npj Biofilms and Microbiomes最新文献_第6页

DJK-5, an anti-biofilm peptide, increases Staphylococcus aureus sensitivity to colistin killing in co-biofilms with Pseudomonas aeruginosa. DJK-5是一种抗生物膜肽，在与铜绿假单胞菌共生物膜中增加金黄色葡萄球菌对粘菌素杀伤的敏感性。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-08 DOI: 10.1038/s41522-024-00637-y

Samuel J T Wardell, Deborah B Y Yung, Anupriya Gupta, Mihnea Bostina, Joerg Overhage, Robert E W Hancock, Daniel Pletzer

{"title":"DJK-5, an anti-biofilm peptide, increases Staphylococcus aureus sensitivity to colistin killing in co-biofilms with Pseudomonas aeruginosa.","authors":"Samuel J T Wardell, Deborah B Y Yung, Anupriya Gupta, Mihnea Bostina, Joerg Overhage, Robert E W Hancock, Daniel Pletzer","doi":"10.1038/s41522-024-00637-y","DOIUrl":"https://doi.org/10.1038/s41522-024-00637-y","url":null,"abstract":"Chronic infections represent a significant global health and economic challenge. Biofilms, which are bacterial communities encased in an extracellular polysaccharide matrix, contribute to approximately 80% of these infections. In particular, pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus are frequently co-isolated from the sputum of patients with cystic fibrosis and are commonly found in chronic wound infections. Within biofilms, bacteria demonstrate a remarkable increase in resistance and tolerance to antimicrobial treatment. We investigated the efficacy of combining the last-line antibiotic colistin with a membrane- and stringent stress response-targeting anti-biofilm peptide DJK-5 against co-biofilms comprised of multidrug-resistant P. aeruginosa and methicillin-resistant S. aureus (MRSA). Colistin lacks canonical activity against S. aureus. However, our study revealed that under co-biofilm conditions, the antibiofilm peptide DJK-5 synergized with colistin against S. aureus. Similar enhancement was observed when daptomycin, a cyclic lipopeptide against Gram-positive bacteria, was combined with DJK-5, resulting in increased activity against P. aeruginosa. The combinatorial treatment induced morphological changes in both P. aeruginosa and S. aureus cell shape and size within co-biofilms. Importantly, our findings also demonstrate synergistic activity against both P. aeruginosa and S. aureus in a murine subcutaneous biofilm-like abscess model. In conclusion, combinatorial treatments with colistin or daptomycin and the anti-biofilm peptide DJK-5 show significant potential for targeting co-biofilm infections. These findings offer promising avenues for developing new therapeutic approaches to combat complex chronic infections.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"8"},"PeriodicalIF":7.8,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11711674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055834","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

Depth heterogeneity of lignin-degrading microbiome and organic carbon processing in mangrove sediments. 红树林沉积物中木质素降解微生物群落的深度异质性及有机碳处理

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-06 DOI: 10.1038/s41522-024-00638-x

Jijuan Ding, Fei Liu, Jiaxiong Zeng, Hang Gu, Jing Huang, Bo Wu, Longfei Shu, Qingyun Yan, Zhili He, Cheng Wang

{"title":"Depth heterogeneity of lignin-degrading microbiome and organic carbon processing in mangrove sediments.","authors":"Jijuan Ding, Fei Liu, Jiaxiong Zeng, Hang Gu, Jing Huang, Bo Wu, Longfei Shu, Qingyun Yan, Zhili He, Cheng Wang","doi":"10.1038/s41522-024-00638-x","DOIUrl":"https://doi.org/10.1038/s41522-024-00638-x","url":null,"abstract":"Mangrove ecosystems are globally recognized for their blue carbon (C) sequestration capacity. Lignocellulosic detritus constitutes the primary C input to mangrove sediments, but the microbial processes involved in its bioprocessing remain unclear. Using lignocellulosic analysis and metagenomic sequencing across five 100-cm sediment cores, we found a high proportion of lignin (95.0-97.7%) within sediments' lignocellulosic detritus, with a small fraction of lignin-degrading genes (1.24-1.98%) of lignin-degrading genes within the carbohydrate-active enzyme coding genes. Depth stratification was observed in genes and microbial communities involved in lignin depolymerization and mineralization of lignin monomer derivatives. Further microbe-centered analyses of biomass production rates and adaptive metabolism revealed diminished microbial C use efficiency potential and augmented \"enzyme latch\" with increasing sediment depths. These findings enhance our understanding of sedimentary organic C cycling and storage in coastal blue C ecosystems.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"5"},"PeriodicalIF":7.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142952378","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: Metaproteomic portrait of the healthy human gut microbiota. 作者更正：健康人类肠道微生物群的元蛋白质组学肖像。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-03 DOI: 10.1038/s41522-024-00635-0

Alessandro Tanca, Antonio Palomba, Giovanni Fiorito, Marcello Abbondio, Daniela Pagnozzi, Sergio Uzzau

引用次数: 0

PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts. 预选：流行率杠杆一致的特征选择解码跨队列的微生物特征。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-03 DOI: 10.1038/s41522-024-00598-2

Yin-Cheng Chen, Yin-Yuan Su, Tzu-Yu Chu, Ming-Fong Wu, Chieh-Chun Huang, Chen-Ching Lin

{"title":"PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts.","authors":"Yin-Cheng Chen, Yin-Yuan Su, Tzu-Yu Chu, Ming-Fong Wu, Chieh-Chun Huang, Chen-Ching Lin","doi":"10.1038/s41522-024-00598-2","DOIUrl":"10.1038/s41522-024-00598-2","url":null,"abstract":"The intricate nature of microbiota sequencing data-high dimensionality and sparsity-presents a challenge in identifying informative and reproducible microbial features for both research and clinical applications. Addressing this, we introduce PreLect, an innovative feature selection framework that harnesses microbes' prevalence to facilitate consistent selection in sparse microbiota data. Upon rigorous benchmarking against established feature selection methodologies across 42 microbiome datasets, PreLect demonstrated superior classification capabilities compared to statistical methods and outperformed machine learning-based methods by selecting features with greater prevalence and abundance. A significant strength of PreLect lies in its ability to reliably identify reproducible microbial features across varied cohorts. Applied to colorectal cancer, PreLect identifies key microbes and highlights crucial pathways, such as lipopolysaccharide and glycerophospholipid biosynthesis, in cancer progression. This case study exemplifies PreLect's utility in discerning clinically relevant microbial signatures. In summary, PreLect's accuracy and robustness make it a significant advancement in the analysis of complex microbiota data.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"3"},"PeriodicalIF":7.8,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11698977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927560","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 dynamic oral-gastric microbial axis connects oral and gastric health: current evidence and disputes. 动态口腔-胃微生物轴连接口腔和胃健康：目前的证据和争议。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-02 DOI: 10.1038/s41522-024-00623-4

Mengying Xia, Lei Lei, Linyong Zhao, Wenqing Xu, Hongyu Zhang, Mingming Li, Jiankun Hu, Ran Cheng, Tao Hu

{"title":"The dynamic oral-gastric microbial axis connects oral and gastric health: current evidence and disputes.","authors":"Mengying Xia, Lei Lei, Linyong Zhao, Wenqing Xu, Hongyu Zhang, Mingming Li, Jiankun Hu, Ran Cheng, Tao Hu","doi":"10.1038/s41522-024-00623-4","DOIUrl":"10.1038/s41522-024-00623-4","url":null,"abstract":"Emerging evidence indicates that oral microbes are closely related to gastric microbes and gastric lesions, including gastric atrophy, intestinal metaplasia and gastric cancer (GC). Helicobacter pylori is a key pathogen involved in GC. However, the increasing prevalence of H. pylori-negative GC and gastric dysbiosis in GC patients emphasize the potential role of other microbial factors. In this review, we discussed the current evidence about the relationship between the oral-gastric microbial axis and oral and gastric health. Epidemiologic evidence indicates that poor oral hygiene is related to greater GC risk. Multiple oral-associated microbes are enriched in the stomach of GC patients. Once colonizing the stomach, oral-associated microbes Streptococcus anginosus and Prevotella melaninogenica, are involved in gastric inflammation or carcinogenesis. Microbial metabolites such as lactate, nitrite, and acetaldehyde promote malignant transformation. The stomach, as a checkpoint of microbial transmission in the digestive tract, is of great importance since the link between oral microbes and intestinal diseases has been emphasized. Still, new technologies and standardized metrics are necessary to identify potential pathogenetic microbes for GC and the core microbiota, interactions, richness, colonization, location and effect (CIRCLE). In the future, oral microbes could be candidates for noninvasive indicators to predict gastric diseases.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"1"},"PeriodicalIF":7.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11696714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142922336","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

Air pollution modifies colonisation factors in beneficial symbiont Snodgrassella and disrupts the bumblebee gut microbiome. 空气污染改变了有益共生体雪草的定植因子，破坏了大黄蜂的肠道微生物群。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-02 DOI: 10.1038/s41522-024-00632-3

Hannah R Sampson, Natalie Allcock, Eamonn B Mallon, Julian M Ketley, Julie A Morrissey

{"title":"Air pollution modifies colonisation factors in beneficial symbiont Snodgrassella and disrupts the bumblebee gut microbiome.","authors":"Hannah R Sampson, Natalie Allcock, Eamonn B Mallon, Julian M Ketley, Julie A Morrissey","doi":"10.1038/s41522-024-00632-3","DOIUrl":"10.1038/s41522-024-00632-3","url":null,"abstract":"Particulate air pollutants, a major air pollution component, are detrimental to human health and a significant risk to wildlife and ecosystems globally. Here we report the effects of particulate pollutant black carbon on the beneficial gut microbiome of important global insect pollinator, the buff-tailed bumblebee (Bombus terrestris). Our data shows that exposure to black carbon particulates alters biofilm structure, gene expression and initial adhesion of beneficial bee gut coloniser, Snodgrassella alvi. Exposure of adult Bombus terrestris to non-toxic black carbon particulates significantly increased viable bacteria on MRS agar and 16S absolute abundance of beneficial bacteria Bombilactobacillus in Post-treated bumblebees compared to Pre-treated, demonstrating disruption of the bumblebee gut microbiome. These findings show that black carbon exposure has direct, measurable effects on bees' beneficial commensal bacteria and microbiome. Together these data highlight that black carbon, a single type of particulate pollution, is an underexplored risk to insect pollinator health.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"2"},"PeriodicalIF":7.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927557","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: Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner. 作者更正：牙龈空间分析揭示了地理上的免疫变异以微生物群依赖和独立的方式存在。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-31 DOI: 10.1038/s41522-024-00636-z

Yasmin Jaber, Avital Sarusi-Portuguez, Yasmin Netanely, Reem Naamneh, Shahd Yacoub, Or Saar, Nadeem Darawshi, Luba Eli-Berchoer, Hagit Shapiro, Eran Elinav, Asaf Wilensky, Avi-Hai Hovav

引用次数: 0

Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis. 艰难梭菌衍生膜囊通过PPARγ/RXRα/ANGPTL4轴抑制滋养细胞运动促进胎儿生长受限。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-31 DOI: 10.1038/s41522-024-00630-5

Zhiqiang Zha, Chunhong Jia, Ruisi Zhou, Qinlan Yin, Yu Hu, Zhipeng Huang, Linyu Peng, Yichi Zhang, Xiaowei Qiu, Ying Chen, Yawen Zhong, Yu Wang, Menglan Pang, Shijing Lu, Chao Sheng, Liping Huang

{"title":"Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis.","authors":"Zhiqiang Zha, Chunhong Jia, Ruisi Zhou, Qinlan Yin, Yu Hu, Zhipeng Huang, Linyu Peng, Yichi Zhang, Xiaowei Qiu, Ying Chen, Yawen Zhong, Yu Wang, Menglan Pang, Shijing Lu, Chao Sheng, Liping Huang","doi":"10.1038/s41522-024-00630-5","DOIUrl":"10.1038/s41522-024-00630-5","url":null,"abstract":"Fetal growth restriction (FGR) is a common complication of pregnancy, which seriously endangers fetal health and still lacks effective therapeutic targets. Clostridium difficile (C. difficile) is associated with fetal birth weight, and its membrane vesicles (MVs) are pathogenic vectors. However, the role of C. difficile and its MVs in FGR remains unclear. Here we found that supplementation with C. difficile altered the characteristics of gut microbiota and reduced the birth weight in mice. Interestingly, C. difficile MVs entered placenta, inhibited trophoblast motility, and induced fetal weight loss in mice. Mechanistically, C. difficile MVs activated the PPAR pathway via enhancing the transcriptional activity of PPARγ promoter, consequently inhibiting trophoblast motility. Moreover, PPARγ expression was significantly elevated in FGR placenta, and negatively correlated with fetal birth weight. Together, our findings reveal the significance of C. difficile and its MVs in FGR, providing new insights into the mechanisms of FGR development.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"158"},"PeriodicalIF":7.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11688498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909898","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 impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms. 抗氧化剂-环丙沙星组合对铜绿假单胞菌生物膜中抗生素耐药性演变的影响

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-30 DOI: 10.1038/s41522-024-00640-3

Doaa Higazy, Marwa N Ahmed, Oana Ciofu

{"title":"The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms.","authors":"Doaa Higazy, Marwa N Ahmed, Oana Ciofu","doi":"10.1038/s41522-024-00640-3","DOIUrl":"10.1038/s41522-024-00640-3","url":null,"abstract":"The evolution of antimicrobial resistance (AMR) in biofilms, driven by mechanisms like oxidative stress, is a major challenge. This study investigates whether antioxidants (AOs) such as N-acetyl-cysteine (NAC) and Edaravone (ED) can reduce AMR in Pseudomonas aeruginosa biofilms exposed to sub-inhibitory concentrations of ciprofloxacin (CIP). In vitro experimental evolution studies were conducted using flow cells and glass beads biofilm models. Results showed that combining CIP with antioxidants (CIP-AOs) effectively reduced the development of CIP resistance. Isolates from biofilms treated with CIP-AO had significantly lower minimum inhibitory concentrations (MICs) of CIP compared to those treated with CIP alone. Whole-genome sequencing (WGS) revealed mutations in the negative regulators of efflux pumps, nfxB, and nalC, in CIP-only treated biofilm populations. The occurrence of nfxB mutations was significantly lower in flow cell biofilms treated with CIP-AO compared to CIP alone. These findings suggest that antioxidants could play a role in mitigating AMR development in biofilms.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"156"},"PeriodicalIF":7.8,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11685532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907362","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

Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic. 牙种植体上形成的早期生物膜结构和组成复杂多样，具有主体特异性和动态性。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-24 DOI: 10.1038/s41522-024-00624-3

Sophie Dieckow, Szymon P Szafrański, Jasmin Grischke, Taoran Qu, Katharina Doll-Nikutta, Matthias Steglich, Ines Yang, Susanne Häussler, Meike Stiesch

{"title":"Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic.","authors":"Sophie Dieckow, Szymon P Szafrański, Jasmin Grischke, Taoran Qu, Katharina Doll-Nikutta, Matthias Steglich, Ines Yang, Susanne Häussler, Meike Stiesch","doi":"10.1038/s41522-024-00624-3","DOIUrl":"10.1038/s41522-024-00624-3","url":null,"abstract":"Biofilm-associated peri-implant infections pose a major problem in modern medicine. The understanding of biofilm development is hampered by biofilm complexity and the lack of robust clinical models. This study comprehensively characterized the dynamics of early biofilm formation in the transmucosal passage of implant abutments in 12 patients. Biofilm structures and compositions were complex, diverse, subject-specific and dynamic. A total of 371 different bacterial species were detected. 100 phylogenetically diverse unnamed species and 35 taxonomically diverse disease-associated species comprised an average 4.3% and 3.1% of the community, respectively, but reached up to 12.7% and 21.7% in some samples. Oral taxa formed numerous positive associations and clusters and were characterized by a high potential for metabolic interactions. The subspecies diversity was highly patient-specific and species-dependent, with 1427 ASVs identified in total. The unprecedented depth of early biofilm characterization in this study will support the development of individualized preventive and early diagnostic strategies.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"155"},"PeriodicalIF":7.8,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886100","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