Microbiome最新文献

{"title":"Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.","authors":"Georgia Vayena, Ginevra Giangeri, Maria Gaspari, Parisa Ghofrani-Isfahani, Panagiotis Tsapekos, Panagiotis G Kougias, Irini Angelidaki","doi":"10.1186/s40168-026-02443-4","DOIUrl":"10.1186/s40168-026-02443-4","url":null,"abstract":"<p><strong>Background: </strong>Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.</p><p><strong>Results: </strong>Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.</p><p><strong>Conclusions: </strong>This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148150604","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":"mPower: a real data-based power analysis tool for microbiome study design.","authors":"Lu Yang, Jun Chen","doi":"10.1186/s40168-026-02427-4","DOIUrl":"10.1186/s40168-026-02427-4","url":null,"abstract":"<p><p>Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/ . Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13450569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148157242","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 Iceman's microbiome: unveiling millennia of microbial diversity and continuity.","authors":"Mohamed S Sarhan, Marco Samadelli, Albert Zink, Frank Maixner","doi":"10.1186/s40168-026-02417-6","DOIUrl":"10.1186/s40168-026-02417-6","url":null,"abstract":"<p><strong>Background: </strong>The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.</p><p><strong>Results: </strong>By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.</p><p><strong>Conclusions: </strong>Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13231656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148150613","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":"Metabolic host-microbe crosstalk in stabilization of epithelial HIF.","authors":"Alexander S Dowdell, Rebecca L Roer, Geetha Bhagavatula, Ian M Cartwright, Rachel H Cohen, Jacob A Countess, Samuel D Koch, J Scott Lee, Lin Liu, Calen A Steiner, Noah T Thompson, Zachary F Villamaria, Nichole Welch, Corey S Worledge, Liheng Zhou, Andrés Vazquez-Torres, Sean P Colgan","doi":"10.1186/s40168-026-02431-8","DOIUrl":"10.1186/s40168-026-02431-8","url":null,"abstract":"<p><strong>Background: </strong>The gastrointestinal tract is home to trillions of microorganisms that interact with their host in profound ways. One mechanism by which these microbes interact with their eukaryotic host is through the establishment of \"physiologic hypoxia\" in the intestinal mucosa, which has been shown to promote gut barrier function and homeostasis in a hypoxia-inducible factor (HIF)-dependent manner. The association between HIF and intestinal homeostasis has been long understood, as activation of HIF signaling has been shown to promote barrier function both in vitro and in vivo. Although it has been previously established that pathogenic bacteria regulate HIF stabilization and activity in the intestinal epithelium independent of short-chain fatty acid metabolism, it is not clear whether this activity extends to noninfectious and/or commensal bacterial species.</p><p><strong>Results: </strong>Here, we demonstrate that nonpathogenic, commensal strains of Escherichia coli stabilize HIF in intestinal epithelial cells in vitro. Further, we show that HIF is transcriptionally active in epithelia and drives a \"pro-barrier\" transcriptional program. This property was found to be dependent on bacterial aerobic respiration, as genetic elimination of E. coli aerobic respiration abolished HIF stabilization and the subsequent transcriptional phenotype. Finally, we observed stabilization of tissue HIF-1α in vivo using antibiotic-treated mice colonized with wild-type, but not respiration-deficient, E. coli.</p><p><strong>Conclusions: </strong>These findings demonstrate a novel ability for commensal E. coli to regulate intestinal homeostasis through activation of HIF and suggest that this mechanism might be a major component of the interaction between facultative anaerobes and the intestinal epithelium in the gut. In addition, we hypothesize that consumption of oxygen by enteric bacteria might be leveraged as a novel therapeutic to combat intestinal inflammation, such as that observed during inflammatory bowel disease (IBD). Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13425931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148055513","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":"Remodelling of cystic fibrosis respiratory microbiota in response to extended elexacaftor-tezacaftor-ivacaftor therapy.","authors":"Helen Gavillet, Lauren R Hatfield, Michelle Hardman, Ryan Marsh, Gisli G Einarsson, Christina S Thornton, Michael D Parkins, Jamie Duckers, Jennifer M Bomberger, Yasmin Hilliam, Stella E Lee, Robert W Lord, Andrew Jones, Alexander Horsley, Thomas W V Daniels, Charlotte C Teneback, Damian W Rivett, Christopher van der Gast","doi":"10.1186/s40168-026-02440-7","DOIUrl":"10.1186/s40168-026-02440-7","url":null,"abstract":"<p><strong>Background: </strong>Cystic fibrosis (CF) has profoundly changed since the introduction of CF Transmembrane Conductance Regulator modulator therapies (CFTRmt), a class of medications that improve function of the CFTR protein encoded by certain CF-causing gene mutations. Amongst these, the triple combination therapy elexacaftor-tezacaftor-ivacaftor (ETI) has been the most impactful and widely used to date. Given chronic respiratory infection and concomitant inflammation is the leading cause of morbidity and early mortality for the majority in CF, what is not certain are the long-term effects of ETI therapy on the respiratory microbiota and pathogens embedded within. Here, we assessed the effects of ETI CFTRmt over 3 years on the respiratory microbiota, using sputum and cough swab samples, from a multi-centre cohort of 276 adults with CF (awCF) from 6 CF centres in the UK, USA, and Canada, and compared to a non-CF healthy cohort.</p><p><strong>Results: </strong>Using Kruskal-Wallis analyses with post hoc Dunn's tests, Wilcoxon signed-rank tests, and PERMANOVA analyses with Bonferroni correction, we determined that respiratory microbiota characteristics (diversity, dominance, and composition) became decreasingly like those of awCF pre-ETI and remodelled to align more with the healthy cohort, where canonical CF pathogens increasingly became less ecologically important in terms of their distributions and abundances across awCF with increased duration on therapy. However, the on-ETI microbiota was impeded from becoming fully 'healthy' due to continued antibiotic exposure and irreversible lung damage experienced by awCF. Specifically, we found that azithromycin, an antibiotic widely used principally for its immunomodulatory benefits, was associated with adverse effects on the respiratory microbiota nullifying the observed positive effects of ETI treatment. Our results indicated that when administered alongside ETI therapy, azithromycin contributed to a pre-ETI microbiota dysbiosis and enabled enhanced persistence of emblematic CF pathogens.</p><p><strong>Conclusions: </strong>The highly anticipated introduction of ETI CFTRmt has greatly changed the course of CF for many people living with this inherited disease. Here, we find that ETI CFTRmt enabled positive remodelling of the respiratory microbiota towards a healthy-like state. However, azithromycin appeared to impede total remodelling, making it an ideal candidate for evaluation for discontinuation in the CFTRmt era. While traditional pathogens become less ecologically important, the potential evolution and emergence of virulent strains should be investigated. Additionally, the impacts and implications of ETI therapy on the understudied fungal microbiota should also be explored. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13430856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148101438","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":"Biosynthesized selenium nanoparticles increase soybean resistance to root rot by recruiting beneficial microbes and reprogramming host metabolism.","authors":"Haixu Liu, Songhan Han, Ke Shi, Yan Zhang, Ying Xu, Shuang Song, Yufei Chen","doi":"10.1186/s40168-026-02439-0","DOIUrl":"10.1186/s40168-026-02439-0","url":null,"abstract":"<p><strong>Background: </strong>Soybean root rot, primarily caused by Fusarium species, is a devastating soil-borne disease that severely threatens global soybean production. Conventional chemical controls are problematic due to their environmental impact and the risk of fostering pathogen resistance. There is therefore an urgent need to develop sustainable and eco-friendly alternative strategies.</p><p><strong>Results: </strong>This study demonstrated that selenium nanoparticles (SeNPs) biosynthesized by Bacillus subtilis ZY56 significantly increased soybean resistance to F. oxysporum. Characterization confirmed that the obtained SeNPs were spherical (approximately 147 nm), consisting of amorphous-state elemental selenium (Se⁰) with a bioactive protein-polysaccharide coating. Treatment with 2.66 mg/L SeNPs significantly promoted seed germination, seedling growth, and antioxidant enzyme activity, while markedly reducing the root rot disease index. Multiomics analyses revealed that SeNPs reprogrammed host metabolism by increasing the levels of key defense-related metabolites (camalexin and isoflavonoids) and upregulating associated biosynthetic pathways. Crucially, SeNPs reshaped the rhizosphere microbiome, enriching beneficial genera (e.g., Bradyrhizobium, Lysobacter, and Nocardioides). Moreover, the analysis predicted enhanced microbial tyrosine metabolism. Integrated correlation analysis identified tyrosine metabolism as a core hub linking microbiome restructuring to host defense, supporting a \"microbe‒plant metabolic division of labor\" model in which microbes supply precursors (e.g., L-tyrosine) for the synthesis of antifungal compounds in the host. This finding was functionally validated, as the accumulated metabolites (camalexin and isoflavonoids) directly inhibited F. oxysporum growth in vitro.</p><p><strong>Conclusions: </strong>Our findings reveal a dual mechanism whereby SeNPs concurrently prime host defenses and modulate beneficial plant-microbe interactions, offering a sustainable nano-enabled strategy for managing soil-borne diseases. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13237894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148055470","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":"Longitudinal analysis of stowaway microorganisms aboard modules and cargo spacecraft of the Chinese Space Station.","authors":"Ying Zhang, Jinglin Ma, Lantao Zhang, Ran Wang, Xi Qu, Tao Wei, Jiangchuan Zhou, Weijie Liu, Xiang Wang","doi":"10.1186/s40168-026-02438-1","DOIUrl":"10.1186/s40168-026-02438-1","url":null,"abstract":"<p><strong>Background: </strong>Although microbial contamination in crewed spacecraft is well studied, quantitative assessment of microorganisms from spacecraft structures and cargo remains overlooked. Here, we investigate 165 microbial samples collected from five critical environments of China Space Station (CSS) missions undertaken in 2016-2024: ground assembly, cargo loading, crewed simulation cabin, test cabin, and on-orbit. The investigation aims to elucidate the impact of cargo- and cabin-derived microorganisms on the CSS microbial community while characterizing the station's unique microbial profile.</p><p><strong>Results: </strong>The calculation results based on the microbial source tracking model revealed that the proportion of cabin-source microbes peaked during initial construction (14.02%) but declined after deployment, whereas cargo-source microbes reached 36.89%. The top three persistent microbial genera in orbit from both sources were Staphylococcus, Acinetobacter, and Corynebacterium. High-abundance CSS microorganisms in the orbital environment are commonly found in both humans and plants, and the few cabin- or cargo-derived microorganisms that entered the interior differed markedly from high-abundance microorganisms found in terrestrial environments. Cargo storage areas and controlled cleanrooms posed a high risk of microbial transfer into orbit, necessitating stricter sterilization measures.</p><p><strong>Conclusions: </strong>These findings systematically characterize, for the first time, the dynamic patterns of structural/cargo-borne microbial contamination during CSS's early phases, providing critical data for biosecurity protocols of long-duration missions. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13417861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148055437","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":"Deterministic assembly of rhizosphere bacterial community enables predictable and stable suppression of Verticillium wilt via microbial homeostasis.","authors":"Jiamin Ai, Jiangying Huang, Chenyuan Wang, Xinrui Wang, Yiduo Zhao, Gehong Wei, Zhefei Li","doi":"10.1186/s40168-026-02432-7","DOIUrl":"10.1186/s40168-026-02432-7","url":null,"abstract":"<p><strong>Background: </strong>The rhizosphere microbiota plays essential roles in maintaining normal physiological function and preventing disease in plants. However, the mechanisms by which soil-borne pathogens break through the microbial defense line in the rhizosphere to infect the host are not well understood.</p><p><strong>Results: </strong>In this study, we observed that the relative abundance of Verticillium dahliae does not significantly differ between healthy and diseased rhizospheres, but the root-associated microbial community structure changes substantially. The invasion of pathogens shifts the assembly process of the microbial community from deterministic to stochastic, making it difficult to predict the disease resistance function of the rhizosphere microbial community. An increase in stochasticity promotes the rapid proliferation of opportunistic bacteria, which deplete carbon sources, disrupt the balance of the original microbial community, and reduce network stability. Consequently, the depletion of beneficial microbes leads to rhizosphere dysbiosis, while fungal pathogenic allies gain a competitive advantage, thereby facilitating the progression of Verticillium wilt. These results are further validated by constructing synthetic microbial communities (SynComs) using strains enriched in different ecological processes. Healthy plants maintain their health by recruiting beneficial microorganisms through deterministic processes. Moreover, the disease-suppressive efficacy of SynComs governed by deterministic processes was less affected by inoculation timing or concentration, making their functional outcomes more predictable. In contrast, the disease resistance levels of SynComs governed by stochastic processes are more sensitive to inoculation timing and concentration, making their function more unpredictable.</p><p><strong>Conclusions: </strong>Overall, our findings emphasize the potential of SynComs designed according to community assembly principles to combat soil-borne diseases, with deterministically assembled SynComs providing more durable disease resistance than stochastically assembled ones. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13411133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148055486","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":"Reproductive aging drives deterministic microbiota assembly to mitigate uterine oxidative phosphorylation impairment via spermidine production in laying hens.","authors":"Dong Dai, Cheng Long, Kaixuan Ma, Wenchang Ma, Pengzu Wang, Guanghai Qi, Zhigang Zhou, Jing Wang","doi":"10.1186/s40168-026-02437-2","DOIUrl":"10.1186/s40168-026-02437-2","url":null,"abstract":"<p><strong>Background: </strong>Reproductive aging represents a critical physiological bottleneck characterized by a progressive decline in tissue homeostasis and physiological function. While the gut microbiota is known to shift during host aging, the ecological forces governing the assembly of the reproductive microbiota and its functional feedback on uterine homeostasis remain poorly understood.</p><p><strong>Results: </strong>We demonstrated that uterine aging drives a transition from stochastic to deterministic microbial community assembly, selecting for a microbiota enriched in Rhodococcus in aged laying hens. Multi-omics analyses revealed that this deterministic shift acts as a compensatory mechanism to counteract age-related energy metabolism decline in the uterus. Mechanistically, the aged uterus suffered from oxidative phosphorylation impairment due to PARP1-mediated NAD+ depletion in response to accumulated DNA damage. However, the specific colonization of Rhodococcus ruber, or the administration of its metabolite spermidine, rescued this phenotype. Spermidine improved uterine energy metabolism by inducing PINK1/Parkin-mediated mitophagy, thereby restoring mitochondrial quality control and ATP production essential for eggshell biomineralization.</p><p><strong>Conclusions: </strong>This study uncovers a previously unrecognized role of the microbiota in reproductive aging: resident microbes enhance oxidative phosphorylation in the aged uterus through the metabolite spermidine, which induces mitophagy. This process alleviates cellular energy deficiency caused by PARP1-mediated NAD + depletion, elucidating a key mechanism of host-microbe interaction in maintaining uterine energy homeostasis during aging. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13411371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148055464","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 bacterial regulation of primate adaptive thermogenesis at high altitude.","authors":"Xiaochen Wang, Mingyi Zhang, Meng Li, Xiaoming Xu, Yue Sun, Yang Teng, Junping Zhao, Huailiang Xu, Da Zhang, Yueqi Yin, Ying Shen, Jiwei Qi, Zuofu Xiang, Christian Roos, Tingbei Bo, Ming Li","doi":"10.1186/s40168-026-02425-6","DOIUrl":"10.1186/s40168-026-02425-6","url":null,"abstract":"<p><strong>Background: </strong>Adaptive thermogenesis is a fundamental physiological process by which mammals maintain their body temperature through shivering and non-shivering thermogenesis to adapt to environmental changes. The activation of brown adipose tissue (BAT) is the core of non-shivering thermogenesis. However, the specific mechanisms by which gut-derived bacteria trigger BAT to activate adaptive thermogenesis remain poorly understood. Environmental variations across different altitudes create unique temperature gradients, providing an ideal condition for identifying bacteria associated with cold adaptation. In this study, we identified Pantoea ananatis, a highland-enriched bacterium, as a key species regulating adaptive thermogenesis and lipid metabolism in Macaca mulatta.</p><p><strong>Results: </strong>Through multi-omics and gavage experiments, we discovered that the gut microbiota of high-altitude macaques can enhance the nutritional absorption capacity of the small intestine of mice, increase the concentration of propionic acid, activate the glycerolipid metabolism and strengthen lipid metabolism. Furthermore, we found that P. ananatis, as one of the main effect bacteria of the high-altitude gut microbiota, can activate BAT, reduce white adipose tissue (WAT) storage, and enhance triglyceride metabolism. Finally, we preliminarily verified that ferulic acid, as one of the potential effector metabolites of P. ananatis, also contributes to the reduction of WAT accumulation.</p><p><strong>Conclusions: </strong>Our work uncovers P. ananatis as a high-altitude-adapted potential probiotic that activates BAT and promotes systemic fat reduction through a gut microbiota-driven mechanism. This breakthrough provides a safe, effective alternative to cold-induced thermogenesis, with profound implications for obesity intervention. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148055480","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}