Microbiome最新文献

{"title":"Dynamic response of gut microbiota mediates the adaptation of Cipangopaludina chinensis to Pomacea canaliculata invasion.","authors":"Mingyuan Liu, Changrun Sui, Wenyu Zhao, Chonghui Fan, Yao Zhang, Zhujun Qiu, Yuqing Wang, Qian Zhang, Ying Liu","doi":"10.1186/s40168-025-02160-4","DOIUrl":"10.1186/s40168-025-02160-4","url":null,"abstract":"<p><strong>Background: </strong>As an invasive species, Pomacea canaliculata exerts significant adverse effects on aquatic ecosystems. It can infect native freshwater snails, such as Cipangopaludina chinensis, by secreting pathogens, leading to increased stress and mortality. Gut microbiota play a crucial role in the survival and adaptation of gastropods, significantly influencing their health and resistance to environmental stressors. By comparing the gut microbiota composition and metabolic profiles between resistant (RE) and sensitive (SE) populations of C. chinensis, this study aims to elucidate the role of the gut microbiota in enhancing the survival of C. chinensis under the invasion pressure from P. canaliculata. And the mechanisms were further explored through gut microbiota transplantation, horizontal and vertical transmission experiments, and field studies. Video Abstract RESULTS: Our findings reveal that RE individuals exhibit greater gut microbiota diversity and a higher abundance of core microbiota, including Psychrobacter, Comamonas, and Pseudomonas, which are correlated with enhanced host survival in the presence of pathogen infections. Analysis of metabolite composition demonstrate that antibiotics and immunological enhancers are the main metabolites, which significantly enhance the host's resistance to pathogen infections. Notably, these core gut microbiota can be transmitted both horizontally and vertically, allowing C. chinensis populations to acquire resistance to the invasion of P. canaliculata. The SE group is enriched in pathogens, such as Mycoplasma. Following the transplantation of RE gut microbiota, SE individuals exhibited improved survival rates and core microbiota abundance. The vital role of core microbiota in maintaining the survival rate of C. chinensis was further confirmed in the field studies.</p><p><strong>Conclusion: </strong>This study highlights the crucial interactions between the gut microbiota and the host's adaptability, offering valuable insights for native species in response of invasive species pressure.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"171"},"PeriodicalIF":12.7,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12291480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708054","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":"Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.","authors":"Philip M Ashton, Leonardos Mageiros, James E Meiring, Angeziwa Chunga-Chirambo, Farhana Khanam, Sabina Dongol, Happy Banda, Abhilasha Karkey, Lorena Preciado-Llanes, Helena Thomaides-Brears, Malick Gibani, Nazmul Hasan Rajib, Nazia Rahman, Prasanta Kumar Biswas, Md Amirul Islam Bhuiyan, Sally Kay, Kate Auger, Olivier Seret, Nicholas R Thomson, Andrew J Pollard, Stephen Baker, Buddha Basnyat, John D Clemens, Christiane Dolecek, Sarah J Dunstan, Gordon Dougan, Robert S Heyderman, Virginia E Pitzer, Firdausi Qadri, Melita A Gordon, Kathryn E Holt, Thomas C Darton","doi":"10.1186/s40168-025-02125-7","DOIUrl":"10.1186/s40168-025-02125-7","url":null,"abstract":"<p><strong>Background: </strong>Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi (S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminated food and water, particularly in settings with poor water and sanitation infrastructure, resulting in over 10 million illnesses annually. As the pathogen invades via the gastrointestinal tract, it is plausible that the gut microbiome may influence the outcome of S. Typhi exposure. There is some evidence that bacteria producing short-chain fatty acids (SCFAs) may create an environment unfavourable to invasive Salmonella, but data from humans is limited.</p><p><strong>Methods: </strong>To investigate the association between the gut microbiome and typhoid fever, we analysed samples collected from three all-age cohorts enrolled in a prospective surveillance study conducted across three settings where typhoid fever is endemic (Dhaka, Bangladesh; Blantyre, Malawi; and Kathmandu, Nepal). Cohorts consisted of acute typhoid fever patients (n = 92), asymptomatic household contacts of typhoid fever patients (representing individuals who were likely exposed to S. Typhi but did not develop the disease, n = 97) and asymptomatic serosurvey participants with high Vi antibody titres (representing individuals who were exposed to S. Typhi and may be carriers, n = 69). The stool microbiomes of each cohort were characterised using shotgun metagenomics, and bacterial diversity, composition and function were compared.</p><p><strong>Results: </strong>We identified 4 bacterial species that were significantly lower in abundance in typhoid fever patients compared with household contacts (i.e. probably exposed), in two of the three participant populations (Bangladesh and Malawi). These bacteria may represent taxa that provide protection against the development of clinical infection upon exposure to S. Typhi and include the inflammation-associated species Prevotella copri clade A and Haemophilus parainfluenzae. Our functional analysis identified 28 specific metabolic gene clusters (MGCs) negatively associated with typhoid fever in Bangladesh and Malawi, including seven MGCs involved in SCFA metabolism. The putative protection provided by microbiome SCFA metabolism was supported by data from a controlled human infection model conducted in a UK population, in which participants who did not develop typhoid fever following ingestion of S. Typhi had a higher abundance of a putative SCFA-metabolising MGC (q-value = 0.22).</p><p><strong>Conclusions: </strong>This study identified the same protective associations between taxonomic and functional microbiota characteristics and non-susceptibility to typhoid fever across multiple human populations. Future research should explore the potential functional role of SCFAs and inflammation-associated bacteria in resistance to S. Typhi and other enteric infections. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"168"},"PeriodicalIF":12.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144690755","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":"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}