Eduard Flores Ventura, María Esteban-Torres, Miguel Gueimonde, Douwe van Sinderen, Omry Koren, Lindsay J Hall, Nicola Segata, Mireia Valles-Colomer, Maria Carmen Collado
{"title":"Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.","authors":"Eduard Flores Ventura, María Esteban-Torres, Miguel Gueimonde, Douwe van Sinderen, Omry Koren, Lindsay J Hall, Nicola Segata, Mireia Valles-Colomer, Maria Carmen Collado","doi":"10.1038/s41522-025-00720-y","DOIUrl":"https://doi.org/10.1038/s41522-025-00720-y","url":null,"abstract":"<p><p>Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, 31 articles from 2009 to 2024 were selected from 2825 screened titles and abstracts. Using a narrative synthesis and meta-analysis, the review focuses on studies employing strain-level metagenomic approaches (Protocol registry CRD: CRD42023490507). Ten studies using shotgun metagenomic sequencing identified specific strains of B. adolescentis, B. angulatum, B. bifidum, B. breve, B. pseudocatenulatum, B. catenulatum, and B. longum shared between mothers and infants. A meta-analysis of 810 mother-infant pairs revealed an overall species transmissibility estimate of 30% (95% CI: 0.17; 0.44), with B. longum strains persisting in infants' guts for up to 6 months. Strain transmissibility was higher in vaginally delivered infants compared to those delivered by caesarean section. This review highlights the high transmission rates of maternal Bifidobacterium strains in early-life gut seeding, particularly B. bifidum and B. longum. Despite ongoing research, uncertainties remain regarding the precise characteristics, transmission routes, and mechanisms of transmitted strains. Comprehensive approaches, including metagenomic sequencing and longitudinal studies, are needed to understand the role of vertical transmission in infant gut microbiome engraftment and its functional implications.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"121"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541646","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}
Yuwei Tan, Yang Zhu, René H Wijffels, Hongxia Zhang, William T Scott, Yan Xu, Vitor Martins Dos Santos
{"title":"Controlling metabolic stability of food microbiome for stable indigenous liquor fermentation.","authors":"Yuwei Tan, Yang Zhu, René H Wijffels, Hongxia Zhang, William T Scott, Yan Xu, Vitor Martins Dos Santos","doi":"10.1038/s41522-025-00729-3","DOIUrl":"https://doi.org/10.1038/s41522-025-00729-3","url":null,"abstract":"<p><p>Steering microbial metabolic stability in fermentation is a recurrent goal in microbial food production. Indigenous liquor fermentation typically relies on complex microbiome metabolism, making it difficult to steer fermentation towards consistent high-quality products. Here, we conducted a three-step experiment to identify instability factors and explore ways to steer fermentation stability in lab-scale settings. We found that the metabolic stability of the microbiome fluctuates due to fermentation parameters, dynamic benefit allocation between yeasts and Lactobacilli, and metabolic network redundancy. In addition to parameters control, short-term metabolic stability requires stable microbial benefit allocation, whereas long-term stability requires proper functional redundancy. Rationally setting initial parameters and the microbial inoculation ratio is a practical way to optimize metabolic stability for stable indigenous liquor fermentation. Our study provides new insights into microbiome metabolism control and shows the feasibility of enhancing fermentation stability through appropriate initial conditions, enabling more controlled and efficient microbial food production systems.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"124"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541639","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}
{"title":"Berberine chloride hydrate impairs Streptococcus mutans biofilm formation via inhibiting sortase A activity.","authors":"Yang Zhou, Fang Huang, Huancai Lin","doi":"10.1038/s41522-025-00756-0","DOIUrl":"https://doi.org/10.1038/s41522-025-00756-0","url":null,"abstract":"<p><p>Dental caries is a biofilm-associated chronic progressive disease, results from the dissolution of mineralized tooth tissue by acidic generated from bacterial sugar fermentation. S. mutans, a prominent pathogen of dental caries, is acknowledged for its role in cariogenic biofilm formation, utilizing Sortase A (SrtA) to catalyse surface proteins, thus promoting biofilm formation. In our previous studies, the inhibitory effect of the berberine chloride hydrate (BH) on S. mutans biofilms was confirmed. Here, we further investigate the influence of BH on S. mutans biofilm-induced bovine enamel caries model and explore the effect of BH on S. mutans SrtA activity. We found that BH inhibited S. mutans biofilm formation in bovine enamel model, leading to a reduction in demineralization. Furthermore, we identified and characterized SrtA, which might catalyze SpaP of S. mutans to form fibrillar amyloid aggregates. Our findings showed that BH inhibited SrtA activity by binding to essential amino acid residues LEU-111, MET-123, and ARG-213. BH inhibited amyloid fibers formation by downregulating the expression of srtA gene, thus disrupting S. mutans biofilm formation. Taken together, our study provides new insight into the mechanism of antibiofilm activity of BH and reveals great potential for anticaries clinical applications.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"120"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541638","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}
Cristina I Amador, Sofia Zoe Moscovitz, Lorrie Maccario, Jakob Herschend, Isabel-Sophie Kramer, Hannah Jeckel, Vaughn S Cooper, Knut Drescher, Thomas R Neu, Mette Burmølle, Henriette L Røder
{"title":"Evolution of genotypic and phenotypic diversity in multispecies biofilms.","authors":"Cristina I Amador, Sofia Zoe Moscovitz, Lorrie Maccario, Jakob Herschend, Isabel-Sophie Kramer, Hannah Jeckel, Vaughn S Cooper, Knut Drescher, Thomas R Neu, Mette Burmølle, Henriette L Røder","doi":"10.1038/s41522-025-00755-1","DOIUrl":"https://doi.org/10.1038/s41522-025-00755-1","url":null,"abstract":"<p><p>Bacterial fitness and adaptability in microbial communities are influenced by interspecies interactions and spatial organization. This study investigated how these factors shape the evolutionary dynamics of Bacillus thuringiensis. A distinct phenotypic variant of B. thuringiensis emerged consistently under both planktonic and biofilm conditions, as well as in monospecies and mixed-species settings, but was strongly selected in biofilms and during coexistence with Pseudomonas defluvii and/or Pseudomonas brenneri. Compared to its ancestor, the variant exhibited shorter generation times, reduced sporulation, auto-aggregation, and lower biomass in mixed-species biofilms. Mutations in the spo0A regulator, which controls sporulation and biofilm matrix production, were identified in all variants. Proteomics revealed a reduction in TasA, a key matrix protein, in the variant but increased levels in co-culture with P. brenneri. These findings highlight how interspecies interactions drive B. thuringiensis diversification, promoting traits like reduced matrix production and species coexistence, with implications for microbial consortia applications in agriculture and biopesticides.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"118"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541640","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}
Emmanuel Amabebe, Madhuri Tatiparthy, Ananth K Kammala, Lauren S Richardson, Brandie D Taylor, Surendra Sharma, Ramkumar Menon
{"title":"Vaginal pharmacomicrobiomics modulates risk of persistent and recurrent bacterial vaginosis.","authors":"Emmanuel Amabebe, Madhuri Tatiparthy, Ananth K Kammala, Lauren S Richardson, Brandie D Taylor, Surendra Sharma, Ramkumar Menon","doi":"10.1038/s41522-025-00748-0","DOIUrl":"https://doi.org/10.1038/s41522-025-00748-0","url":null,"abstract":"<p><p>Bacterial vaginosis (BV) is the most commonly diagnosed vaginal infection in women of reproductive age, with most patients unaware that they have BV due to its asymptomatic nature. BV is a dysbiotic condition defined by a deviation from the healthy Lactobacillus dominance to a polymicrobial anaerobic bacterial community that increases the risk of sexually transmitted infections and adverse reproductive outcomes, including spontaneous preterm birth. The increasing number of infectious agents in BV, biofilm persistence and antibiotic resistance in the vaginal canal hinder effective treatments with antibiotics leading to consistent recurrence of BV in many women (30-70%). Like in the gut, these vaginal drug-microbiome interactions termed pharmacomicrobiomics could alter drug disposition, mechanism of action, and toxicity that reduce the efficacy of antibiotics and increase the risk of persistent and recurrent BV and its sequelae. For instance, both vaginal epithelial and bacterial cells co-exist and possess enzymes that metabolize antibiotics, and transporter proteins that expel drugs and toxins, rendering them ineffective. Despite significant progress on pharmacomicrobiomics in the gut, little is known about this phenomenon in the vaginal microenvironment, which harbors a consequential microbiota and a major source of infection and antibiotic resistance. Therefore, to improve therapeutic outcomes and reduce the rate of persistent/recurrent BV and infection-associated preterm birth, we present an overview of the evidence pertaining to the effect of vaginal microbiome-drug interactions and efficacy of antibiotics against recurrent BV. We also highlight plausible mechanistic underpinnings of these interactions and implications for treatment modalities to combat infection-associated preterm birth.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"115"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541648","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}
Cristina Rosell-Cardona, John F Cryan, Gerard Clarke, Sarah Kittel-Schneider
{"title":"Host-microbiome relationship in depression: can human induced pluripotent stem cells play a role in unravelling mechanisms?","authors":"Cristina Rosell-Cardona, John F Cryan, Gerard Clarke, Sarah Kittel-Schneider","doi":"10.1038/s41522-025-00749-z","DOIUrl":"https://doi.org/10.1038/s41522-025-00749-z","url":null,"abstract":"<p><p>Depression is highly prevalent, with many patients not responding to existing treatments. The gut microbiota plays a key role in its pathophysiology, offering new therapeutic avenues. Human-based research is essential to uncover mechanisms and validate new targets. Given CNS inaccessibility, human induced pluripotent stem cells (hiPSCs) offer an innovative model. This review explores the emerging field of hiPSCs and their potential in advancing microbiota-gut-brain axis science and depression research.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"117"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541642","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}
Kevin H Mwangi, Yue Qu, Peilun Hu, Toshitatsu Nagayasu, Jia-Feng Liu, Xiumei Wang
{"title":"Microanatomy related biocidal activity at cellular resolution and bone reconstruction potential of PEG EGaIn nanocapsules.","authors":"Kevin H Mwangi, Yue Qu, Peilun Hu, Toshitatsu Nagayasu, Jia-Feng Liu, Xiumei Wang","doi":"10.1038/s41522-025-00724-8","DOIUrl":"https://doi.org/10.1038/s41522-025-00724-8","url":null,"abstract":"<p><p>Critical bone defects, exacerbated by infections, pose significant challenges to bone healing and homeostasis, necessitating the development of dual-functional biomimetics that combine anti-infective and reparative capabilities. The EGaIn holds promise across various disciplines, though its interactions with microbial cells require further elucidation. This investigation evaluates the antimicrobial efficacy of PEG-EGaIn nanocapsules against a spectrum of bacterial, employing electron microscopy. Constructs containing 1.5% PEG-EGaIn hinder biofilm-producing bacteria, while 3% concentrations amplify the biocidal effect. Furthermore, the nanocapsules promoted osteogenic differentiation rBMSCs, evidenced by enhanced mineralization and upregulation of key osteogenic genes. In addressing large bone defects, PEG-EGaIn-Col-Ap-lamellar and ethanolic-mediated Col-Ap-lamellar constructs serve as potential solutions for bone resorption mitigation and osteo-angiogenesis. Bone-remodeling were validated through μ-CT and histomorphometry confirming no evidence of chronic inflammation or fibrosis. In this study, PEG-EGaIn nanocapsules emerge as potent biocide and bone repair, underscoring their potential in combating antibiotic resistance and enhancing bone healing.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"123"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541644","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}
Miyang Luo, Jiayou Luo, Atipatsa C Kaminga, Jia Wei, Wen Dai, Yan Zhong, Ningan Xu, Xiongwei Li, Haixiang Zhou, Xiongfeng Pan
{"title":"Targeted metabolomics reveals bioactive inflammatory mediators from gut into blood circulation in children with NAFLD.","authors":"Miyang Luo, Jiayou Luo, Atipatsa C Kaminga, Jia Wei, Wen Dai, Yan Zhong, Ningan Xu, Xiongwei Li, Haixiang Zhou, Xiongfeng Pan","doi":"10.1038/s41522-025-00706-w","DOIUrl":"https://doi.org/10.1038/s41522-025-00706-w","url":null,"abstract":"<p><p>Altered gut metabolites are important for the inflammatory progression in children with NAFLD. Fecal and plasma samples were collected from 145 subjects including 53 non-alcoholic fatty liver (NAFL), 39 nonalcoholic steatohepatitis (NASH) and 53 obese controls. We performed G350 targeted integrative metabolomics using high performance liquid chromatography mass spectrometry for fecal and plasma analysis of NAFL, NASH, and obese children. We found 9 metabolites involved in metabolic reprogramming of inflammation in NAFLD, such as lipid, carbohydrate, amino acid metabolism, and TCA cycle pathway. Moreover, 7 inflammation-related metabolites could discriminate NAFLD severity by machine learning model. This study identified three novel elevated inflammatory pathogenic metabolites and the relationship between increased inflammation, may be involved in TLR5/MYD88/NFκB pathway. These findings reveal that specific inflammatory metabolites entering the blood circulation from the gut are associated with disease severity and inflammatory pathogenesis in children with NAFLD.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"119"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541647","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}
JunHong Xing, TianMing Niu, Tong Yu, BoShi Zou, ShuHui Fan, ChunFeng Wang, ChunWei Shi, DongXing Zhang, Nan Wang, YanLong Jiang, HaiBin Huang, Xin Cao, Yan Zeng, JianZhong Wang, Di Zhang, GuiLian Yang, WenTao Yang
{"title":"Gut microbiota-derived isovaleric acid ameliorates influenza virus infection via gut-lung axis.","authors":"JunHong Xing, TianMing Niu, Tong Yu, BoShi Zou, ShuHui Fan, ChunFeng Wang, ChunWei Shi, DongXing Zhang, Nan Wang, YanLong Jiang, HaiBin Huang, Xin Cao, Yan Zeng, JianZhong Wang, Di Zhang, GuiLian Yang, WenTao Yang","doi":"10.1038/s41522-025-00753-3","DOIUrl":"https://doi.org/10.1038/s41522-025-00753-3","url":null,"abstract":"<p><p>H9N2 influenza virus infections represent a significant respiratory health concern, yet the functional role of gut microbiota during infection progression remains poorly understood. Here, we show that H9N2 infection causes dose-dependent alterations in gut microbial communities in a mammalian infection model, particularly the depletion of Prevotella species. Prophylactic administration of Prevotella copri improved survival and clinical outcomes in infected mice by restructuring the gut microbiome, promoting beneficial bacteria, and suppressing pathogens. Metabolomic profiling revealed increased isovaleric acid levels in the intestine and serum. Isovaleric acid pretreatment reduced pulmonary inflammation, alleviated tissue damage, and preserved epithelial integrity. Isovaleric acid pretreatment alleviates lung inflammation, reduces tissue damage, and maintains epithelial integrity. Additionally, isovaleric acid mitigates infection caused by the H1N1 influenza virus. These findings highlight the immunomodulatory role of gut commensals and their metabolites in antiviral defense, offering a new approach to influenza virus treatment.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"116"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541641","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}
{"title":"Iron limitation-induced endophytic Ammoniphilus assemblage promotes root apoplastic iron remobilization by attenuation of salicylic acid pathways.","authors":"Lin Zhu, Aijing Zhang, Jiansheng Guo, Huabing Liu, Yue Xie, Xiaomin Lu, Congsheng Yan, Jianfei Wang, Cheng Zhou","doi":"10.1038/s41522-025-00765-z","DOIUrl":"https://doi.org/10.1038/s41522-025-00765-z","url":null,"abstract":"<p><p>Plants establish symbiotic associations with root-colonizing microbes to adapt to adverse conditions. However, how root-associated microbiota interacted with their hosts to improve plant growth under nutrient deficient conditions remains poorly understood. In this study, we explored an interaction between tomato plants and root-associated microbiota under iron (Fe) limitation, mediated by bacterial secretion of glutamine. 16S rRNA gene sequencing revealed that Fe-limited conditions altered the composition of root-associated microbiomes, resulting in the enrichment of Ammoniphilus sp. This taxon was isolated and shown to alleviate Fe deficiency symptoms. Moreover, Fe deficiency triggered salicylic acid (SA)-induced hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) burst, thereby inhibiting the exudation of Fe-mobilizing phenolics from the roots. However, bacterial secretion of Gln greatly attenuated the SA-induced H<sub>2</sub>O<sub>2</sub> production in the roots, thereby enhancing bacterial colonization and promoting apoplastic Fe remobilization. Collectively, these results underscored a microbial strategy for orchestrating plant SA pathways to facilitate the reutilization of root apoplastic Fe.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"125"},"PeriodicalIF":7.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541643","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}