Yi Zhou, Min Jiang, Ke Shen, Tao He, Siyu Zhou, Aibin Shao, Xiaoyu Li, Jiao Wang, Rongrong Wu, Rajeev K Singla, Jonathan P Jacobs, Bairong Shen
{"title":"Optimizing breast cancer chemotherapy by harnessing gut microbiota with insights from artificial intelligence.","authors":"Yi Zhou, Min Jiang, Ke Shen, Tao He, Siyu Zhou, Aibin Shao, Xiaoyu Li, Jiao Wang, Rongrong Wu, Rajeev K Singla, Jonathan P Jacobs, Bairong Shen","doi":"10.1038/s41522-025-00825-4","DOIUrl":"10.1038/s41522-025-00825-4","url":null,"abstract":"<p><p>Optimizing chemotherapy for breast cancer (BC) remains a critical challenge. Gut microbiota (GM) dysbiosis, varying across BC subtypes and stages, influences BC development and chemotherapy response through immune and metabolic pathways. Chemotherapy also disrupts the microbiota, creating a complex bidirectional interaction. Integrating artificial intelligence (AI) allows the identification of hidden patterns, deepening our understanding of the microbiota's role. This integrated approach promises to revolutionize BC treatment with novel insights and personalized interventions.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"198"},"PeriodicalIF":9.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12511378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145258633","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}
Yuli Wu, Guo Ji, Dongyan Han, Youhua Zhang, Xingchen Zhu, Hao Li, Man Li, Yaohui Gao, Ruting Xie, Min Xu, Ling Lu, Zixin Deng, Qing Wei, Huanlong Qin, Dexi Bi
{"title":"Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer.","authors":"Yuli Wu, Guo Ji, Dongyan Han, Youhua Zhang, Xingchen Zhu, Hao Li, Man Li, Yaohui Gao, Ruting Xie, Min Xu, Ling Lu, Zixin Deng, Qing Wei, Huanlong Qin, Dexi Bi","doi":"10.1038/s41522-025-00826-3","DOIUrl":"10.1038/s41522-025-00826-3","url":null,"abstract":"<p><p>Non-nucleatum Fusobacterium may play a nonnegligible role in colorectal cancer (CRC) and certain Fusobacterium lineages (namely, L1 and L5) have shown specific associations with CRC. We aim to clarify the complex connections between Fusobacterium and CRC. We found that the widely adopted quantitative PCR (qPCR) method could overestimate F. nucleatum abundance and, in fact, reflect L1 levels in clinical samples. A lineage-specific qPCR assay targeting L1/L5 was developed and validated using mock and clinical samples. Its application in independent cohorts confirmed that L1 was overabundant in CRC, whereas L5 correlated with lymphovascular invasion. Importantly, faecal L1 abundance was more predictive of CRC than F. nucleatum, supported also by cross-population metagenomic data. CRC-associated virulence and colonisation genes were found in various L1 species other than F. nucleatum. Our results highlight the clinical importance of L1/L5 in CRC with high-diversity Fusobacterium contexts and suggest that non-nucleatum Fusobacterium may also contribute to CRC.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"197"},"PeriodicalIF":9.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12511565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145258643","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}
{"title":"TNF-α modulation by rice bran peptides: implications for gut microbiota stability and cognitive health in aging.","authors":"Jianfei Mu, Qinlu Lin, Shuang Wang, Mingfeng Chen, Jianqiang Wang, Yajuan Chen, Yusheng Li, Ying Liang","doi":"10.1038/s41522-025-00830-7","DOIUrl":"10.1038/s41522-025-00830-7","url":null,"abstract":"<p><p>Aging-related neuroinflammation drives cognitive decline; however, the mechanisms by which gut microbiota-modulating bioactive compounds, such as rice bran peptide KF-8, mitigate this process remain unclear. Here, KF-8 was shown to ameliorate age-related traits in aged mice by reshaping gut microbiota, notably by stabilizing Akkermansia muciniphila (AKK), to suppress systemic inflammation and cognitive deficits. Specifically, antibiotic-treated mice receiving KF-8 exhibited neuroinflammation and declined cognition. KF-8 and AKK synergistically attenuated pro-inflammatory pathways, particularly TNF-α, in the blood and in the hippocampus. While TNF-α antibodies mirrored KF-8's benefits, TNF-α recombinant protein negated KF-8's protective effects. Combined KF-8 and AKK interventions aligned with TNF-α antibody outcomes, underscoring TNF-α's pivotal role. Our findings reveal that KF-8 enhances healthy aging by modulating gut microbiota, sustaining AKK, and suppressing TNF-α-driven neuroinflammation, thereby rescuing cognitive function in aged mice.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"195"},"PeriodicalIF":9.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12511609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145258654","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}
Rebecca A Gabrilska, Khalid Omeir, Jacob Ancira, Clint Miller, Craig D Tipton, Kendra P Rumbaugh, Joseph Wolcott, Ashley Noe, Kumudu Subasinghe, Megan Rowe, Nicole Phillips, Caleb D Phillips
{"title":"Functionally enriched human polymorphisms associate to species in the chronic wound microbiome.","authors":"Rebecca A Gabrilska, Khalid Omeir, Jacob Ancira, Clint Miller, Craig D Tipton, Kendra P Rumbaugh, Joseph Wolcott, Ashley Noe, Kumudu Subasinghe, Megan Rowe, Nicole Phillips, Caleb D Phillips","doi":"10.1038/s41522-025-00831-6","DOIUrl":"10.1038/s41522-025-00831-6","url":null,"abstract":"<p><p>Chronic wounds are a burden to millions of patients worldwide and impaired wound closure has been shown to be associated with wound microbiota. Recent evidence suggests human genetics may shape differences in composition of wound microbiomes. Here, a microbiome genome-wide association study was used to test effects of human genetics on the relative abundances of bacterial species in chronic wounds. Sixteen species were associated with 193 genetic loci distributed across 25 non-overlapping genomic regions, with per-species heritability estimates ranging up to 20%. Functional analyses on genomic regions and species resulted in overrepresentation of pathways relevant to microbial infection and wound healing. Species associated with host genetics exhibited co-occurrence relationships with common wound pathogens including Staphylococcus aureus. Moreover, the genetic distance among patients was significantly related to differences in their overall wound microbiome composition. Identification of genetic biomarkers reveals predictive risk factors and new mechanistic insight for chronic wounds.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"194"},"PeriodicalIF":9.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12511294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145258656","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}
{"title":"UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.","authors":"Shuang Liu, Bo Feng, Zhenyang Zhang, Jian Miao, Xueshuang Lai, Wei Zhao, Qinqin Xie, Xiaowei Ye, Caiyun Cao, Pengfei Yu, Jiabao Sun, Jianwei Guo, Zhen Wang, Qishan Wang, Zhe Zhang, Yuchun Pan","doi":"10.1038/s41522-025-00828-1","DOIUrl":"10.1038/s41522-025-00828-1","url":null,"abstract":"<p><p>The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"196"},"PeriodicalIF":9.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12511339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145258586","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}
Fang Liu, Jiahao Ren, Peihua Zhang, Wenliang Sun, Wan Liu, Allen D Smith, Robert W Li, Haiyan Yang
{"title":"Exploiting strong synergies between punicalagin and cefoperazone to combat methicillin-resistant Staphylococcus aureus infections.","authors":"Fang Liu, Jiahao Ren, Peihua Zhang, Wenliang Sun, Wan Liu, Allen D Smith, Robert W Li, Haiyan Yang","doi":"10.1038/s41522-025-00822-7","DOIUrl":"10.1038/s41522-025-00822-7","url":null,"abstract":"<p><p>Methicillin-resistant Staphylococcus aureus (MRSA) represents a serious public health threat. The effectiveness of existing antibiotics to treat MRSA infections is diminishing. This study aims to develop novel antimicrobial alternatives to fight MRSA infections. We conducted an anti-virulence screening targeting the L-lectin module (SLL) of the S. aureus cell wall protein serine-rich adhesin for platelets (SraP) against a database consisting of >14,000 natural products. The top candidates identified, including the polyphenol punicalagin (PA), were validated using surface plasmon resonance and a range of microbiological assays, including cell adhesion and invasion, biofilm formation, checkboard assays, microbiome studies, and RNAseq, for their properties to combat MRSA. The efficacy of punicalagin in treating MRSA infections, alone or in combination with existing antibiotics, was investigated using mouse models. PA was bound to the virulence factor SraP with high affinity and was highly effective in inhibiting MRSA colonization. PA significantly reduced the expression of multiple genes associated with ß-lactam resistance and disrupted biofilm formation. The synergistic effects between PA and cefoperazone (CF), a well-known bactericidal, were remarkable. The combination of PA and CF reduced the bacterial load in key murine organs by >98.9% and completely protected mice infected by MRSA. PA restored native gut microbiota disrupted by antibiotics, enriched butyrate-producing species, and repressed tissue inflammation. PA acted as a potent anti-virulence agent in addition to its intrinsic anti-inflammatory properties. Taking advantage of the strong synergism between PA and CF represents a promising strategy for combating MRSA infection and antibiotic resistance.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"193"},"PeriodicalIF":9.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12508159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145252052","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}
Cristina Cuesta-Marti, Benjamin Valderrama, Thomaz Bastiaanssen, John F Cryan, Catherine Stanton, Siobhain M O'Mahony, Gerard Clarke, Harriët Schellekens
{"title":"In vitro assessment of bacterial supernatants on hypothalamic gene expression: implications for appetite regulation.","authors":"Cristina Cuesta-Marti, Benjamin Valderrama, Thomaz Bastiaanssen, John F Cryan, Catherine Stanton, Siobhain M O'Mahony, Gerard Clarke, Harriët Schellekens","doi":"10.1038/s41522-025-00820-9","DOIUrl":"10.1038/s41522-025-00820-9","url":null,"abstract":"<p><p>Bacterial metabolites, such as short-chain fatty acids (SCFAs), influence energy balance, appetite, and endocrine function. Investigating cell-free (CFSs) and cell-free conditioned supernatants (CCSs) containing SCFAs and other microbial metabolites may help unravel the mechanisms underpinning these potential benefits for metabolic health. This study evaluated the neuroactive potential of two bacterial species, Bifidobacterium longum APC1472 and Limosilactobacillus reuteri ATCC PTA 6475, known for their metabolic health benefits. In silico analysis predicted the capacity of these bacteria to produce neuroactive metabolites involved in gut-brain communication. Next, untargeted metabolomics was used to evaluate the predicted functional capability of these two species to produce metabolites under different growth conditions. CFSs and CCSs were tested on embryonic and adult mouse hypothalamic cells to assess their effects on appetite-regulating gene expression. Results revealed supernatant type- and species-specific metabolite profiles, identifying B. longum APC1472 and L. reuteri ATCC PTA 6475 as acetate producers, with B. longum APC1472 also identified as a tryptophan producer. The distinct metabolite profiles of CFSs and CCSs from these two species induced specific effects on the modulation of ghrelin receptor and glucagon-like receptor 1 gene expression in hypothalamic cells. These findings validate an in vitro approach to identify bacterial metabolites with potential neuroactive and metabolic health benefits, demonstrated through modulation of mouse hypothalamic gene expression.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"192"},"PeriodicalIF":9.2,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12494950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225646","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}
Chaofan Chen, Qi Su, Min Zi, Xiaokun Hua, Zhiyun Zhang
{"title":"Harnessing gut microbiota for colorectal cancer therapy: from clinical insights to therapeutic innovations.","authors":"Chaofan Chen, Qi Su, Min Zi, Xiaokun Hua, Zhiyun Zhang","doi":"10.1038/s41522-025-00818-3","DOIUrl":"10.1038/s41522-025-00818-3","url":null,"abstract":"<p><p>Colorectal cancer (CRC) remains a leading cause of cancer morbidity and mortality worldwide, yet improvements in survival have been modest despite advances in conventional therapies. The gut microbiota has emerged as a critical player in CRC pathogenesis and a promising therapeutic target to enhance clinical outcomes. Mounting evidence implicates specific microorganisms, notably Escherichia coli, Fusobacterium nucleatum, and Bacteroides fragilis, in tumor initiation and progression through DNA damage, inflammatory modulation, and immunosuppressive mechanisms. Clinical trials investigating microbiome modulators-including faecal microbiota transplantation, probiotics, prebiotics, and engineered biotherapeutics-highlight their potential to augment chemotherapy, radiotherapy, immunotherapy, and surgical recovery, with encouraging preliminary efficacy in treatment-resistant CRC subtypes. Nonetheless, translating microbiome interventions into standardized clinical practice requires rigorous mechanistic validation, robust biomarker development, and careful management of safety concerns. Future research must focus on integrating high-resolution multi-omics, spatial microbiome mapping, artificial intelligence analytics, and innovative microbiome-targeted nanotechnologies to precisely reshape gut microbial communities, thereby ushering in a new era of precision oncology in colorectal cancer management.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"190"},"PeriodicalIF":9.2,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200526","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}
Lei Zhang, Ding-Ding Zhou, Jia Feng, Zhi-Jun Liao, Xian-Long Shu, Rui-Meng Yang, Yong-Chao Gao, Hong-Hao Zhou, Wei Zhang, You Zou, Rong Liu
{"title":"Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis.","authors":"Lei Zhang, Ding-Ding Zhou, Jia Feng, Zhi-Jun Liao, Xian-Long Shu, Rui-Meng Yang, Yong-Chao Gao, Hong-Hao Zhou, Wei Zhang, You Zou, Rong Liu","doi":"10.1038/s41522-025-00827-2","DOIUrl":"10.1038/s41522-025-00827-2","url":null,"abstract":"<p><p>Gut microbiota influence on the effectiveness of immune checkpoint inhibitors (ICIs), but research on fungi-an essential component of the microbiome-has been limited. This multi-cohort meta-analysis of 976 fecal metagenomes across 8 cohorts, representing melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC), identified fungal species associated with ICI efficacy. In melanoma, Rhizophagus irregularis and Debaryomyces hansenii were correlated with poor responses, whereas Aspergillus avenaceus was associated with great efficacy. In NSCLC, an increased abundance of Aspergillus pseudonomiae was associated with a favorable prognosis. Stronger bacterial-fungal interactions were observed in responders. The presence of certain fungi in fungal enterotypes, like Aspergillus or Saccharomyces, was linked to better efficacy to ICIs. Mouse models revealed Debaryomyces hansenii impaired ICI efficacy by reducing CD8+ T cells. Our findings highlight specific fungal signatures that may inform strategies to enhance ICI efficacy and encourage further research on microbial impacts on treatment outcomes.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"188"},"PeriodicalIF":9.2,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12475161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145177004","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}