Microbiome最新文献

{"title":"Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.","authors":"Julia Krasenbrink, Buck T Hanson, Anna S Weiss, Sabrina Borusak, Tomohisa Sebastian Tanabe, Michaela Lang, Georg Aichinger, Bela Hausmann, David Berry, Andreas Richter, Doris Marko, Marc Mussmann, David Schleheck, Bärbel Stecher, Alexander Loy","doi":"10.1186/s40168-025-02175-x","DOIUrl":"10.1186/s40168-025-02175-x","url":null,"abstract":"<p><strong>Background: </strong>Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.</p><p><strong>Results: </strong>¹³CO₂ breath tests with germ-free C57BL/6 mice gavaged with ¹³C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.</p><p><strong>Conclusions: </strong>Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"184"},"PeriodicalIF":12.7,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12330013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799567","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":"Sulfated dietary fiber protects gut microbiota from antibiotics.","authors":"Fuqing Wu, Xiaoqian Annie Yu, David Angeles-Albores, Susan E Erdman, Eric J Alm","doi":"10.1186/s40168-025-02176-w","DOIUrl":"10.1186/s40168-025-02176-w","url":null,"abstract":"<p><strong>Background: </strong>Antibiotics, while essential for combating pathogens, also disrupt commensal bacteria, leading to gut microbiota imbalance and associated diseases. However, strategies to mitigate such collateral damage remain largely underexplored.</p><p><strong>Result: </strong>In this study, we found that fucoidan, a marine polysaccharide derived from brown seaweed, provides broad-spectrum growth protection against multiple classes of antibiotics for human gut microbial isolates in vitro and for fecal communities ex vivo. This protective effect is dependent on the structural integrity, molecular weight, and sulfur content of the polysaccharide. Transcriptomic analysis showed that while fucoidan had minimal impact on baseline gene expression, it counteracted about 60% of the genes induced by kanamycin, suggesting a potential inhibition of kanamycin. Mass spectrometry results further showed that this inhibition may be due to the non-specific binding of fucoidan to kanamycin in solution. Finally, animal model experiments revealed that fucoidan facilitated the recovery of gut microbes following antibiotic treatment in vivo.</p><p><strong>Conclusion: </strong>These findings suggest fucoidan could serve as a potential intervention to help protect gut microbiota during antibiotic therapy. Further studies are needed to evaluate its clinical potential and ensure it does not compromise antimicrobial efficacy. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"183"},"PeriodicalIF":12.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794889","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":"Lipid accumulation inhibition strategies alleviate Fusobacterium nucleatum-infected colorectal cancer.","authors":"Zhongkun Zhou, Yuqing Niu, Yunhao Ma, Dekui Zhang, Yiqing Wang, Rui Ji, Jianfang Zhao, Chi Ma, Hongmei Zhu, Yingqian Liu, Lixue Tu, Juan Lu, Baizhuo Zhang, Hua Zhang, Xin Ma, Peng Chen","doi":"10.1186/s40168-025-02133-7","DOIUrl":"10.1186/s40168-025-02133-7","url":null,"abstract":"<p><strong>Background: </strong>Fusobacterium nucleatum (F. nucleatum) is prevalent in colorectal cancer (CRC), and it can promote proliferation and induce chemoresistance via multiple pathways. The development of treatment strategies for F. nucleatum-infected CRC is of great importance.</p><p><strong>Methods: </strong>Shotgun metagenomic and metabolomic analyses of human feces, as well as metabolomic analysis of human blood, were performed to reveal the dysbiosis and metabolic dysregulation in CRC. Furthermore, the effects of Bifidobacterium animalis (B. animalis) on F. nucleatum and CRC were assessed in vitro and in vivo. Using a mouse CRC model, the function of bile salt hydrolase (BSH) in B. animalis was verified through heterologous expression in Escherichia coli (E. coli). Bile acids and drug library screening experiments were performed to inhibit F. nucleatum and tumor proliferation.</p><p><strong>Results: </strong>We identified an increase in F. nucleatum, enrichment of lipid metabolites, and depletion of Bifidobacterium in CRC patients. Furthermore, B. animalis inhibited F. nucleatum and CRC cells growth in an acid-dependent manner and reduced F. nucleatum-induced tumor increasement in mice. Mechanistically, F. nucleatum caused lipid accumulation, exacerbated inflammation, and intestinal barrier disruption, whereas B. animalis alleviated these changes, increased the Simpson diversity index, reduced lipid metabolites, and altered secondary bile acid composition in mice. Moreover, E. coli-BSH and ursodeoxycholic acid (UDCA) inhibited F. nucleatum-induced lipid accumulation and FASN/CPT1/NF-κB upregulation. Additionally, they alleviated F. nucleatum-related intestinal tumorigenesis in vivo. Targeting F. nucleatum-infected CRC cells and subcutaneous tumors in mice, penfluridol or the combination of orlistat and 5-FU exhibited superior inhibitory effects compared to 5-FU alone.</p><p><strong>Conclusions: </strong>F. nucleatum and lipid metabolites are enriched in CRC patients. Furthermore, BSH-expressing E. coli, UDCA, and penfluridol can alleviate F. nucleatum-induced lipid accumulation and tumor growth in mice. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"181"},"PeriodicalIF":12.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12326762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794888","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":"Dual-transcriptomics on microdissected cells reveals functional specialisation of symbiont-bearing-cells and contrasted responses to nutritional stress in the cereal weevil.","authors":"Nikoletta Galambos, Nicolas Parisot, Agnès Vallier, Claudia Bevilacqua, Séverine Balmand, Carole Vincent-Monégat, Rita Rebollo, Benjamin Gillet, Sandrine Hughes, Abdelaziz Heddi, Anna Zaidman-Rémy","doi":"10.1186/s40168-025-02164-0","DOIUrl":"10.1186/s40168-025-02164-0","url":null,"abstract":"<p><strong>Background: </strong>Insects thriving on a nutritionally imbalanced diet often establish long-term relationships with intracellular symbiotic bacteria (endosymbionts), which complement their nutritional needs and improve their physiological performances. Endosymbionts are in host specialised cells, called the bacteriocytes, which in many insects group together to form a symbiotic organ, the bacteriome. The cereal weevil Sitophilus oryzae houses multiple bacteriomes at the adult mesenteric caeca.</p><p><strong>Results: </strong>Using microscopic cell imaging, we revealed that bacteriomes consist of several cell types, including progenitor cells, peripheral bacteriocytes, central bacteriocytes and epithelial cells. By combining laser capture microdissection and dual RNA-sequencing, we showed that both host cell types and their associated endosymbionts express distinct transcriptional profiles. The comparison between peripheral bacteriocytes and midgut cells from insects artificially deprived from endosymbionts (aposymbiotic) unravelled cellular pathways modulated by the presence of endosymbionts. The cell-specific response to endosymbionts in peripheral bacteriocytes includes a boost of fatty-acid and amino acid metabolisms. We found that central bacteriocytes overexpress transport and G-protein signalling-related genes when compared to peripheral bacteriocytes, indicating a signalling and/or transport function of these cells. Diet composition strongly impacts host and endosymbiont gene expression and reveals a molecular trade-off among metabolic pathways.</p><p><strong>Conclusions: </strong>This study provides evidence on how endosymbionts interfere and enhance metabolic performances of insect bacteriocytes and highlights key genes involved in the bacteriocyte differentiation and metabolic pathways. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"182"},"PeriodicalIF":12.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12326831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794887","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":"Expanded genetic and functional diversity of oceanic fungi.","authors":"Xuefeng Peng, David L Valentine","doi":"10.1186/s40168-025-02162-2","DOIUrl":"10.1186/s40168-025-02162-2","url":null,"abstract":"<p><strong>Background: </strong>Fungi are known members of marine microbiomes that can act as saprotrophs, parasites, and pathogens. Although a few studies utilizing cultivation-based methods and metabarcoding have been conducted, the diversity, ecological roles, and functional activities of fungi in the open ocean remain vastly underexplored. This gap in knowledge is particularly notable in oxygen minimum zones (OMZ) of the ocean, which have expanded over the past 50 years, affecting marine ecosystems and biogeochemical cycles. The eastern tropical North Pacific Ocean (ETNP) is the largest oxygen minimum zone where fungi have been implicated in the production of the potent greenhouse gas nitrous oxide. Nevertheless, anaerobic metabolisms have rarely been investigated for fungi within the oxygen-depleted water columns of the ocean.</p><p><strong>Results: </strong>We report previously unrecognized diversity and activity of fungi in the ETNP OMZ. Phylogenetic analysis based on ribosomal proteins and carbohydrate-active enzyme (CAZyme) gene families revealed that oceanic fungi form distinct evolutionary clades that diverge from their terrestrial counterparts, challenging earlier models of multiple, intermingled marine-terrestrial transitions. Despite comprising a very low percentage of the total DNA and RNA pool, fungi accounted for a disproportionate share of extracellular CAZyme expression, with glycoside hydrolase family 7 (GH7) emerging as the dominant enzyme. The high expression of fungal GH7 genes suggests a specialized role fungi play in particle degradation, potentially acting on cellulose derived from dinoflagellates and pelagic tunicates, as well as chitosan derived from bacterial deacetylation of chitin. The strong correlation between the gene expression of fungal GH7 and bacterial chitin deacetylase suggests a potential synergy between bacteria and fungi in the degradation of chitin. Moreover, the correlation between dissimilatory nitrogen cycling processes and fungal hydrolytic activities provides new evidence for fungi as key players in linking carbon remineralization and nitrogen cycling in oxygen minimum zones.</p><p><strong>Conclusions: </strong>Our results point to fungi as pivotal contributors to particle remineralization in the ocean, potentially modulating the coupled cycles of carbon and nitrogen in OMZs. Integrating these fungal processes into marine ecosystem models may therefore be essential for improving our understanding of global biogeochemical dynamics and predicting responses to ocean deoxygenation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"179"},"PeriodicalIF":12.7,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12323267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144784578","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":"Lactiplantibacillus plantarum attenuate gossypol-induced hepatic lipotoxicity by altering intestinal microbiota for enriching microbial tryptophan metabolites in Nile tilapia (Oreochromis niloticus).","authors":"Fei-Fei Ding, Nan-Nan Zhou, Yue-Jian Mao, Jing Yang, Samwel M Limbu, Jorge Galindo-Villegas, Zhen-Yu Du, Mei-Ling Zhang","doi":"10.1186/s40168-025-02172-0","DOIUrl":"10.1186/s40168-025-02172-0","url":null,"abstract":"<p><strong>Background: </strong>Free fatty acids (FFAs) are the main cause of fatty liver disease, which can be alleviated by modulation of intestinal microbiota. Lactiplantibacillus plantarum plays a key role in maintaining liver health, but the underlying mechanism remains unclear.</p><p><strong>Results: </strong>Here, a strain affiliated to Lactiplantibacillus plantarum was isolated from the intestine of Nile tilapia (Oreochromis niloticus). We used a gossypol-induced fatty liver disease model, which only increased the FFAs level in liver, to investigate the effectiveness of L. plantarum (YC17) in alleviating FFAs-induced lipotoxicity liver injury. We found that dietary gossypol (GOS) induced a significant increase of FFAs in liver, resulting in lipotoxicity in Nile tilapia compared to control. L. plantarum YC17 supplementation reduced FFAs content by restoring esterification process, and then relieved liver injury. Addition of L. plantarum YC17 effectively increased the abundances of Lactobacillus, Clostridium and Cetobacterium in fish intestine, as well as serum levels of the microbial tryptophan metabolites, notably indole-3-propionic acid (IPA) and indole-3-acetic acid (IAA). The addition of L. plantarum YC17 significantly inhibited P53 signaling pathway and up-regulated the expression of FFAs esterification genes. In vitro experiments demonstrated that IPA inhibited P53 through ubiquitination and enhanced FFAs esterification in an aryl hydrocarbon receptor (Ahr) dependent manner.</p><p><strong>Conclusion: </strong>The gut microbiota-derived tryptophan metabolites (IPA and IAA) alleviated FFAs induced lipotoxic liver injury by activating Ahr, which promoted P53 ubiquitination, leading to the enhanced FFAs esterification. Our findings demonstrated that gut microbial metabolites alleviated lipotoxicity by promoting the esterification of FFAs in the liver, offering new insights into the study of probiotics and microbial tryptophan metabolites in fatty liver disease. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"180"},"PeriodicalIF":12.7,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12323027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144784643","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":"The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach.","authors":"Edgar L Reinoso-Peláez, María Saura, Carmen González, Manuel Ramón, Jorge H Calvo, Magdalena Serrano","doi":"10.1186/s40168-025-02165-z","DOIUrl":"10.1186/s40168-025-02165-z","url":null,"abstract":"<p><strong>Background: </strong>Despite advancements in artificial insemination, sheep fertility rates remain suboptimal. Recent studies in other species highlight the critical role of reproductive microbiota in influencing fertility outcomes. This research explores the relationship between ovine vaginal microbiota, associated functional pathways, and fertility using advanced nanopore long-reading metagenomic sequencing on 297 ewes from three Spanish breeds across four herds. The study aimed to describe a core vaginal microbiota, analyse the complex interactions with herd, breed, age, and parity factors, and identify taxa and genes associated with reproductive success by artificial insemination.</p><p><strong>Results: </strong>The study identified Staphylococcus, Escherichia, and Histophilus as the most abundant genera. Microbial communities varied considerably between breeds and herds, with high predictive accuracy (> 90%) in classification models. Differential abundance analysis revealed that the genera Histophilus, Fusobacterium, Bacteroides, Campylobacter, Streptobacillus, Gemella, Peptoniphilus, Helococcus, Treponema, Tissierella, and Phocaeicola were more abundant in non-pregnant ewes. Some of these taxa were also associated with four COG entries and one KEGG orthologue significantly linked to non-pregnancy, primarily involving carbohydrate metabolism, defence mechanisms, and structural resilience. Age and parity were also associated with microbiota composition, particularly in ewes older than five years or with more than three parturitions, suggesting that cumulative physiological changes may contribute to microbial shifts over time.</p><p><strong>Conclusions: </strong>The ewe's vaginal microbiome appears to be mainly influenced by both herd and breed, though distinguishing genetic from environmental factors is challenging within our study design. While the overall microbiota showed a subtle effect on pregnancy, certain genera had a significant negative impact, likely due to pathogenic or inflammatory properties that disrupt reproductive health. The metagenomic approach used here enabled not only comprehensive taxonomic classification but also detailed functional analysis, providing deeper insights into the microbiome's role in reproductive outcomes. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"177"},"PeriodicalIF":12.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12315406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765067","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":"Granular activated carbon (GAC)-driven microbial electron shuttle boosts denitrification and mitigates N₂O in cold and carbon-limited biofilm system.","authors":"Xiangyu Yang, Mingchen Yao, Peng Li, Jan Peter van der Hoek, Lujing Zhang, Gang Liu","doi":"10.1186/s40168-025-02161-3","DOIUrl":"10.1186/s40168-025-02161-3","url":null,"abstract":"<p><strong>Background: </strong>Denitrification in wastewater treatment is severely limited under low-temperature and low-carbon (\"dual-low\") conditions, hindering sustainable nitrogen removal. Biofilm systems, though energy-efficient, suffer from reduced efficiency in such environments due to impaired interspecies electron transfer (IET). Granular activated carbon (GAC), a conductive mediator, offers potential to enhance IET between electroactive microorganisms (EAMs) and denitrifiers, yet its role in dual-low systems remains underexplored. This study investigates GAC's capacity to optimize biofilm functionality and mitigate greenhouse gas (GHG) emissions under these constraints.</p><p><strong>Results: </strong>Under dual-low conditions (4-6°C, C/N = 4), GAC increased denitrification efficiency by 19.4-21.9% and reduced N₂O emissions by 10.6-22.9%. Metatranscriptomes revealed upregulation of denitrifying genes (e.g., nosZ) and electron transport pathways (e.g., omcB in Geobacter). FISH/SEM confirmed GAC-driven coacervates of EAMs and denitrifiers, linked by nanowires, enhancing direct electron transfer. Microbial diversity decreased, but functional redundancy improved, with Pseudomonas fluorescens and Geobacter sulfurreducens dominating. TOC removal rose under low temperatures, indicating enhanced carbon utilization.</p><p><strong>Conclusions: </strong>GAC fosters synergistic EAM-denitrifier partnerships, enabling efficient denitrification and GHG mitigation in cold and carbon-limited (\"dual-low\") biofilm systems, advancing sustainable wastewater management. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"178"},"PeriodicalIF":12.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12315362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765066","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":"Soil microbial legacy mediated by buckwheat flavonoids enhances cabbage resistance to clubroot disease.","authors":"Jiabing Wu, Shilin Hu, Jing Chen, Lili Zhou, Shengdie Yang, Na Zhou, Lei Wu, Guoqing Niu, Yong Zhang, Xuesong Ren, Qinfei Li, Jun Yuan, Hongyuan Song, Jun Si","doi":"10.1186/s40168-025-02166-y","DOIUrl":"10.1186/s40168-025-02166-y","url":null,"abstract":"<p><strong>Background: </strong>The legacy of plant growth significantly impacts the health of subsequent plants, yet the mechanisms by which soil legacies in crop rotation systems influence disease resistance through rhizosphere plant-microbiome interactions remain unclear. Using a buckwheat-cabbage rotation model, we investigated how microbial soil legacies shape cabbage growth and clubroot disease resistance.</p><p><strong>Results: </strong>Three-year field trials revealed that buckwheat rotation sustainably reduced clubroot severity by 67%-97%, regardless of pathogen load. Soil sterilization eliminated this suppression, implicating a microbial basis. Using 16S rRNA sequencing, we identified buckwheat-enriched bacterial taxa (Microbacterium, Stenotrophomonas, Ralstonia) that colonized subsequent cabbage roots. Metabolomic profiling pinpointed buckwheat root-secreted flavonoids - 6,7,4'-trihydroxyisoflavone and 7,3',4'-trihydroxyflavone - as key drivers of microbial community restructuring. These flavonoids synergistically enhanced the efficacy of a synthetic microbial community (SynCom1, containing Microbacterium keratanolyticum, Stenotrophomonas maltophilia, and Ralstonia pickettii), boosting disease suppression by 34% in greenhouse trials. Co-application of flavonoids and SynCom1 improved bacterial colonization in root niches. Although SynCom1 partially activated jasmonic acid (JA)-associated defenses, its effectiveness depended primarily on flavonoid-driven microbial recruitment rather than direct immune induction.</p><p><strong>Conclusions: </strong>Buckwheat rotation induces flavonoid-mediated soil microbiomes that prime JA-dependent immunity in subsequent cabbage crops, thereby decoupling disease severity from pathogen load. This study elucidates how specialized metabolites orchestrate cross-crop microbial legacies for sustainable disease control, providing a blueprint for designing rotation systems through precision microbiome engineering. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"176"},"PeriodicalIF":12.7,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12309073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144742600","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":"Metabolite-mediated interactions and direct contact between Fusobacterium varium and Faecalibacterium prausnitzii.","authors":"Koji Hosomi, Satoko Maruyama, Tsubasa Matsuoka, Mari Furuta, Yoko Tojima, Keita Uchiyama, Makiko Morita, Hitoshi Kawashima, Toshiki Kobayashi, Jun Kunisawa","doi":"10.1186/s40168-025-02168-w","DOIUrl":"10.1186/s40168-025-02168-w","url":null,"abstract":"<p><strong>Background: </strong>The human gut harbors a diverse microbiota that is crucial for maintaining health but also contributes to several diseases. Understanding how microbial communities are assembled and maintained is critical for advancing gut health.</p><p><strong>Results: </strong>We identified a unique interaction between the pathobiont Fusobacterium varium and the symbiont Faecalibacterium prausnitzii, both members of the gut microbial community; their interaction is driven by metabolites and direct cell-to-cell contact. Growth of F. varium was inhibited in the presence of F. prausnitzii because of a decrease in pH and an increase in β-hydroxybutyric acid. Conversely, the growth of F. prausnitzii was promoted in the presence of F. varium, likely via direct contact.</p><p><strong>Conclusions: </strong>These findings highlight the importance of metabolite-driven interactions and direct contact in shaping gut microbial communities and emphasize the potential of interactions between F. prausnitzii and F. varium in influencing gut health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"175"},"PeriodicalIF":12.7,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732065","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}