npj Biofilms and Microbiomes最新文献_第3页

Genome-resolved discovery of Candidatus Vitaminotrophota reveals carbon fixation and multi-vitamin biosynthetic potential in hot springs. 基因组解析的发现揭示了温泉中的碳固定和多种维生素的生物合成潜力。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-13 DOI: 10.1038/s41522-026-01093-6

Yuan-Guo Xie, Xing-Ru Cao, Yan-Ling Qi, Lei Chen, Yan-Huan Mao, Yang Li, Ci-Jian Wang, Ze-Wei Li, Yan-Ni Qu, Wen-Jun Li, Zheng-Shuang Hua

{"title":"Genome-resolved discovery of Candidatus Vitaminotrophota reveals carbon fixation and multi-vitamin biosynthetic potential in hot springs.","authors":"Yuan-Guo Xie, Xing-Ru Cao, Yan-Ling Qi, Lei Chen, Yan-Huan Mao, Yang Li, Ci-Jian Wang, Ze-Wei Li, Yan-Ni Qu, Wen-Jun Li, Zheng-Shuang Hua","doi":"10.1038/s41522-026-01093-6","DOIUrl":"https://doi.org/10.1038/s41522-026-01093-6","url":null,"abstract":"Geothermal environments harbor abundant microbial diversity, yet rare lineages remain poorly resolved, limiting understanding of ecosystem function and evolutionary innovation under energy limitation. Here, we describe Candidatus Vitaminotrophota, a previously unrecognized bacterial phylum represented by 35 metagenome-assembled genomes (MAGs) from Tengchong hot spring sediments, China. Phylogenomic analyses support a coherent internal taxonomy comprising one order, two families and four candidate genera. Metabolic reconstruction indicates a predominantly anaerobic, mixotrophic lifestyle, with widespread carbon fixation potential via the Wood-Ljungdahl pathway and a noncanonical CODH/ACS architecture featuring divergent acsA paralogs. Nitrogenase structural genes (nifHDK) occur in two genera, suggesting diazotrophic potential in part of the lineage. All MAGs encode complete or near-complete cobalamin and pantothenate biosynthesis pathways, and most retain conserved thiamine pathway components, alongside transport systems consistent with corrinoid and metal acquisition. Ca. Vitaminotrophota dominated community-level cobalamin biosynthetic potential in several samples, reaching 99.11% and accounting for >50% in nearly half of the samples. Conserved flagellar and chemotaxis gene sets suggest capacity to navigate steep physicochemical gradients. These findings expand the phylogenetic and functional landscape of geothermal bacteria and identify Ca. Vitaminotrophota as a candidate contributor to carbon fixation and vitamin-mediated metabolic interactions in nutrient-limited hot springs.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437511","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 rugged life: how host-microbiome adaptations associated with the semi-feral lifestyle of gayal (Bos frontalis). 崎岖的生活：寄主-微生物群的适应如何与半野生的生活方式相关联。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-11 DOI: 10.1038/s41522-026-01095-4

Yuming Chen, Juntao Ma, Zhifan Guo, Junren Chen, Xiaonan Wang, Jian Xiao, Dexiang Hu, Jifan Yan, Weidong Deng, Zhizhong Nu, Husheng He, Wenliang He, Jing Luo, Ya-Ping Zhang, Yan Li

{"title":"A rugged life: how host-microbiome adaptations associated with the semi-feral lifestyle of gayal (Bos frontalis).","authors":"Yuming Chen, Juntao Ma, Zhifan Guo, Junren Chen, Xiaonan Wang, Jian Xiao, Dexiang Hu, Jifan Yan, Weidong Deng, Zhizhong Nu, Husheng He, Wenliang He, Jing Luo, Ya-Ping Zhang, Yan Li","doi":"10.1038/s41522-026-01095-4","DOIUrl":"https://doi.org/10.1038/s41522-026-01095-4","url":null,"abstract":"The semi-domesticated gayal (Bos frontalis) is an endangered browsing ruminant inhabiting the rugged Eastern Himalayan foothills, and maintains an energy-intensive lifestyle on nutrient-poor, fiber-rich feed. However, the dietary, microbial, and host physiological features underlying this adaptation remain poorly understood. Here, we analyzed fecal metagenomes from ten bovine populations (n = 334) to characterize dietary composition. Then we profiled the four-chambered (FC) stomach microbiome in adult gayal (Bos frontalis), yak (Bos grunniens), and taurine cattle (Bos taurus). Host transcriptomes were profiled across the FC stomach in adult individuals from gayal, yak and cattle. Dietary analysis revealed a woody plant-dominated, bamboo-rich dietary pattern in gayal. Gastric metagenomes in gayal showed high population-level microbial diversity, pronounced individual-associated community structure, and functional potentials related to aromatic compound transformation, nitrogen metabolism, and metabolic flexibility. Transcriptomes revealed compartment-specific specialization in the gayal stomach, including rumen immune signatures and reticulum contractile/electrophysiological features. Exploratory compartment-level integration further suggested possible consistency between host transcriptomic features and microbial functional potential. Together, these multi-omics findings suggest a host-microbiome system potentially associated with the utilization of chemically complex, low-quality forage, providing a framework for understanding digestive features of browsing ruminants and for conserving host-associated gastrointestinal microbiomes.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422934","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

Lactiplantibacillus plantarum promotes intestinal goblet cell differentiation via indole-3-lactic acid-AHR signaling in pigs. 植物乳杆菌通过吲哚-3-乳酸- ahr信号通路促进猪肠杯状细胞分化。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-11 DOI: 10.1038/s41522-026-01085-6

Ziyu Liu, Haiqin Wu, Samantha Howe, Bin Zuo, Yang Tian, Xiaofan Wang, Hailemariam Abrha Assress, Renny Shang-Lun Lan, Chunlong Mu, Yingping Xiao, Yan Huang, Michael Looper, Tsungcheng Tsai, Jiangchao Zhao

{"title":"Lactiplantibacillus plantarum promotes intestinal goblet cell differentiation via indole-3-lactic acid-AHR signaling in pigs.","authors":"Ziyu Liu, Haiqin Wu, Samantha Howe, Bin Zuo, Yang Tian, Xiaofan Wang, Hailemariam Abrha Assress, Renny Shang-Lun Lan, Chunlong Mu, Yingping Xiao, Yan Huang, Michael Looper, Tsungcheng Tsai, Jiangchao Zhao","doi":"10.1038/s41522-026-01085-6","DOIUrl":"https://doi.org/10.1038/s41522-026-01085-6","url":null,"abstract":"The swine intestinal microbiota dynamically remodels during development and supports gut homeostasis. However, whether stage-specific microbial shifts, are associated with epithelial development remains poorly understood. Here, longitudinal metagenomic profiling of the swine gut microbiome identified Lactiplantibacillus plantarum as a transiently enriched nursery-stage bacterium positively associated with goblet cell numbers. Dietary supplementation with L. plantarum validated this association, showing increased goblet cell numbers and MUC2 expression in the ileum of nursery piglets. Co-culture with porcine ileum organoids further demonstrated that L. plantarum cell-free supernatant promoted ileal organoid growth and goblet cell differentiation. Integrated untargeted metabolomic analyses of ileal samples and bacterial culture supernatants identified indole-3-lactic acid (ILA) as a potential key microbial metabolite from L. plantarum. Mechanistically, ILA promoted intestinal stem cell proliferation and MUC2 expression, accompanied by increased expression of aryl hydrocarbon receptor (AHR) and its downstream target CYP1A1 in ileal organoids. Consistently, activation of AHR using FICZ increased MUC2 expression, whereas inhibition with CH-223191 suppressed MUC2 expression in ileal organoids. Collectively, these findings uncover a L. plantarum-ILA-AHR signaling axis that promotes intestinal goblet cell differentiation, providing mechanistic insight into microbial metabolite-mediated regulation of epithelial homeostasis during post-weaning period in pigs.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422967","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

Uncovering microbial life-history strategies under disturbance: a trait-based computational analysis of anaerobic systems. 揭示扰动下的微生物生活史策略：厌氧系统的基于特性的计算分析。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-10 DOI: 10.1038/s41522-026-01067-8

Soheil A Neshat, Ezequiel Santillan, Stefan Wuertz

{"title":"Uncovering microbial life-history strategies under disturbance: a trait-based computational analysis of anaerobic systems.","authors":"Soheil A Neshat, Ezequiel Santillan, Stefan Wuertz","doi":"10.1038/s41522-026-01067-8","DOIUrl":"https://doi.org/10.1038/s41522-026-01067-8","url":null,"abstract":"Trait-based approaches are helpful in simplifying ecosystem complexity to explore disturbance-diversity-function relationships. These frameworks classify organisms based on their functional characteristics-traits that influence growth, survival and reproduction-providing a mechanistic basis to understand how communities respond to changes in their environment. The application of these approaches has been successful in ecology, but to date has only been tested in a few microbial ecosystems, namely, soil microbial communities and aerobic bioreactors treating wastewater. Here, we employed Grime's competitor-stress-tolerant-ruderal framework in replicated mesophilic anaerobic bioreactors exposed to a disturbance (biomass removal) with varied frequencies at a constant number of disturbance events for 90 days. Bioreactors were inoculated with sludge from full-scale anaerobic digesters and fed with a mixture of primary and waste activated sludge. A genome-resolved metagenomics approach was utilised to assess the microbial communities in terms of composition and functional potential. We found that communities across the disturbance range were clustered into three groups, suggesting the adoption of a three-way life-history strategy. This study demonstrates, for the first time, the applicability of trait-based life-history strategies in anaerobic microbial systems under disturbance using genome-resolved techniques, providing a new perspective for understanding and managing microbial ecosystems under disturbance conditions.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422987","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

The Cat Gut Microbial Genome Collection reveals global structure of the feline gut microbiome. 猫肠道微生物基因组收集揭示了猫肠道微生物组的全球结构。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-09 DOI: 10.1038/s41522-026-01088-3

Zhixin Lei, Hengming Liu, Yue Zhang, Xiaobo Li, Chenghaotian Xiao, Guorui Xing, Ruochun Guo, Yidi Zhang, Jie Xu, Wei Yang, Huixiang Chen, Min Li, Tong Lu, Shenghui Li, Yaping Lu, Qiulong Yan

{"title":"The Cat Gut Microbial Genome Collection reveals global structure of the feline gut microbiome.","authors":"Zhixin Lei, Hengming Liu, Yue Zhang, Xiaobo Li, Chenghaotian Xiao, Guorui Xing, Ruochun Guo, Yidi Zhang, Jie Xu, Wei Yang, Huixiang Chen, Min Li, Tong Lu, Shenghui Li, Yaping Lu, Qiulong Yan","doi":"10.1038/s41522-026-01088-3","DOIUrl":"https://doi.org/10.1038/s41522-026-01088-3","url":null,"abstract":"The gut microbiome is a critical determinant of mammalian health, yet our understanding is largely derived from humans and laboratory models. The ecological principles governing the microbiome of globally important companion animals, such as cats, remain poorly defined. We generated the Cat Gut Microbial Genome Collection (CGMGC), a comprehensive resource encompassing over 40,000 microbial genomes. This collection spans 874 prokaryotic species, 6 fungal species, and 5543 viral operational taxonomic units, derived from feline gut samples across diverse geographical regions. Our analysis reveals that the cat gut microbiome is a highly host-specific ecosystem whose structure is primarily driven by geography rather than host genetics or diet. Over 50% of the identified prokaryotic species are unique to felines and contain novel taxonomic lineages. Functionally, the virome encodes a vast repertoire of auxiliary metabolic genes, indicating pervasive inter-kingdom control over bacterial hosts. Surprisingly, the feline gut shares significantly more microbial species with humans than with laboratory mice, suggesting convergent evolution in cohabiting species. The core ecological principles of the feline gut are profound host-specificity, geographic structuring, and pervasive viral modulation of bacterial function. This work redefines the feline microbiome as a unique model for host-microbe co-evolution and establishes a genomic foundation for a new era of evidence-based veterinary medicine.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422965","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

Maternal cold exposure improves offspring metabolic health via a milk lithocholic acid-microbiota-Th17 axis. 母体低温暴露通过乳石胆酸-微生物群- th17轴改善子代代谢健康。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-09 DOI: 10.1038/s41522-026-01092-7

Xuejie Han, Hui Yu, Qianhui Gao, Dongze Li, Linwei Zhang, Qi Kang, Chaowen Sui, Qian Zhao, Xuanrui Ji, Hanwen Liu, Yuchen Wang, Changming Zhao, Shuting Li, Li Sun, Yun Zhang, Yue Li

{"title":"Maternal cold exposure improves offspring metabolic health via a milk lithocholic acid-microbiota-Th17 axis.","authors":"Xuejie Han, Hui Yu, Qianhui Gao, Dongze Li, Linwei Zhang, Qi Kang, Chaowen Sui, Qian Zhao, Xuanrui Ji, Hanwen Liu, Yuchen Wang, Changming Zhao, Shuting Li, Li Sun, Yun Zhang, Yue Li","doi":"10.1038/s41522-026-01092-7","DOIUrl":"https://doi.org/10.1038/s41522-026-01092-7","url":null,"abstract":"Metabolic diseases are rising with a trend toward earlier onset, yet effective preventive strategies remain limited. While cold exposure improves metabolic health in adults, its role during pregnancy in shaping offspring metabolic outcomes remains unknown. Herein, we demonstrate that maternal cold exposure in early pregnancy markedly improved offspring glucose tolerance, insulin sensitivity, and hepatic lipid metabolism when challenged with a Western diet, and the benefits persisted into late adulthood. Transcriptomic and immunophenotyping analyses revealed that offspring with cold-exposed dams exhibited suppressed Th17 activity and IL-17 signaling. Cross-fostering and metabolomics identified elevated lithocholic acid (LCA) in maternal milk as a critical mediator of these effects. LCA supplementation recapitulates these benefits through gut microbiota-dependent conversion to 3-oxo-LCA. Furthermore, Clostridium scindens supplementation enhanced 3-oxo-LCA production, suppressed Th17 responses, and alleviated diet-induced hepatic steatosis. Clinically, analysis of the UK Biobank cohort showed that winter conception was associated with a lower risk of metabolic dysfunction-associated steatotic liver disease in offspring. A similar association was observed in the CHARLS cohort in colder northern China. Together, these results identify a maternal cold-microbiota-bile acid-Th17 axis that programs offspring metabolic health and highlight microbial bile acid metabolism as a potential therapeutic target for metabolic diseases.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422952","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

MicroICS: predictive phenotyping of Listeria monocytogenes biofilms from three-dimensional structural features. MicroICS：从三维结构特征预测单核增生李斯特菌生物膜的表型。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-08 DOI: 10.1038/s41522-026-01083-8

Nika Janež, Blaž Škrlj, Aljaž Osojnik, Márta Ladányi, Martin Breskvar, Matej Petković, Boštjan Kokot, Petra Čotar, Bojan Papić, Majda Golob, Tjaša Peternel, Jerica Sabotič

{"title":"MicroICS: predictive phenotyping of Listeria monocytogenes biofilms from three-dimensional structural features.","authors":"Nika Janež, Blaž Škrlj, Aljaž Osojnik, Márta Ladányi, Martin Breskvar, Matej Petković, Boštjan Kokot, Petra Čotar, Bojan Papić, Majda Golob, Tjaša Peternel, Jerica Sabotič","doi":"10.1038/s41522-026-01083-8","DOIUrl":"https://doi.org/10.1038/s41522-026-01083-8","url":null,"abstract":"Biofilms underpin microbial survival, yet their three-dimensional structure remains difficult to quantify systematically. We present the Microbial Image Classification Suite (MicroICS), an open-source framework for predictive phenotyping of microbial communities from 3D biofilm images. MicroICS consists of three independent but interoperable modules: feature extraction from 3D biofilm images, machine learning-based classification, and an inference module for applying trained models to new, unseen images. Each module can be run independently, and the classification module accepts externally generated features, enabling integration with existing quantitative image analysis tools. As a pilot study, we demonstrate the framework using eight epidemiologically diverse Listeria monocytogenes strains, with strain differentiation and trait-based grouping as proof-of-principle tasks. MicroICS extracted over 2,700 quantitative structural features from Syto 9-labelled biofilm images. An optimised random forest model achieved human baseline-level accuracy in strain classification on previously unseen images, including biofilms experimentally perturbed by food extracts. BiofilmQ-derived features incorporated into the classification module yielded higher accuracy with fewer features than either tool alone, confirming the framework's extensibility. Extending the framework to clonal complex-based clinical grouping demonstrates utility beyond strain identity. MicroICS is applicable to any organism or condition for which suitable 3D biofilm images can be obtained.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148412420","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

Periodontitis aggravates bone loss through gut microbiota alterations in ovariectomized mice. 在去卵巢小鼠中，牙周炎通过肠道菌群改变加重骨质流失。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-08 DOI: 10.1038/s41522-026-01084-7

Hua Nie, Nannan Wang, Haowei Mao, Yuan Wei, Jun Qian, Rixin Chen, Qiao Yuan, Yin Xiao, Li Zhang, Fuhua Yan

{"title":"Periodontitis aggravates bone loss through gut microbiota alterations in ovariectomized mice.","authors":"Hua Nie, Nannan Wang, Haowei Mao, Yuan Wei, Jun Qian, Rixin Chen, Qiao Yuan, Yin Xiao, Li Zhang, Fuhua Yan","doi":"10.1038/s41522-026-01084-7","DOIUrl":"https://doi.org/10.1038/s41522-026-01084-7","url":null,"abstract":"Epidemiological evidence suggests a bidirectional relationship between periodontitis and osteoporosis, yet the underlying mechanisms remain unclear. In this study, using a mouse model combining ovariectomy-induced osteoporosis and ligature-induced periodontitis, we demonstrated that periodontitis significantly aggravated both alveolar and femoral bone loss, impaired intestinal barrier integrity, and elevated systemic inflammation. Gut microbiota and metabolomic analyses revealed that periodontitis induced distinct alterations in gut microbial composition and intestinal metabolic profiles, potentially contributing to systemic inflammation and bone metabolic dysregulation. Furthermore, fecal microbiota transplantation demonstrated that gut microbiota from periodontitis donors aggravated bone loss and inflammation in recipient mice, whereas microbiota from donors that received periodontal treatment partially alleviated inflammatory responses and skeletal deterioration. Collectively, these findings suggest that periodontitis may aggravate osteoporosis via gut microbiota-mediated mechanisms, highlighting the importance of maintaining oral health to mitigate the adverse impact of periodontitis on systemic bone metabolism.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148412428","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

Role of starvation survival response mechanisms on ribosome integrity, antibiotic tolerances, and virulence of Pseudomonas aeruginosa biofilms. 饥饿生存反应机制对铜绿假单胞菌生物膜核糖体完整性、抗生素耐受性和毒力的影响。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-08 DOI: 10.1038/s41522-026-01061-0

Kerry S Williamson, Michael J Franklin

{"title":"Role of starvation survival response mechanisms on ribosome integrity, antibiotic tolerances, and virulence of Pseudomonas aeruginosa biofilms.","authors":"Kerry S Williamson, Michael J Franklin","doi":"10.1038/s41522-026-01061-0","DOIUrl":"10.1038/s41522-026-01061-0","url":null,"abstract":"Bacterial biofilms contain physiologically diverse subpopulations of cells, including cells that are nutrient stressed or dormant. We determined how two dormancy pathways, ribosome hibernation and the stringent response, contribute to the survival and antibiotic tolerance of Pseudomonas aeruginosa biofilms. Analyses of whole biofilms and single cells showed that these pathways have differing effects on biofilm cell physiology. Ribosome hibernation, mediated by hibernation promoting factor (HPF), is essential for optimal survival and resuscitation of starved biofilm cells. In the absence of HPF, starved cells progressively lose ribosome integrity. However, loss of HPF does not increase the sensitivity of P. aeruginosa biofilm cells to ciprofloxacin or tobramycin. In contrast, the stringent response, mediated by RelA and SpoT, is not required for viability or ribosome integrity in starved biofilm cells, but does affect biofilm antibiotic tolerance. In a plant model of biofilm infection, disruption of either ribosome hibernation or the stringent response reduced bacterial virulence. The results show that ribosome hibernation preserves ribosomal integrity necessary for recovery from starvation and for pathogenesis, while the stringent response is required for growth arrest, antibiotic tolerance, and pathogenesis. These two ribosome-mediated pathways play distinct yet complementary roles in regulating dormancy and persistence of P. aeruginosa biofilms.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13503843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405287","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

Dissection of mammary cell landscape in ruminal dysbiosis-induced mastitis by single-cell RNA sequencing. 单细胞RNA测序分析瘤胃生态失调性乳腺炎乳腺细胞景观。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-07 DOI: 10.1038/s41522-026-01076-7

Caijun Zhao, Zhuohan Li, Miao Liu, Lijuan Bao, Chongshan Yuan, Yihong Zhao, Keyi Wu, Min Qiu, Yuhong He, Naisheng Zhang, Xiaoyu Hu, Yun Zhang, Fanglei Han, Yunhe Fu

{"title":"Dissection of mammary cell landscape in ruminal dysbiosis-induced mastitis by single-cell RNA sequencing.","authors":"Caijun Zhao, Zhuohan Li, Miao Liu, Lijuan Bao, Chongshan Yuan, Yihong Zhao, Keyi Wu, Min Qiu, Yuhong He, Naisheng Zhang, Xiaoyu Hu, Yun Zhang, Fanglei Han, Yunhe Fu","doi":"10.1038/s41522-026-01076-7","DOIUrl":"https://doi.org/10.1038/s41522-026-01076-7","url":null,"abstract":"Growing evidence has underscored the contribution of gastrointestinal dysbiosis to the onset of mastitis, however, the local cellular changes responsible for the pathological processes of ruminal dysbiosis-induced mastitis (RDIM) are still unclear. Here, we profiled mammary single-cell transcriptomes in goats with RDIM, complemented by ruminal metagenomic and untargeted metabolomic analyses of rumen fluid and serum. Our results indicated that compromised lactation and barrier integrity in LumSec were linked to RDIM. Increased inflammatory macrophages and DCs, γδT and CD4+ TH cell populations, along with reduced Tex/Treg and B cells were implicated in RDIM. Fibroblasts exhibited increased gene expression related to the extracellular matrix, while lymphatic endothelial cells and Vas-venous structures displayed elevated inflammatory gene expression. Tight junction integrity and apelin signaling pathways were compromised in Vas-capillary during RDIM. Notably, metagenomic analysis indicated that RDIM correlated with reduced ruminal microbial diversity and shifts in microbial community composition. Key metabolic pathways including microbial tryptophan metabolism, secondary bile acid biosynthesis, and vitamin metabolism were significantly diminished during RDIM. Furthermore, tryptophan-induced AHR signaling and secondary bile acid receptor GPBAR1, primarily expressed in vascular endothelial cells and macrophages, respectively, which were reduced during RDIM. Collectively, our study provides a comprehensive atlas of mammary cell landscapes in RDIM, which may enhance the understanding of mastitis pathogenesis.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405308","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