Microbiome最新文献

{"title":"Disruption of hindgut microbiome homeostasis promotes postpartum energy metabolism disorders in dairy ruminants by inhibiting acetate-mediated hepatic AMPK-PPARA axis.","authors":"Shuo Wang, Fanlin Kong, Xinyue Zhang, Dongwen Dai, Chen Li, Zhijun Cao, Yajing Wang, Wei Wang, Shengli Li","doi":"10.1186/s40168-025-02150-6","DOIUrl":"10.1186/s40168-025-02150-6","url":null,"abstract":"<p><strong>Background: </strong>Postpartum energy metabolism disorders pose a significant challenge to the health and productivity of dairy ruminants, yet their underlying pathogenesis remains poorly understood. The critical role of the gut microbiota in regulating host metabolic processes via the \"gut-liver axis\" has garnered increasing attention, but its specific mechanisms in dairy ruminant energy metabolism disorders are still unclear. This study uses dairy cows as a model and employs a large-scale case-control analysis to systematically investigate the pathophysiological basis of postpartum energy metabolism disorders through the lens of the \"gut-liver axis.\"</p><p><strong>Results: </strong>Postpartum energy metabolism disorders in dairy cows are characterized by elevated blood β-hydroxybutyrate (BHB) and aspartate aminotransferase (AST) levels, and hepatic steatosis. A random forest model based on gut microbiota effectively predicts disease occurrence (AUC = 0.74). Multi-omics (metagenomics, metabolomics, and transcriptomics) analysis further identified key microbes, including Faecousia species (sp017465625 and sp017380435), Methanosphaera species (sp016282985), and Bifidobacterium globosum. These microbes regulate acetate concentration in the gut, which is significantly correlated with key genes in the hepatic PPAR and PI3K-AKT pathways, as well as with blood BHB levels. Primary hepatocyte culture experiments further confirmed that sodium acetate effectively inhibits hepatic fat deposition induced by mixed fatty acids through the hepatic AMPK-PPARA axis and reduces the production of BHB in the culture medium.</p><p><strong>Conclusion: </strong>This study demonstrates that key gut microbes and their metabolic product (acetate) inhibit the occurrence of metabolic disorders through the hepatic AMPK-PPARA axis. These findings provide new insights and potential therapeutic targets for understanding and mitigating postpartum metabolic disorders in dairy ruminants. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"167"},"PeriodicalIF":13.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649881","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":"Sulfur-rich deposits associated with the deep submarine volcano Fani Maoré support broad microbial sulfur cycling communities.","authors":"Stéven Yvenou, Mélanie Le Moigne, Olivier Rouxel, Johanne Aubé, Blandine Trouche, Cécile Cathalot, Emmanuel Rinnert, Xavier Philippon, Sandrine Chéron, Audrey Boissier, Vivien Guyader, Yoan Germain, Anne Godfroy, Erwan G Roussel, Karine Alain","doi":"10.1186/s40168-025-02153-3","DOIUrl":"10.1186/s40168-025-02153-3","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;In 2018, the island of Mayotte located in the western Indian ocean, has experienced a seismo-volcanic crisis linked to the birth of an impressive intraplate submarine volcano at the east of the island. This volcano, named Fani Maoré, which has not yet been the subject of microbiological studies, triggered the largest submarine eruptive event ever recorded. Close to the volcano's summit is a singular meter-size structure containing abundant native sulfur mineralizations. While a wide variety of ecosystems, with more or less well documented microbial communities, are found in active volcanoes on the ocean floor, knowledge on microbial communities hosted in habitats such as sulfur-rich intraplate volcanoes, that are not located on hotspots, remains limited. Genome-resolved metagenomics, culture-based functional approaches, geochemical and mineralogical analyses were combined to characterize the geological and physico-chemical constraints of the environment surrounding the yellow deposit part of this hotspot volcano and the composition and functions of its microbial community.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Geological and geochemical analyses indicated that this volcanic habitat had high concentrations in various sulfur species, including native sulfur, hydrogen sulfide and sulfate. Twenty-three Metagenome Assembled Genomes (MAGs) belonging to 8 different bacterial phyla, mainly Pseudomonadota, Bacteroidota and Campylobacterota, were reconstructed from the sulfur-rich deposit and analyzed. The vast majority of MAGs encoded genes for complete sulfur cycling metabolic pathways, in particular sulfur oxidation. Estimation of the cultivable microbial fraction revealed a diversity of microorganisms, with high growth rates for sulfur reduction, sulfate reduction with dihydrogen, and sulfur oxidation. Sulfur compound (S&lt;sup&gt;0&lt;/sup&gt;, SO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt; and S&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt;) disproportionation was also observed in cultures. The versatile genus Sulfurimonas was prevalent in culture at 6 and 20 °C, in the presence of different sulfur redox couples.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Microbial communities, including taxa commonly found in ridge hydrothermal systems, were composed of autotrophic, heterotrophic or mixotrophic taxa using a large range of electron donors and acceptors to fuel their catabolism, particularly sulfur compounds in all common oxidation states. They had the genetic potential and physiological capacity to carry out all the metabolic reactions of the microbial sulfur cycle using the abiotic sulfur compounds present in their habitat. Representatives of the Sulfurimonas genus were among the main chemoautotrophs, since they predominated in eleven different temperature-redox pair culture combinations. Based on the observations, a conceptual model was proposed to describe the interactions in this sulfur-rich deposit that may occur between the microorganisms, the physico-chemical con","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"166"},"PeriodicalIF":13.8,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12261689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642926","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":"DnaK of Parvimonas micra extracellular vesicles interacts with the host fibroblasts BAG3-IKK-γ axis to accelerate TNF-α secretion in oral lichen planus.","authors":"Xiaoli Ji, Mengfan Zhi, Xiufeng Gu, Ying Han, Xiang Lan, Lixiang Song, Peipei Sun, Jingyuan Li, Xiangmin Qi, Qiang Feng","doi":"10.1186/s40168-025-02151-5","DOIUrl":"10.1186/s40168-025-02151-5","url":null,"abstract":"<p><strong>Background: </strong>Oral lichen planus (OLP) is one of the most frequent oral mucosal diseases associated with chronic inflammation, despite a profoundly limited understanding of its underlying pathogenic mechanisms.</p><p><strong>Results: </strong>The microbiome analysis was conducted on buccal and lip mucosae, tongue dorsum, and saliva in nonerosive/erosive OLP patients and healthy individuals. Significant variations were observed in the oral microbiome of OLP patients, particularly in the buccal mucosa. Network, random forest, and NetShift analysis collectively indicated that Parvimonas micra (P. micra) emerged as a crucial bacterium in OLP. In vivo analysis further demonstrated that P. micra was abundant at the junction of epithelial and connective tissue layers in OLP lesions. Single-cell RNA sequencing data implicated fibroblasts as potential targets, characterized by upregulation of the NF-κB pathway linked to TNF-α. Co-culturing of P. micra or its extracellular vesicles (EVs) with fibroblasts showed that P. micra and EVs could activate the NF-κB signaling pathway and suppress autophagy in buccal mucosal fibroblasts. Among the pathogenic effectors, DnaK from P. micra EVs was identified to interact with BAG3 in fibroblasts. The interaction of DnaK with BAG3 subsequently activated the NF-κB pathway and decreased autophagy flux. Additionally, we identified that IKK-γ was the key downstream protein that could bind with DnaK-BAG3, thereby inhibiting autophagy and promoting TNF-α secretion.</p><p><strong>Conclusions: </strong>We initially revealed that P. micra was a crucial pathogen in the development of OLP and demonstrated that P. micra's EVs induce the inhibition of autophagy and enhanced TNF-α secretion in OLP fibroblasts via the DnaK-BAG3-IKK-γ axis. This study offers novel insights into the pathogenic mechanisms underlying OLP. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"164"},"PeriodicalIF":13.8,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12261604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144637432","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":"Correction: Gut bacterium Acinetobacter sp. assists Camellia weevil with host plant adaptation by degrading tea saponin via the benzoate pathway.","authors":"Feng Song, Jinping Shu, Shouke Zhang","doi":"10.1186/s40168-025-02167-x","DOIUrl":"10.1186/s40168-025-02167-x","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"165"},"PeriodicalIF":13.8,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12261690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144637431","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":"Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants.","authors":"Yijun Tang, Pengchao Zhan, Yingjian Wu, Tao Zhang, Di Yin, Yunlong Gao, Yueying Yu, Shengnan Qiu, Jiaqi Zhao, Xue Zhang, Zhe Ma, Yanting Chen, Liang Zhao, Shengyong Mao, Jinhu Huang, Wei-Hua Chen, Jinxin Liu","doi":"10.1186/s40168-025-02139-1","DOIUrl":"10.1186/s40168-025-02139-1","url":null,"abstract":"<p><strong>Background: </strong>Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes-especially their impact on diversity, adaptation, and dietary responsiveness-remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation.</p><p><strong>Results: </strong>Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs-a ~ 216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE ( https://rummge.liulab-njau.com ), to support further research.</p><p><strong>Conclusions: </strong>This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"162"},"PeriodicalIF":13.8,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619027","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":"Cetobacterium somerae-derived argininosuccinic acid promotes intestinal and liver ureagenesis to alleviate ammonia intoxication.","authors":"Shidong Wang, Xue Li, Muzi Zhang, Ming Li","doi":"10.1186/s40168-025-02152-4","DOIUrl":"10.1186/s40168-025-02152-4","url":null,"abstract":"<p><strong>Background: </strong>Ammonia generated from amino acid metabolism is a cytotoxin that can adversely affect cell function and overall health and potentially lead to cellular toxicity and death due to its accumulation. Previous studies have shown that acute ammonia intoxication (AI) can increase the intestinal C. somerae abundance, hinting at a possible involvement of C. somerae in the host's reaction to AI. Nonetheless, the precise mechanism through which C. somerae mitigates the effects of AI is uncertain.</p><p><strong>Results: </strong>This research elucidated the metabolic mechanism of transplanting Cetobacterium somerae ceto (CSC) to assist the host in managing AI. Our results suggest that (I) AI resulted in impaired ureagenesis pathway. This was manifested by elevated levels of ammonia in the blood, liver, and intestines, along with decreased urea levels. (II) Supplementing orally with live CSC facilitated its colonization in the intestines, mitigating AI by reversing depletion of intestinal argininosuccinic acid (ARA) and promoting ureagenesis. (III) CSC synthesized ARA from aspartate and asparagine through the asnA-ansA/B-argG gene cluster. Additionally, CSC assimilated fumaric acid and malic acid from the environment, dampening the degradation of ARA by CSC's fumA-fumB-argH gene cluster. (IV) Live CSC provided ARA support for ureagenesis in the intestine and liver, reducing endogenous ammonia levels of pseudo-sterile yellow catfish. (V) Supplementation of ARA decreased systemic ammonia levels by promoting ureagenesis. Inhibiting the expression of argininosuccinate lyase in the liver through RNA interference can impede arginine synthesis, thereby eliminating the ammonia-lowering effect of ARA.</p><p><strong>Conclusion: </strong>In summary, this study found that the role of probiotics in enhancing the host's resistance to AI depends on the function of ARA generated by CSC. AI can lead to depletion of ARA and interrupting ureagenesis, while CSC-produced ARA supplements ureagenesis in the liver and intestines, facilitating ammonia detoxification into urea. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"163"},"PeriodicalIF":13.8,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619026","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":"Nucleotides enriched under heat stress recruit beneficial rhizomicrobes to protect plants from heat and root-rot stresses.","authors":"Haijiao Liu, Yingwei Su, Chen Ye, Denghong Zuo, Luotao Wang, Xinyue Mei, Weiping Deng, Yixiang Liu, Huichuan Huang, Jianjun Hao, Jiangchao Zhao, Dongli Wang, Xin Zhang, Youyong Zhu, Junfeng Liu, Min Yang, Shusheng Zhu","doi":"10.1186/s40168-025-02126-6","DOIUrl":"10.1186/s40168-025-02126-6","url":null,"abstract":"<p><strong>Background: </strong>Plants thrive under biotic and abiotic stresses with the help of rhizomicrobiota. Root exudates play a pivotal role in recruiting beneficial microbes that assist plants in surviving environmental challenges, but the mechanisms of plant-microbiome interactions to resist multiple stresses remain elusive. We investigated how heat stress alters the rhizomicrobiomes of Panax notoginseng and how these heat stress-regulated microbes confer enhanced heat tolerance and disease resistance.</p><p><strong>Results: </strong>We revealed that heat stress at 36 °C caused thermal damage to plants while enhancing heat tolerance and disease resistance for the survival of subsequent plants. Specifically, the beneficial microbes Burkholderia sp. and Saitozyma podzolica were recruited by the heat-stressed P. notoginseng and were confirmed to be responsible for resisting multiple stresses. Heat stress-induced plant roots secrete nucleotides such as purines and pyrimidines to promote the proliferation of these two beneficial microbes rather than root-rot pathogens. The exogenous application of these nucleotides to natural soil also resulted in the enrichment of the same beneficial microbes. Cross-species validation experiments in Capsicum annuum (pepper) and Solanum lycopersicum (tomato) further demonstrated that co-application of nucleotides with beneficial microbes synergistically enhanced heat tolerance.</p><p><strong>Conclusions: </strong>Our findings highlight a plant strategy for thriving under multiple adversities and propose a potential pathway by leveraging nucleotide-mediated recruitment of beneficial microbes for enhancing plant resilience against multiple stresses. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"160"},"PeriodicalIF":13.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144584322","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":"Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.","authors":"Jiaying Zhu, Min-Zhi Jiang, Xue Chen, Min Li, Yu-Lin Wang, Chang Liu, Shuang-Jiang Liu, Wei-Hua Chen","doi":"10.1186/s40168-025-02156-0","DOIUrl":"10.1186/s40168-025-02156-0","url":null,"abstract":"<p><strong>Background: </strong>Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.</p><p><strong>Methods: </strong>We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the \"PairInteraX\" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.</p><p><strong>Results: </strong>Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.</p><p><strong>Conclusions: </strong>This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"161"},"PeriodicalIF":13.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144584323","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":"Organic fertilizer enhances the secretion of microRNAs from tomato roots to facilitate beneficial rhizosphere microorganism expansion and suppress Ralstonia solanacearum proliferation.","authors":"Shuo Liu, Hai-Yang Li, Tao Zhang, Yang-Kai Li, Xin-Di Liao, Si-Cheng Xing","doi":"10.1186/s40168-025-02137-3","DOIUrl":"10.1186/s40168-025-02137-3","url":null,"abstract":"<p><strong>Background: </strong>Key members of the rhizomicrobiome, plant root exudates, and pathogen inhibition are important for the immune system functions of disease-suppressive soils, and a \"cry for help\" mechanism is proposed to describe this immune response process. However, there is still a gap in the understanding of rhizomicrobiome functional genes that are regulated by plants; to date, most studies have shown that the \"cry for help\" process is mediated by root exudates. The cross-talk between eukaryotes and prokaryotes through microRNAs (miRNAs) represents a new route for research on host and microbe interactions.</p><p><strong>Results: </strong>After six generations of plantings, the disease index of the tomato plants significantly decreased compared with that of the first-generation plants (P < 0.05) in both the organic fertilizer (OF) and chemical fertilizer (CF) groups, and the effectiveness of OF in reducing the disease index of the tomato plants was obviously greater than that of CF. Furthermore, tomato miRNAs were identified in the rhizosphere soil, and exosome-like extracellular vesicles were found to be their potential carriers. Subsequent experiments confirmed that the tomato roots secreted sly-miR159 and sly-miR319c-3p, which were both crucial miRNAs that inhibited the proliferation of Ralstonia solanacearum and that sly-miR159 promoted the growth of beneficial bacteria belonging to the Streptomyces and Bacillus genera. The active functional components of organic fertilizer included soluble macromolecular compounds (nonmicrobial components) and microbial components. Among these, the nonmicrobial components induced the roots of tomato plants to secrete key microRNAs (sly-miR159 and sly-miR319c-3p), whereas the microbial components provided beneficial microbial communities for the rhizosphere of plants, jointly promoting the inhibition of Ralstonia solanacearum.</p><p><strong>Conclusions: </strong>In this study, the role of organic manure in promoting the establishment of disease-suppressive soil for combating bacterial wilt disease in tomato plants was comprehensively investigated. Moreover, this study provides a new perspective for research on rhizosphere immunity; that is, the presence of plant-derived exosomal miRNAs in the rhizosphere could serve as a new way to explain interactions between plants and the rhizosphere microbial community. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"159"},"PeriodicalIF":13.8,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12228361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144567632","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":"Adaptive strategies of Caribbean sponge holobionts beyond the mesophotic zone.","authors":"Benoît Paix, Alexane Thivet, Celso Domingos, Özlem Erol, Niels van der Windt, Young H Choi, Nicole J de Voogd","doi":"10.1186/s40168-025-02146-2","DOIUrl":"10.1186/s40168-025-02146-2","url":null,"abstract":"<p><strong>Background: </strong>Marine sponges and their microbiomes function together as holobionts, playing essential roles in ecosystem dynamics and exhibiting remarkable adaptability across depth gradients. This study utilized a multi-omics approach, integrating microbiome and metabolome analyses, to investigate adaptive strategies in sponge holobionts inhabiting the mesophotic (80-125 m), upper-rariphotic (125-200 m), and lower-rariphotic (200-305 m) zones of Curaçao. We hypothesized that depth-related environmental factors drive distinct adaptive strategies, similar to patterns observed in fish and coral assemblages.</p><p><strong>Results: </strong>Results revealed major differences in holometabolomes and microbial communities between Demospongiae and Hexactinellida sponges, reflecting class-specific adaptive strategies. Notably, phospholipid homeoviscous adaptation to temperature and pressure might emerge as a key mechanism in phosphorus metabolism. Adaptations in nitrogen metabolism were linked to diverse ammonia oxidizing archaea (AOA) symbionts, and dissolved organic matter cycling. Hexactinellid microbiomes exhibited intra-specific heterogeneity; however, species-specific associations with AOA symbionts such as Cenarchaeum and Nitrosopumilus were observed. Additionally, the lower-rariphotic hexactinellid holometabolomes highlighted the significance of the nested ecosystem concept through the identification of secondary metabolites produced by their associated fauna (aphrocallistins by zoanthids and xanthurenic acid by shrimp).</p><p><strong>Conclusions: </strong>This study highlights the ecological significance of sponge holobionts in mesophotic and rariphotic ecosystems, revealing diverse adaptations to unique physicochemical conditions and biotic interactions. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"157"},"PeriodicalIF":13.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553960","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}