npj Biofilms and Microbiomes最新文献_第4页

Evolutionary adaptation of probiotics in the gut: selection pressures, optimization strategies, and regulatory challenges. 肠道中益生菌的进化适应：选择压力、优化策略和监管挑战。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-06-07 DOI: 10.1038/s41522-025-00734-6

Julia Leeflang, Josephine A Wright, Daniel L Worthley, M Omar Din, Susan L Woods

{"title":"Evolutionary adaptation of probiotics in the gut: selection pressures, optimization strategies, and regulatory challenges.","authors":"Julia Leeflang, Josephine A Wright, Daniel L Worthley, M Omar Din, Susan L Woods","doi":"10.1038/s41522-025-00734-6","DOIUrl":"10.1038/s41522-025-00734-6","url":null,"abstract":"Probiotics and live bacterial therapeutics are garnering increased attention for use in human health and have the potential to revolutionise the treatment of gastrointestinal diseases. However, a pervasive feature of bacteria that must be considered in the design of safe and effective probiotics and live bacterial therapeutics is their capacity for rapid evolution, both at the individual (epi)genetic level and in terms of population dynamics. Here we summarise gastrointestinal-specific evolution of bacteria, focussing on genetic and population levels of adaptation to factors such as carbon source availability, environmental stressors, and interactions with the native microbiome. We also address regulatory and safety considerations for the development of probiotics and live biotherapeutics from an evolutionary perspective, with a discussion of methods that utilise evolution to improve probiotic safety and efficacy via directed evolution, in comparison to another popular approach, genetic engineering.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"96"},"PeriodicalIF":7.8,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12145451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248955","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

Harnessing vaginal inflammation and microbiome: a machine learning model for predicting IVF success. 利用阴道炎症和微生物组：预测试管婴儿成功的机器学习模型。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-06-05 DOI: 10.1038/s41522-025-00732-8

Ofri Bar, Stylianos Vagios, Omer Barkai, Joseph Elshirbini, Irene Souter, Jiawu Xu, Kaitlyn James, Charles Bormann, Makiko Mitsunami, Jorge E Chavarro, Philipp Foessleitner, Douglas S Kwon, Moran Yassour, Caroline Mitchell

{"title":"Harnessing vaginal inflammation and microbiome: a machine learning model for predicting IVF success.","authors":"Ofri Bar, Stylianos Vagios, Omer Barkai, Joseph Elshirbini, Irene Souter, Jiawu Xu, Kaitlyn James, Charles Bormann, Makiko Mitsunami, Jorge E Chavarro, Philipp Foessleitner, Douglas S Kwon, Moran Yassour, Caroline Mitchell","doi":"10.1038/s41522-025-00732-8","DOIUrl":"10.1038/s41522-025-00732-8","url":null,"abstract":"Humans are the only species with a commensal Lactobacillus-dominant vaginal microbiota. Reproductive tract microbes have been linked to fertility outcomes, as has intrauterine inflammation, suggesting immune response may mediate adverse outcomes. In this pilot study, we compared vaginal microbiota composition and immune marker concentrations between patients with unexplained or male factor infertility (MFI), as a control. We applied a supervised machine learning algorithm that integrated microbiome and inflammation data to predict pregnancy outcomes.Twenty-eight participants provided vaginal swabs at three IVF cycle time points; 18 achieved pregnancy. Pregnant participants had lower microbial diversity and inflammation. Among them, MFI cases had higher diversity but lower inflammation than those with unexplained infertility. Our model showed the highest prediction accuracy at time point 2 of the IVF cycle. These findings suggest that vaginal microbiota and inflammation jointly impact fertility and can inform predictive tools in reproductive medicine.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"95"},"PeriodicalIF":7.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12141462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234670","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

Activity of GS-linked chimeric endolysin CHAPk-SH3bk against methicillin-resistant Staphylococcus aureus biofilms: an in-vitro, ex-vivo and in-vivo study. gs连接嵌合内溶素CHAPk-SH3bk对耐甲氧西林金黄色葡萄球菌生物膜的活性：体外、离体和体内研究

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-06-03 DOI: 10.1038/s41522-025-00728-4

Manisha Behera, Priyanka Singh, Anita Kamra Verma, Sachinandan De, Soma M Ghorai

{"title":"Activity of GS-linked chimeric endolysin CHAPk-SH3bk against methicillin-resistant Staphylococcus aureus biofilms: an in-vitro, ex-vivo and in-vivo study.","authors":"Manisha Behera, Priyanka Singh, Anita Kamra Verma, Sachinandan De, Soma M Ghorai","doi":"10.1038/s41522-025-00728-4","DOIUrl":"10.1038/s41522-025-00728-4","url":null,"abstract":"The evolution of antibiotic resistance and the propensity of methicillin-resistant Staphylococcus aureus to form biofilms impedes antibiotic therapy, which enkindles the rummage for novel therapeutic agents like bacteriophage endolysins. This study investigates the biofilm degradation activity of novel chimeric endolysin CHAPk-SH3bk compared to single domain construct CHAPk. The in-vitro biofilm degradation assay displayed higher antibiofilm activity of CHAPk-SH3bk compared to CHAPk on glass and steel surfaces. Treatment of CHAPk-SH3bk effectively inhibited biofilm formation of hospital-associated and bovine-origin MRSA. The in-vivo results displayed a higher reduction of 24 h MRSA-biofilm using CHAPk-SH3bk compared to CHAPk in mice skin infection model. Further, confocal laser scanning microscopy, scanning electron microscopy, and immunohistochemistry confirmed the in-vivo results. The study indicated that attachment of SH3b using glycine-serine linker to CHAPk increased the catalytic domains biofilm reduction ability. The study demonstrates that construction of novel chimeric endolysins by shuffling parental endolysin domains may increase their antibiofilm activity.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"94"},"PeriodicalIF":7.8,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216420","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

TSP50 deficiency in neural stem cells aggravates colitis in mice by altering intestinal microbiome. 神经干细胞TSP50缺乏通过改变肠道微生物群加重小鼠结肠炎。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-06-03 DOI: 10.1038/s41522-025-00737-3

Xiaoli Li, Rong Jin, Zhaoxia Wang, Chunxue Niu, Zhenbo Song, Xiaoling Liu, Jian Huang, Huan Zhang, Xia Qian, Feng Gao, Shuyue Wang, Chunlei Yu, Luguo Sun, Yanxin Huang, Lihua Zheng, Guannan Wang, Ying Sun, Xiaoguang Yang, Yongli Bao, Jiawei Li

{"title":"TSP50 deficiency in neural stem cells aggravates colitis in mice by altering intestinal microbiome.","authors":"Xiaoli Li, Rong Jin, Zhaoxia Wang, Chunxue Niu, Zhenbo Song, Xiaoling Liu, Jian Huang, Huan Zhang, Xia Qian, Feng Gao, Shuyue Wang, Chunlei Yu, Luguo Sun, Yanxin Huang, Lihua Zheng, Guannan Wang, Ying Sun, Xiaoguang Yang, Yongli Bao, Jiawei Li","doi":"10.1038/s41522-025-00737-3","DOIUrl":"10.1038/s41522-025-00737-3","url":null,"abstract":"Inflammatory bowel disease (IBD) is a complex disease characterized by persistent chronic inflammation of the gastrointestinal tract and periodic episodes. Despite the increasing number of related studies, the detailed pathogenesis of IBD has not been elucidated. In recent years, host-microbiota interactions in the pathogenesis of IBD have received extensive attention. Testes-specific protease 50 (TSP50) is a potential risk gene for IBD, but whether it can affect the susceptibility of colitis by regulating the gut microbiome is still unclear. Here, we showed that TSP50 deficiency in neural stem cells (NSCs) aggravated colitis in mice by altering intestinal microbiome. Mechanistically, TSP50 maintained the level of neurotransmitter acetylcholine (ACh) by degrading acetylcholinesterase (AChE), thereby maintaining intestinal mucosa and intestinal microecological homeostasis and reducing the susceptibility to colitis. These findings provide a new perspective on the interaction between host and commensal microbiota, which may be beneficial for developing potential therapeutic strategies for IBD.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"93"},"PeriodicalIF":7.8,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216421","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

Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women. 宏基因组分析揭示了阴道乳杆菌在中国健康孕妇中的新作用。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-30 DOI: 10.1038/s41522-025-00731-9

Xudong Wang, Qingru Jiang, Xiaohui Tian, Wei Chen, Junrui Mai, Gan Lin, Yingfang Huo, Haiyang Zheng, Dandan Yan, Xiaohong Wang, Tian Li, Yu Gao, Xiangyu Mou, Wenjing Zhao

{"title":"Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women.","authors":"Xudong Wang, Qingru Jiang, Xiaohui Tian, Wei Chen, Junrui Mai, Gan Lin, Yingfang Huo, Haiyang Zheng, Dandan Yan, Xiaohong Wang, Tian Li, Yu Gao, Xiangyu Mou, Wenjing Zhao","doi":"10.1038/s41522-025-00731-9","DOIUrl":"10.1038/s41522-025-00731-9","url":null,"abstract":"This study investigated the relationship between vaginal microbiota and women's health conditions in 95 Chinese pregnant women in their third trimester. We conducted vaginal metagenomic analysis, examining species, functional pathways, and genes, and utilized correlation and LEfSe analyses to link microbiota to health conditions. Results revealed that healthy participants exhibited higher levels of Lactobacillus iners, with its abundance associated with tetrahydrofolate biosynthesis pathways. They also possessed more glycosyltransferase and ErmB antibiotic resistance genes compared to women with diagnosed conditions. Comparative genomics demonstrated that L. iners strains linked to bacterial vaginosis (BV) possessed more genes encoding biofilm-associated YhgE/Pip domain-containing proteins than healthy-associated strains. Notably, three BV-associated L. iners strains exhibited stronger biofilm formation abilities than four healthy-associated strains isolated in this study. Also, four out of seven L. iners strains inhibited the growth of Gardnerella vaginalis. Overall, L. iners may help maintain vaginal ecosystem stability in Chinese pregnant women.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"92"},"PeriodicalIF":7.8,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12125259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187390","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

Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains. 综合多组学揭示了特应性皮炎的长双歧杆菌菌株的不同宿主串扰。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-29 DOI: 10.1038/s41522-025-00714-w

Hoon Je Seong, Yoon Mee Park, Bong-Soo Kim, Hyun Ju Yoo, Taeyune Kim, Sun Mi Yoon, Jeong-Hyun Kim, So-Yeon Lee, Yun Kyung Lee, Dong-Woo Lee, Myung Hee Nam, Soo-Jong Hong

{"title":"Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.","authors":"Hoon Je Seong, Yoon Mee Park, Bong-Soo Kim, Hyun Ju Yoo, Taeyune Kim, Sun Mi Yoon, Jeong-Hyun Kim, So-Yeon Lee, Yun Kyung Lee, Dong-Woo Lee, Myung Hee Nam, Soo-Jong Hong","doi":"10.1038/s41522-025-00714-w","DOIUrl":"10.1038/s41522-025-00714-w","url":null,"abstract":"The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"91"},"PeriodicalIF":7.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12122682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182932","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

Mediation effect and metabolic pathways of gut microbiota in the associations between lifestyles and dyslipidemia. 肠道菌群在生活方式与血脂异常之间的中介作用和代谢途径。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-28 DOI: 10.1038/s41522-025-00721-x

Lijun Zeng, Bin Yu, Peibin Zeng, Zhuoma Duoji, Haojiang Zuo, Jian Lian, Tingting Yang, Yingxue Dai, Yuemei Feng, Peng Yu, Jiqi Yang, Shujuan Yang, Qingyu Dou

引用次数: 0

Applying the theory of broken windows to microbiome studies. 将破窗理论应用于微生物组研究。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-27 DOI: 10.1038/s41522-025-00726-6

Delia Mercedes Bianco, Flavio De Maio

引用次数: 0

Distal gut colonization by oral bacteria during intensive chemotherapy: direct evidence from strain-level analysis of paired samples. 强化化疗期间口腔细菌的远端肠道定植：来自成对样本的菌株水平分析的直接证据。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-26 DOI: 10.1038/s41522-025-00725-7

Suravi Raychaudhuri, Hakan Gem, Kevin Chung, Jeffrey S McLean, Kristopher A Kerns, Meredith A J Hullar, Elissa Elmorr, Jacob B Appelbaum, Mary-Elizabeth M Percival, Roland B Walter, Anna B Halpern, Samuel S Minot, Katie Kim, Alexander S Zevin, Armin Rashidi

{"title":"Distal gut colonization by oral bacteria during intensive chemotherapy: direct evidence from strain-level analysis of paired samples.","authors":"Suravi Raychaudhuri, Hakan Gem, Kevin Chung, Jeffrey S McLean, Kristopher A Kerns, Meredith A J Hullar, Elissa Elmorr, Jacob B Appelbaum, Mary-Elizabeth M Percival, Roland B Walter, Anna B Halpern, Samuel S Minot, Katie Kim, Alexander S Zevin, Armin Rashidi","doi":"10.1038/s41522-025-00725-7","DOIUrl":"10.1038/s41522-025-00725-7","url":null,"abstract":"Oral bacteria have been found in the colon in pathologies such as inflammatory bowel disease. To ascertain niche coalescence, 2 elements are essential: (i) paired oral/fecal samples and (ii) strain-level resolution. We profiled the microbiota in 283 samples from 39 patients undergoing intensive chemotherapy at baseline (saliva: 49, plaque: 51, stool: 43), week 2 (saliva: 18, plaque: 17, stool: 17), week 3 (saliva: 18, plaque: 21, stool: 21), and week 4 (saliva: 8, plaque: 10, stool: 10) of chemotherapy. Through strain-level analysis of paired samples, we demonstrate strong evidence for a breakdown of niche separation in most patients. The extent of overlap increased with time, particularly in patients with intestinal mucositis. Our findings provide definitive evidence for ectopic colonization of the distal gut by oral bacteria in a disease state, likely facilitated by intestinal mucositis. Microbiota contribution by the mouth to the colon may have consequences for the host.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"88"},"PeriodicalIF":7.8,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12106833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151236","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

Multiomic analysis of different horse breeds reveals that gut microbial butyrate enhances racehorse athletic performance. 对不同马品种的多组学分析表明，肠道微生物丁酸盐可以提高赛马的运动成绩。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-05-24 DOI: 10.1038/s41522-025-00730-w

Cunyuan Li, Xiaoyue Li, Kaiping Liu, Junli Xu, Jinming Yu, Zhuang Liu, Núria Mach, Wei Ni, Chen Liu, Ping Zhou, Limin Wang, Shengwei Hu

{"title":"Multiomic analysis of different horse breeds reveals that gut microbial butyrate enhances racehorse athletic performance.","authors":"Cunyuan Li, Xiaoyue Li, Kaiping Liu, Junli Xu, Jinming Yu, Zhuang Liu, Núria Mach, Wei Ni, Chen Liu, Ping Zhou, Limin Wang, Shengwei Hu","doi":"10.1038/s41522-025-00730-w","DOIUrl":"10.1038/s41522-025-00730-w","url":null,"abstract":"Gut microbes play a vital role in host physiology, but whether specific bacterial functions contribute to the exceptional athletic performance of racehorses needs to be better understood. Here, we identify an association of gut butyrate-producing bacteria with athletic performance in racehorses (Thoroughbred horse). Butyrate-producing bacteria and microbial butyrate synthesis genes were significantly enriched in the racehorse gut, and the GC-MS results confirmed this conclusion. Using a mouse model, we demonstrated that sodium butyrate is sufficient to increase treadmill run time performance. We also show that butyrate improves the host response to exercise, significantly altering muscle fibre type in skeletal muscle, and increasing muscle mitochondrial function and activity. In addition, in-depth analysis of the published data showed that the gene for the synthesis of butyrate was also significantly enriched in the gut microbes of human athletes. Overall, our study indicates that gut microbial butyrate improves run time via the gut-muscle axis, providing novel insights into gut microbial functions and paving the way for improving athletic performance by targeted gut microbiome manipulation.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"87"},"PeriodicalIF":7.8,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132659","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