"Shuyuan Zhang, Frederick Clasen, Haizhuang Cai, Thuy Do, Saeed Shoaie, Guy H Carpenter","doi":"10.1038/s41522-025-00689-8","DOIUrl":"https://doi.org/10.1038/s41522-025-00689-8","url":null,"abstract":"Nitrate, an inorganic anion found in various foods is also present in saliva and has emerged as a potential prebiotic for the oral microbiome. Salivary glands concentrate nitrate from the bloodstream and release it into the oral cavity via the anion transporter sialin SLC17A5. In previous studies dietary nitrate supplementation altered oral bacteria composition, favouring genera like Rothia and Neisseria while reducing Streptococcus, Veillonella, Prevotella, and Actinomyces. The present study hypothesized that taste intensity might adapt to changes in the oral microbiome caused by nitrate supplementation. Participants underwent taste tests before, during, and after supplementation. All subjects showed greater levels of salivary nitrate during supplementation and had higher levels of Neisseria compared to before. Subjects were then grouped according to taste tests (before vs. during) as responders (ANOVA p < 0.05, n = 7), and non-responders (ANOVA p > 0.05, n = 6) and their salivary metabolome and oral microbiome further analysed. Responders had significantly less 5-amino pentanoate, formate, propionate and butyrate in saliva while non-responders showed no metabolite changes between before and during supplementation. In contrast, non-responders had increased Capnocytophaga gingivalis and altered lysosomal degradation pathways. Overall, nitrate supplementation shifted the oral microbiome composition in all subjects and when taste intensity was altered this correlated to bacteria-derived short-chain fatty acid production. This suggests taste perception is affected by the oral microbiome.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"69"},"PeriodicalIF":7.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12048645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144030351","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