Microbiome最新文献

{"title":"Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes.","authors":"Robert Heyer, Maximilian Wolf, Dirk Benndorf, Sergio Uzzau, Jana Seifert, Lucia Grenga, Martin Pabst, Heike Schmitt, Bart Mesuere, Tim Van Den Bossche, Sven-Bastiaan Haange, Nico Jehmlich, Mariagrazia Di Luca, Manuel Ferrer, Sergio Serrano-Villar, Jean Armengaud, Helge B Bode, Patrick Hellwig, Catherine Robbe Masselot, Renaud Léonard, Paul Wilmes","doi":"10.1186/s40168-025-02119-5","DOIUrl":"10.1186/s40168-025-02119-5","url":null,"abstract":"<p><p>One Health seeks to integrate and balance the health of humans, animals, and environmental systems, which are intricately linked through microbiomes. These microbial communities exchange microbes and genes, influencing not only human and animal health but also key environmental, agricultural, and biotechnological processes. Preventing the emergence of pathogens as well as monitoring and controlling the composition of microbiomes through microbial effectors including virulence factors, toxins, antibiotics, non-ribosomal peptides, and viruses holds transformative potential. However, the mechanisms by which these microbial effectors shape microbiomes and their broader functional consequences for host and ecosystem health remain poorly understood. Metaproteomics offers a novel methodological framework as it provides insights into microbial dynamics by quantifying microbial biomass composition, metabolic functions, and detecting effectors like viruses, antimicrobial resistance proteins, and non-ribosomal peptides. Here, we highlight the potential of metaproteomics in elucidating microbial effectors and their impact on microbiomes and discuss their potential for modulating microbiomes to foster desired functions.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"134"},"PeriodicalIF":13.8,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132625","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":"Gut symbiotic bacteria enhance reproduction in Spodoptera frugiperda (J.E. Smith) by regulating juvenile hormone III and 20-hydroxyecdysone pathways.","authors":"Bo Chu, Shishuai Ge, Wei He, Xiaoting Sun, Jiajie Ma, Xianming Yang, Chunyang Lv, Pengjun Xu, Xincheng Zhao, Kongming Wu","doi":"10.1186/s40168-025-02121-x","DOIUrl":"10.1186/s40168-025-02121-x","url":null,"abstract":"<p><strong>Background: </strong>The insect gut microbiota forms a complex, multifunctional system that significantly affects phenotypic traits linked to environmental adaptation. Strong reproductive potential underpins the migratory success, population growth and destructive impact of the fall armyworm, Spodoptera frugiperda (J.E. Smith). However, the precise role of gut bacteria in S. frugiperda reproductive processes, distribution and transmission dynamics remains unclear.</p><p><strong>Results: </strong>We examined the gut microbiota of S. frugiperda a major invasive agricultural pest, identifying Enterococcus, Enterobacter, and Klebsiella as core microorganisms present throughout its life cycle. These microbes showed heightened activity during the egg stage, early larval stages and pre-oviposition period in females. Using an axenic insect re-infection system, Enterococcus quebecensis FAW181, Klebsiella michiganensis FAW071 and Enterobacter hormaechei FAW049 were found to significantly enhance host fecundity, increasing egg production by 62.73%, 59.95%, and 56.71%, respectively. Metagenomic and haemolymph metabolomic analyses revealed a positive correlation between gut symbiotic bacteria and hormone metabolism in female S. frugiperda. Further analysis of metabolites in the insect hormone biosynthesis pathway, along with exogenous injection of juvenile hormone III and 20-hydroxyecdysone, revealed that gut microbes regulate these hormones, maintaining levels equivalent to those in control insects. This regulation supports improved fecundity in S. frugiperda, aiding rapid colonization and population expansion.</p><p><strong>Conclusions: </strong>These findings emphasize the pivotal role of gut bacteria E. quebecensis FAW181, E. hormaechei FAW049, and K. michiganensis FAW071 in enhancing S. frugiperda reproduction by modulating JH III levels through JHAMT regulation and concurrently modulating the levels of 20E and its precursors via PHM. Our results provide novel insights into microbe-host symbiosis and pest management strategies for alien invasive species. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"132"},"PeriodicalIF":13.8,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101018/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132623","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":"Fecal microbiota transplantation for hypertension: an exploratory, multicenter, randomized, blinded, placebo-controlled trial.","authors":"Luyun Fan, Junru Chen, Qi Zhang, Jie Ren, Youren Chen, Jinfeng Yang, Lu Wang, Zihong Guo, Peili Bu, Bingpo Zhu, Yanyan Zhao, Yang Wang, Xiaoyan Liu, Wenjie Wang, Zhenzhen Chen, Qiannan Gao, Lemin Zheng, Jun Cai","doi":"10.1186/s40168-025-02118-6","DOIUrl":"10.1186/s40168-025-02118-6","url":null,"abstract":"<p><strong>Background: </strong>On the basis of the contribution of the gut microbiota to hypertension development, a novel strategy involving fecal microbiota transplantation (FMT) has been proposed to treat hypertension, but its efficacy has not been investigated in the clinic.</p><p><strong>Methods: </strong>In a randomized, blinded, placebo-controlled clinical trial (2021/03-2021/12, ClinicalTrials.gov, NCT04406129), hypertensive patients were recruited from seven centers in China, and received FMT or placebo capsules orally at three visits. The patients were randomized at a 1:1 ratio in blocks of four and stratified by center by an independent statistician. The intention-to-treat principle was implemented, as all randomized participants who received at least one intervention were included. The primary outcome was the decrease in office systolic blood pressure (SBP) from baseline to the day 30 visit. Adverse events (AEs) were recorded through the 3-month follow-up to assess safety measures. Alterations in BP, the fecal microbiome, and the plasma metabolome were assessed via exploratory analyses.</p><p><strong>Results: </strong>This study included 124 patients (mean age 43 years, 73.4% men) who received FMT (n = 63) or placebo (n = 61) capsules. The numbers of participants who experienced AEs (13 (20.6%) vs. 9 (14.8%), p = 0.39) and the primary outcome (6.28 (11.83) vs. 5.77 (10.06) mmHg, p = 0.62) were comparable between the groups. The FMT group presented a decrease in SBP after 1 week of FMT, with a between-arm difference of - 4.34 (95% CI, - 8.1 to - 0.58; p = 0.024) mmHg, but this difference did not persist even after repeated intervention. After FMT, shifts in microbial richness and structure were identified and the abundance of the phyla Firmicutes and Bacteroidetes was altered. Decreases in the abundances of Eggerthella lenta, Erysipelatoclostridium ramosum, Anaerostipes hadrus, Gemella haemolysans, and Streptococcus vestibularis and increases in the abundances of Parabacteroides merdae, Prevotella copri, Bacteroides galacturonicus, Eubacterium sp. CAG 180, Desulfovibrio piger, Megamonas hypermegale, Collinsella stercoris, Coprococcus catus, and Allisonella histaminiformans were identified and correlated with office SBP. Those species were also correlated with responding and inversely office SBP-associated metabolites including tyrosine, glutamine, aspartate, phenylalanine, methionine, serine, sarcosine, and/or asparagine.</p><p><strong>Conclusions: </strong>Safety but unsustainable BP reduction was observed in the first trial of the effects of FMT on hypertension. Additional intervention studies on specific microbes with metabolite-targeting and BP-modulating features are needed. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"133"},"PeriodicalIF":13.8,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100813/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132622","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":"Variation in diet concentration and bacterial inoculum size in larval habitats shapes the performance of the Asian tiger mosquito, Aedes albopictus.","authors":"Vincent Raquin, Edwige Martin, Guillaume Minard, Claire Valiente Moro","doi":"10.1186/s40168-025-02067-0","DOIUrl":"10.1186/s40168-025-02067-0","url":null,"abstract":"<p><strong>Background: </strong>Ecological niches present unique environmental and biological trademarks such as abiotic conditions, nutrient availability, and trophic interactions that may impact the ecology of living organisms. Female mosquitoes deposit their eggs in aquatic niches with fluctuating diet sources and microbial communities. However, how niche's diet and microbial composition impact mosquito performance (i.e., traits that maximize mosquito fitness) are not well understood. In this study, we focused on the Asian tiger mosquito, Aedes albopictus, one of the most invasive species in the world and a competent vector for human pathogens. To remove any external microbes, Ae. albopictus eggs were surface-sterilized then hatching larvae were exposed to a gradient of bacterial inoculum (i.e., initial microbial load) and diet concentrations while their impact on mosquito performance traits during juvenile development was measured.</p><p><strong>Results: </strong>Our results showed that Ae. albopictus larvae develop faster and give larger adults when exposed to microbiota in rearing water. However, mosquito performance, up to the adult stage, depends on both bacterial inoculum size and diet concentration in the aquatic habitat. Upon low inoculum size, larvae survived better if the diet was in sufficient amounts whereas a higher inoculum size was associated with optimal larvae survival only in the presence of the lower amount of diet. Inoculum size, and to a lesser extent diet concentration, shaped bacterial community structure and composition of larval-rearing water allowing the identification of bacterial taxa for which their abundance in larvae-rearing water correlated with niche parameters and/or larval traits.</p><p><strong>Conclusions: </strong>Our work demonstrates that both diet concentration and bacterial inoculum size impact mosquito performance possibly by shaping bacterial community structure in the larval habitat, which accounts for a large part of the juvenile's microbiota. Host-microbe interactions influence several mosquito life-history traits, and our work reveals that niche parameters such as inoculum size and diet concentration could have numerous implications on the microbiota assembly and host evolutionary trajectory. This underlies that host-microbe-environment interactions are an important yet overlooked factor of mosquito adaptation to its local environment, with potential future implications for vector control and vector ecology. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"130"},"PeriodicalIF":13.8,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128141","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":"Porcine nasal organoids to model interactions between the swine nasal microbiota and the host.","authors":"Laura Bonillo-Lopez, Noelia Carmona-Vicente, Ferran Tarrés-Freixas, Karl Kochanowski, Jorge Martínez, Mònica Perez, Marina Sibila, Florencia Correa-Fiz, Virginia Aragon","doi":"10.1186/s40168-025-02088-9","DOIUrl":"10.1186/s40168-025-02088-9","url":null,"abstract":"<p><strong>Background: </strong>Interactions between the nasal epithelium, commensal nasal microbiota, and respiratory pathogens play a key role in respiratory infections. Currently, there is a lack of experimental models to study such interactions under defined in vitro conditions. Here, we developed a porcine nasal organoid (PNO) system from nasal tissue of pigs as well as from cytological brushes.</p><p><strong>Results: </strong>PNOs exhibited similar structure and cell types to the nasal mucosa, as evaluated by immunostaining. PNOs were inoculated with porcine commensal strains of Moraxella pluranimalium, Rothia nasimurium, and the pathobiont Glaesserella parasuis for examining host-commensal-pathogen interactions. All strains adhered to the PNOs, although at different levels. M. pluranimalium and G. parasuis strains stimulated the production of proinflammatory cytokines, whereas R. nasimurium induced the production of IFNγ and diminished the proinflammatory effect of the other strains.</p><p><strong>Conclusions: </strong>Overall, PNOs mimic the in vivo nasal mucosa and can be useful to perform host-microbe interaction studies. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"131"},"PeriodicalIF":13.8,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128139","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":"Microbiota alterations leading to amino acid deficiency contribute to depression in children and adolescents.","authors":"Teng Teng, Fang Huang, Ming Xu, Xuemei Li, Lige Zhang, Bangmin Yin, Yuping Cai, Fei Chen, Luman Zhang, Jushuang Zhang, Aoyi Geng, Chengzhi Chen, Xiaofei Yu, Jing Sui, Zheng-Jiang Zhu, Kai Guo, Chenhong Zhang, Xinyu Zhou","doi":"10.1186/s40168-025-02122-w","DOIUrl":"10.1186/s40168-025-02122-w","url":null,"abstract":"<p><strong>Background: </strong>Major depressive disorder (MDD) in children and adolescents is a growing global public health concern. Metabolic alterations in the microbiota-gut-brain (MGB) axis have been implicated in MDD pathophysiology, but their specific role in pediatric populations remains unclear.</p><p><strong>Results: </strong>We conducted a multi-omics study on 256 MDD patients and 307 healthy controls in children and adolescents, integrating plasma metabolomics, fecal metagenomics, and resting-state functional magnetic resonance imaging (rs-fMRI) of the brain. KEGG enrichment analysis of 360 differential expressed metabolites (DEMs) indicated significant plasma amino acid (AA) metabolism deficiencies (p-value < 0.0001). We identified 58 MDD-enriched and 46 MDD-depleted strains, as well as 6 altered modules in amino acid metabolism in fecal metagenomics. Procrustes analysis revealed the association between the altered gut microbiome and circulating AA metabolism (p-value = 0.001, M² = 0.932). Causal analyses suggested that plasma AAs might mediate the impact of altered gut microbiota on depressive and anxious symptoms. Additionally, rs-fMRI revealed that connectivity deficits in the frontal lobe are associated with depression and 22 DEMs in AA metabolism. Furthermore, transplantation of fecal microbiota from MDD patients to adolescent rats induced depressive-like behaviors and 14 amino acids deficiency in the prefrontal cortex (PFC). Moreover, the dietary lysine restriction increased depression susceptibility in adolescent rats by reducing the expression of excitatory amino acid transporters in the PFC.</p><p><strong>Conclusions: </strong>Our findings highlight that gut microbiota alterations contribute to AAs deficiency, particularly lysine, which plays a crucial role in MDD pathogenesis in children and adolescents. Targeting AA metabolism may offer novel therapeutic strategies for pediatric depression. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"128"},"PeriodicalIF":13.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102129","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":"Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces.","authors":"Tianyu Sun, Hongwei Liu, Ningqi Wang, Mingcong Huang, Samiran Banerjee, Alexandre Jousset, Yangchun Xu, Qirong Shen, Shimei Wang, Xiaofang Wang, Zhong Wei","doi":"10.1186/s40168-025-02120-y","DOIUrl":"10.1186/s40168-025-02120-y","url":null,"abstract":"<p><strong>Background: </strong>Streptomyces spp. are known for producing bioactive compounds that suppress phytopathogens. However, previous studies have largely focused on their direct interactions with pathogens and plants, often neglecting their interactions with the broader soil microbiome. In this study, we hypothesized that these interactions are critical for effective pathogen control. We investigated a diverse collection of Streptomyces strains to select those with strong protective capabilities against tomato wilt disease caused by Ralstonia solanacearum. Leveraging a synthetic community (SynCom) established in our lab, alongside multiple in planta and in vitro co-cultivation experiments, as well as transcriptomic and metabolomic analyses, we explored the synergistic inhibitory mechanisms underlying bacterial wilt resistance facilitated by both Streptomyces and the soil microbiome.</p><p><strong>Results: </strong>Our findings indicate that direct antagonism by Streptomyces is not sufficient for their biocontrol efficacy. Instead, the efficacy was associated with shifts in the rhizosphere microbiome, particularly the promotion of two native keystone taxa, CSC98 (Stenotrophomonas maltophilia) and CSC13 (Paenibacillus cellulositrophicus). In vitro co-cultivation experiments revealed that CSC98 and CSC13 did not directly inhibit the pathogen. Instead, the metabolite of CSC13 significantly enhanced the inhibition efficiency of Streptomyces R02, a highly effective biocontrol strain in natural soil. Transcriptomic and metabolomic analyses revealed that CSC13's metabolites induced the production of Erythromycin E in Streptomyces R02, a key compound that directly suppressed R. solanacearum, as demonstrated by our antagonism tests.</p><p><strong>Conclusions: </strong>Collectively, our study reveals how beneficial microbes engage with the native soil microbiome to combat pathogens, suggesting the potential of leveraging microbial interactions to enhance biocontrol efficiency. These findings highlight the significance of intricate microbial interactions within the microbiome in regulating plant diseases and provide a theoretical foundation for devising efficacious biocontrol strategies in sustainable agriculture. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"126"},"PeriodicalIF":13.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102126","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":"Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces.","authors":"Hanpeng Liao, Chang Wen, Dan Huang, Chen Liu, Tian Gao, Qiyao Du, Qiu-E Yang, Ling Jin, Feng Ju, Mengting Maggie Yuan, Xiang Tang, Pingfeng Yu, Shungui Zhou, Pedro J Alvarez, Ville-Petri Friman","doi":"10.1186/s40168-025-02117-7","DOIUrl":"10.1186/s40168-025-02117-7","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.</p><p><strong>Results: </strong>Multi-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.</p><p><strong>Conclusion: </strong>Our study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"127"},"PeriodicalIF":13.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102121","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":"Tissue-resident microbiota signature in nasopharyngeal carcinoma.","authors":"Xi-Rong Tan, Han Qiao, Ying-Qing Li, Wei Jiang, Sheng-Yan Huang, Sha Gong, Wen-Fei Li, Ling-Long Tang, Guan-Qun Zhou, Ye-Lin Liang, Hui Li, Qing-Mei He, Jie-Wen Bai, Ming-Liang Ye, Jing-Yun Wang, Sai-Wei Huang, Jun-Yan Li, Chun-Qiao Gan, Ying-Qin Li, Yin Zhao, Ying Sun, Jun Ma, Na Liu","doi":"10.1186/s40168-025-02114-w","DOIUrl":"10.1186/s40168-025-02114-w","url":null,"abstract":"<p><strong>Background: </strong>Emerging evidence reveals that microbiota plays a crucial role in multiple cancers. Nasopharyngeal carcinoma (NPC) tissues harbour microbiota, highlighting the need to investigate the clinical implications of tissue-resident microbiota in the development of NPC. Here, we aim to clarify the specific profile of tissue-resident microbiota and its influence on NPC outcomes.</p><p><strong>Results: </strong>This retrospective study included 491 NPC patients from Sun Yat-sen University Cancer Center (Guangzhou, China) and the Affiliated Hospital of Guilin Medical College (Guilin, China). We profiled the microbial composition of 343 NPC and 36 normal nasopharyngeal tissues through sequencing of the genes encoding the 16S rRNA subunit of bacterial ribosomes. There were significant differences in microbial composition, alpha diversity (Shannon index, P = 0.007; Simpson index, P = 0.036), and beta diversity (Bray-Curtis distance: R² = 0.016, F = 5.187, P = 0.001; unweighted UniFrac distance: R² = 0.017, F = 5.373, P = 0.001) between NPC and normal nasopharyngeal tissues. A bacterial signature comprising four risk bacterial genera, including Bacteroides, Alloprevotella, Parvimonas, and Dialister, was constructed in the training cohort (n = 171). Patients in the high-risk group had shorter disease-free (HR 2.80, 95% CI 1.51-5.18, P < 0.001), distant metastasis-free (HR 4.00, 95% CI 1.77-9.01, P < 0.001), and overall survival (HR 3.45, 95% CI 1.77-6.72, P < 0.001) than those of patients in the low-risk group. Similar results were yielded in the internal validation (n = 172) and external validation (n = 148) cohorts. Integrated multi-omics analysis revealed that NPC tissues harbouring abundant risk bacteria were characterised by deficient immune infiltration, which was verified by multiplex immunohistochemistry.</p><p><strong>Conclusions: </strong>This study developed and validated the applicability of a four-bacteria signature as a prognostic tool for NPC prognostication. Integrated multi-omics analysis further uncovered that the tumour immune microenvironment was perturbed by tissue-resident microbiota, which might pave the way towards the era of microbiota-targeted precision medicine for NPC. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"125"},"PeriodicalIF":13.8,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094178","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":"Multi-omics analysis reveals that Bacillus spp. enhance mucosal antiviral immunity in teleost fish by mediating diglyceride production through lipid metabolism.","authors":"Gaofeng Cheng, Weiguang Kong, Ruiqi Lin, Zhihao Jiang, Xinyou Wang, Xueying Qin, Yong Shi, Peng Yang, Xiaoyun Chen, Lu Xia, Zhen Xu","doi":"10.1186/s40168-025-02124-8","DOIUrl":"10.1186/s40168-025-02124-8","url":null,"abstract":"<p><strong>Background: </strong>Symbiotic microbiota in vertebrates play critical roles in establishing and enhancing host resistance to pathogenic infections as well as maintaining host homeostasis. The interactions and mechanisms of commensal microbiota-mediated mucosal immune systems have been extensively studied in mammals and, to a lesser extent, in birds. However, despite several studies emphasizing the role of mucosal microbiota in controlling pathogen infections in teleost fish, limited knowledge exists regarding the core microbiota and the mechanisms by which they contribute to resistance against viral infections.</p><p><strong>Results: </strong>Our findings suggest that viral infections shape clinical manifestations of varying severity in infected fish. An increased abundance of Bacillus spp. in the mild phenotype indicates its crucial role in influencing fish immunity during viral infections. To confirm that Bacillus spp. act as a core contributor against viral infection in fish, we isolated a representative strain of Bacillus spp. from largemouth bass (Micropterus salmoides), which was identified as Bacillus velezensis (Bv), and subsequently conducted feeding trials. Our study demonstrated that dietary supplementation with Bv significantly reduced mortality from largemouth bass virus (LMBV) infection in bass by enhancing host immunity and metabolism as well as by regulating the microbial community. Furthermore, multi-omics analysis elucidated the mechanism by which Bacillus spp. confer resistance to viral infections by regulating the production of diglyceride (DG) during lipid metabolism.</p><p><strong>Conclusions: </strong>Our study provides the first evidence that Bacillus spp. are a core microbiota for combating viral infections in teleost fish, shedding light on the conserved functions of probiotics as a core microbiota in regulating microbial homeostasis and mucosal immunity across the vertebrate lineage.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"123"},"PeriodicalIF":13.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086155","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}