Microbiome最新文献

{"title":"Gut microbiota-derived riboflavin mediates protective effects of MUC2 in acute pancreatitis via CD40-macrophage pathway.","authors":"Yang Fu, Nuoming Yin, Zehua Huang, Wenfei Qin, Binqiang Xu, Huizhen Huang, Jia Hu, Mengyan Cui, Qixiang Mei, Junjie Fan, Yingying Lu, Qiaoli Jiang, Junjie Hu, Chunlan Huang, Yue Zeng","doi":"10.1186/s40168-026-02375-z","DOIUrl":"10.1186/s40168-026-02375-z","url":null,"abstract":"<p><strong>Background: </strong>Gut barrier dysfunction is critical in the pathogenesis of acute pancreatitis (AP), yet the underlying mechanisms remain unclear. Mucin 2 (MUC2), the primary component of the intestinal mucus layer, is essential for gut homeostasis and microbial eubiosis. This study aimed to elucidate the protective mechanism of intestinal MUC2 in AP.</p><p><strong>Results: </strong>We reported that intestinal MUC2 expression was decreased in AP patients and correlated with disease severity. Intestinal epithelial-specific Muc2 knockout (Muc2^ΔIEC) mice demonstrated exacerbated AP in a gut microbiota-dependent manner. Decreased abundance of Lactobacillus and correlated reduced levels of riboflavin were found in Muc2^ΔIEC mice after AP induction. Supplementation with riboflavin effectively ameliorated AP in Muc2^ΔIEC mice, whereas administration of an engineered strain deficient in riboflavin synthesis failed to provide a protective effect. MUC2 deficiency aggravated a macrophage-dominant immune imbalance in the pancreas, which was reversed by riboflavin. In vitro experiments revealed that riboflavin suppresses pro-inflammatory macrophage activation by inhibiting the CD40 signaling pathway. This inhibition preserved mitochondrial function and reversed the histone H3 acetylation at pro-inflammatory gene promoters.</p><p><strong>Conclusion: </strong>Our study demonstrates that intestinal MUC2 deficiency is associated with reduced levels of microbiota-derived riboflavin, which could partially suppress pro-inflammatory macrophage activation via the CD40 pathway. Targeting the microbiota-derived riboflavin in AP may help to ameliorate the disease course. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13602806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149030774","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 changes in gut microbiota across reproductive states in wild baboons.","authors":"Chelsea A Southworth, Logan Barrios, Mauna R Dasari, Laurence R Gesquiere, Jack A Gilbert, Susan C Alberts, Jenny Tung, Elizabeth A Archie","doi":"10.1186/s40168-026-02494-7","DOIUrl":"10.1186/s40168-026-02494-7","url":null,"abstract":"<p><strong>Background: </strong>In humans and other mammals, female reproduction is linked to extensive changes in physiology, immunity, hormones, and behavior. These changes likely shape, and may be shaped by, the composition of gut microbial communities. Characterizing the dynamics of gut microbial change across reproductive states, including its relationship to female physiology, is important for understanding how the gut microbiota influences female and offspring health.</p><p><strong>Results: </strong>Here we characterize longitudinal changes in gut microbiota across reproduction by combining 16S rRNA gene sequencing data from 4,462 stool samples (spanning 14 years of sample collection) with life history data on multiple reproductive events in 169 female baboons. These baboons were members of a well-studied, natural baboon population in Kenya where reproductive state (ovarian cycling, pregnancy, and postpartum amenorrhea) is tracked daily and microbiota data could be paired with measurements of fecal-derived estrogen, progesterone, and glucocorticoid levels. We found extensive changes in baboon gut microbiota as females transitioned between reproductive states. Pregnancy was linked to distinct patterns of ASV richness, community composition, and taxonomic abundances compared to postpartum amenorrhea and ovarian cycling. The most dramatic shifts occurred as females transitioned from the first to second trimester of pregnancy, with altered abundances of taxa that have been linked, in humans and model systems, to host immunity, weight gain, or hormone levels. Host identity was consistently the strongest predictor of gut microbiota composition across states, and this individual signature was strongest during pregnancy. Estrogen and progesterone levels had robust associations with the gut microbiota overall, but the microbial taxa involved in these associations were reproductive state-dependent. Glucocorticoid concentrations were not a major predictor of gut microbiota composition in any state.</p><p><strong>Conclusions: </strong>Together, our results support the idea that gut microbiota contribute to the complex physiological changes necessary during pregnancy, but that microbial changes during pregnancy are somewhat unique to each female. Variation in steroid hormones is associated with some, but not all, of these relationships, emphasizing the importance of considering steroid hormone levels in studies of gut microbiota variation. Our results motivate future work on how gut microbiota contribute to reproductive outcomes, including both maternal and offspring health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13602499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149030783","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-protective metabolic phenotype for diarrhoeal remission caused by an environmental probiotic thermophile.","authors":"Hirokuni Miyamoto, Hideyuki Takahashi, Wataru Suda, Haruki Yamano, Yudai Inabu, Hiroaki Kodama, Yumiko Nakanishi, Shigeharu Moriya, Takashi Satoh, Tamotsu Kato, Chie Shindo, Naoko Tsuji, Makiko Matsuura, Chitose Ishii, Teruno Nakaguma, Tetsuji Etoh, Yuji Shiotsuka, Motoaki Udagawa, Atsushi Kurotani, Kenta Suzuki, Hiroshi Masuya, Satoshi Wada, Shinji Fukuda, Yukihiro Tashiro, Hisashi Miyamoto, Jun Kikuchi, Masahira Hattori, Takumi Nishiuchi, Naoki Yamamoto, Hiroshi Ohno","doi":"10.1186/s40168-026-02476-9","DOIUrl":"10.1186/s40168-026-02476-9","url":null,"abstract":"<p><strong>Background: </strong>Controlling diarrhoea in humans and livestock is a global challenge with diverse aetiologies. However, the dynamics of the microbiome for diarrhoeal remission are not sufficiently understood, and effective intervention strategies based on environmental microorganisms have not been fully explored.</p><p><strong>Methods: </strong>We investigated the metabolic structure associated with diarrhoeal remission using a combination of statistical, genomic, and proteomic approaches in a cattle model. Oral administration of the compost-derived thermophile Caldifermentibacillus hisashii significantly ameliorated persistent diarrhoea. Faecal bacterial populations and metabolites were characterised by a multi-step statistical pipeline comprising difference-in-differences (DID) analysis, Cliff's delta effect size estimation with permutation-based validation. The functional importance of the selected feature components was validated through genomic and proteomic analysis of C. hisashii N11 (AP028807.1).</p><p><strong>Results: </strong>Oral administration of C. hisashii significantly ameliorated persistent diarrhoea in calves. Although no significant differences in faecal bacterial community composition were observed, integrated analysis of faecal metabolites identified butyrate and 2-aminoisobutyrate (AIB) as the most discriminative features associated with diarrhoeal remission. Genomic and proteomic analyses of C. hisashii confirmed biosynthetic gene clusters for butyrate and AIB-containing lantibiotics, supporting the structural importance of these metabolites in diarrhoeal remission.</p><p><strong>Conclusion: </strong>These findings suggest that diarrhoeal remission observed in this study involves characteristic shifts in faecal metabolite profiles rather than marked changes in overall gut microbial community composition, highlighting a protective role of C. hisashii as an environmental probiotic against diarrhoeal dysbiosis through modulation of gut microbial metabolic output. This offers a perspective that bridges environmental microbiology and gut health within a One Health framework. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148685017","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 iron modulates beneficial maize microbiome feedbacks in rotations with wheat.","authors":"Jan Waelchli, Henry Janse van Rensburg, Katja Stengele, Viola D'Adda, Selma Cadot, Veronica Caggìa, Valentin Gfeller, Klaus Schlaeppi","doi":"10.1186/s40168-026-02493-8","DOIUrl":"https://doi.org/10.1186/s40168-026-02493-8","url":null,"abstract":"<p><strong>Background: </strong>Plants change their surrounding soil microbiome by root exudates and these conditioned microbiomes impact the performance of the present as well as the next plant generation as for example in crop rotations. The big challenge is that such 'microbiome feedbacks' are highly context-dependent, i.e. they vary in strength and direction dependent on the local soil environment - of which the driving factor(s) remain unknown. Including maize in crop rotations involves benzoxazinoids (BXs), which are exuded from roots and alter the soil microbiome, which in turn affects growth and defence of the following crop.</p><p><strong>Results: </strong>Here, we grew wild-type and BX-depleted maize in the field to differentially condition their soil microbiome and we found varying feedbacks on wheat performance dependent on the local physicochemical soil parameters. Using multivariate, correlation and modelling approaches and including additional data from two previous field experiments, we identified plant-available (PA) iron to be associated with BX-dependent microbiome feedbacks on wheat. The BX-conditioned soil microbiome caused wheat to grow taller at low levels of soil PA-iron but smaller at high levels. This finding was generalized by testing these maize microbiome feedbacks on the model plant Arabidopsis thaliana using soil batches containing different levels of iron. Consistent with wheat, a significant inverse relationship between soil PA-iron levels and plant growth was found. This relationship was experimentally validated with Arabidopsis thaliana grown at low levels of soil iron where iron supplementation abolished the beneficial feedback of the BX-conditioned soil microbiome.</p><p><strong>Conclusion: </strong>Together, these findings revealed that beneficial microbiome feedbacks occur at low levels of plant-available iron, i.e. when plants grow in a suboptimal soil, but they are lost when plants are nutritionally well supported. These results underscore the importance of iron availability in soil for beneficial microbial feedbacks on plant growth and predict agronomic benefits of incorporating maize in crop rotations on low iron soils. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13628717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149111642","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":"Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery.","authors":"Tanner G Richie, Hallie Wiechman, Brooke Vogt, Carson Ingold, Leah Heeren, Abigail Kamke, Sophia Pogranichniy, Kourtney Monk, Trey Summers, Qinghong Ran, Soumyadev Sarkar, Brandon L Plattner, Ashley M Sidebottom, Eugene B Chang, Sonny T M Lee","doi":"10.1186/s40168-026-02457-y","DOIUrl":"10.1186/s40168-026-02457-y","url":null,"abstract":"<p><strong>Background: </strong>Certain microbes inhabiting the gut have been implicated in maintaining gut homeostasis and promoting gut damage repair. Lachnospiraceae members were highly detected in dysbiotic IL-10 KO mice that displayed similar physiological outcomes as control mice. Lachnospiraceae is a highly diverse family of microbes that have been shown to display both commensal and pathogenic characteristics in the colon environment.</p><p><strong>Results: </strong>We investigated the impact of genetic variation in five Lachnospiraceae strains on lowering cellular inflammation and reactive oxygen species (ROS) levels. Cell-free spent media (CFSM) from Eubacterium rectale resulted in lowered ROS, and nitric oxide levels in stressed colon cells and colon organoids. CFSM-treated organoids showed reduced ROS accumulation, improved epithelial integrity, and partial recovery of barrier function compared to oxidatively stressed controls. We demonstrated through shotgun metagenomics, metabolomics, host RNA sequencing, and molecular techniques that glutathione (GSH) biosynthesized by E. rectale alleviated host ROS damage. We showed downregulation of cell stress and immune response genes, indicating recovery from ROS stress. Chemical depletion of GSH in CFSM confirmed the role of microbial derived GSH in alleviation of ROS in colon cells.</p><p><strong>Conclusions: </strong>In this study, we identify E. rectale as a potential probiotic by lowering colon inflammation and ROS damage through production of reduced glutathione. Microbially derived GSH has not been well established in the Lachnospiraceae family which are a large member of the overall gut microbiota. Understanding more about the impacts of microbial functions including GSH on lowering inflammation is needed to develop potential probiotics or therapies for chronic inflammatory conditions. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148684991","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":"Untapped enzymatic potential: dehalogenase- and peroxidase-driven PVC degradation by gene carriers in Tibetan plateau pikas.","authors":"Chunxiu Zhou, Baotong Fu, Xiaoxiao Hou, Wei-Min Wu, Aman Khan, Chunjie Li, Huawen Han, Xiangkai Li","doi":"10.1186/s40168-026-02478-7","DOIUrl":"10.1186/s40168-026-02478-7","url":null,"abstract":"<p><strong>Background: </strong>Wide distribution of polyvinyl chloride microplastics (PVC-MPs) has been documented in remote regions such as the Qinghai-Tibet Plateau (QTP). Microbial degradation of plastics is frequently coupled with lignocellulose-degrading enzymatic machinery. As a ubiquitous biological sampler on the QTP, the herbivore plateau pika (Ochotona curzoniae), which harbors diverse lignocellulose-degrading enzymes, represents a promising reservoir for novel PVC-degrading enzymes.</p><p><strong>Results: </strong>In this study, a PVC-MPs feeding trial of plateau pikas revealed gut microbiota recruitment of plastic degraders. Subsequent enrichment experiment yielded a PVC-degrading consortium that depolymerized PVC into long-chain alkanes, with Rhodococcus and Leifsonia identified as PVC-response specialist and generalist, respectively. Multi-omics analysis supported a putative degradation pathway initiated by haloalkane dehalogenase (HLD) and involving oxidases. Furthermore, novel RhHLD (from Rhodococcus MAG) released 11.5 mg L^-1 chloride ions from PVC films, whereas dye-decolorizing peroxidase LeDyP from Leifsonia MAG generated PVC-degrading intermediates. Analysis of 39 metagenomic datasets further confirmed that haloalkane dehalogenase and dye-decolorizing peroxidase are prevalent in the gut of wild pikas.</p><p><strong>Conclusions: </strong>This study elucidates the PVC-degrading potential of herbivore gut microbiota and expands the catalytic toolkit for plastic bioremediation, underscoring the bioprospecting potential in extreme ecosystems Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990522","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":"Integrated landscape of salivary metagenome and multi-biofluid metabolome characterizes a microbial-metabolic axis in upper gastrointestinal cancer progression.","authors":"Shuai Zhang, Nan Zhang, Xiaofeng Zhang, Yanxiu Liu, Yukun Feng, Junling Xiang, Jun Zhang, Hengmin Ma, Youhua Lu, Tao Zhang","doi":"10.1186/s40168-026-02475-w","DOIUrl":"10.1186/s40168-026-02475-w","url":null,"abstract":"<p><strong>Background: </strong>Upper gastrointestinal cancer (UGIC) imposes a major global health burden, yet the stage-specific molecular changes along the microbial-metabolic axis remain limited understood. We aimed to delineate this molecular landscape across UGIC progression and evaluate its potential as non-invasive methods for precision screening.</p><p><strong>Results: </strong>Derived from a multi-center population-based UGIC screening program, we enrolled 420 individuals, stratified into normal, low-grade intraepithelial neoplasia (LGIN), high-grade intraepithelial neoplasia (HGIN), and UGIC (n = 105 per group). Integrated salivary metagenomics and paired salivary/plasma metabolomics were performed to capture local and systemic dysregulation. We uncovered distinct stage-specific divergence during UGIC progression: profound remodeling of the salivary microbiota (104 differential species) and salivary metabolomics (80 differential metabolites) initiated early at the LGIN stage, whereas plasma metabolic dysregulation (40 differential metabolites) peaked significantly later at the HGIN stage. Integrative analysis revealed salivary microbiota related more closely with salivary metabolome than plasma metabolome. Moreover, statistical evidence suggested that dysbiotic salivary microbiota was associated with altered lysine- and tryptophan-related catabolic pathways converging on Acetyl-CoA-related metabolic nodes, supporting a potential metabolic mechanism in precancerous lesions. Finally, the discriminative model integrating metagenomic and metabolomic markers demonstrated promising diagnostic performance in distinguishing these precancerous lesions (LGIN: area under the curve [AUC] = 0.83; HGIN: AUC = 0.77) and UGIC (AUC = 0.76) from normal.</p><p><strong>Conclusion: </strong>This study characterizes a stage-specific microbial-metabolic axis that facilitates the comprehensive understanding of UGIC pathogenesis. These multi-biofluid signatures offer a promising non-invasive triage strategy for detecting precancerous lesions and optimizing endoscopic resource allocation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13560389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148930436","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":"Toxic metals differentially affect bacterial and fungal seed endophytes in Arabidopsis arenosa.","authors":"Agnieszka Domka, Ayesha Aziz, Roman J Jędrzejczyk, Oleksandra Kutinova, Weronika Kosowicz, Artur Pliszko, Piotr Rozpądek, Rafał Ważny","doi":"10.1186/s40168-026-02497-4","DOIUrl":"10.1186/s40168-026-02497-4","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Seed endophytes are the earliest microbial companions of plants. They play a beneficial role in seed germination, seedling development, and plant growth. Endophytes help plants to adapt to changing environments; however, their role in the aspect of toxic metal-polluted environments is poorly known. We investigated the impact of metal toxicity on the structure of seed-associated microbiota in Arabidopsis arenosa and explored the role of these microbes in host plant adaptation to metal-rich, post-mining environments.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Toxic metals markedly altered the alpha and beta diversity of bacterial seed endophytes, whereas fungal endophyte diversity was largely unaffected. Similar patterns were observed in a vertical transmission experiment, indicating that metal exposure can influence seed-associated microbiota across generations. To explore the functional relevance of these changes, we assembled synthetic microbial communities from culturable bacterial and fungal isolates recovered from seeds of plants originating from non-metalliferous and metalliferous sites. A synthetic community composed of isolates from non-metalliferous populations enhanced plant growth under metal stress, whereas the community assembled from metalliferous populations showed no growth-promoting effect. Crude seed extracts also did not reproduce the growth-promoting effect of the defined synthetic community. Further fractionation indicated that the beneficial effect was mainly associated with the fungal component, while bacterial fractions did not enhance plant growth under the tested metal-stress conditions. Fungal isolates from non-metalliferous populations promoted plant biomass under metal stress, whereas this effect was not observed for isolates from metalliferous populations under the tested conditions.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Long-term exposure to toxic metals exerts strong selective pressure on seed-associated microbiota, markedly reducing bacterial diversity and reshaping community composition while leaving fungal diversity largely unaffected. Metal toxicity causes losses in the abundance of bacteria. High metal tolerance of these microorganisms indicates rather that metal exposure affects the interaction between the microbe and its host and the ability of the microbe to be retained in the seeds. Fungal endophytes from metal-free populations proved more effective in promoting plant growth under metal stress than those from metalliferous populations, suggesting that intrinsic strain-level traits, rather than prior environmental adaptation, are key to enhancing host tolerance. This challenges the assumption that endophytes from contaminated sites are inherently better suited for phytoremediation and highlights the potential of \"naive\" microbial sources. Together, these results expand our understanding of vertical transmission, microbial adaptation, and host-microbe interactions under heavy metal stress, ","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13602735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149039682","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 Metaproteomics Initiative: five years of community-driven progress.","authors":"Tim Van Den Bossche, Lucia Grenga, Gelio Alves, Magnus Ø Arntzen, Dirk Benndorf, Madita Brauer, Daniel Figeys, Celine Henry, Robert L Hettich, Robert Heyer, Pratik D Jagtap, Nico Jehmlich, Manuel Kleiner, Leyuan Li, Bart Mesuere, Martin Pabst, Jagroop Pandhal, Phillip B Pope, Jana Seifert, Anke Trautwein-Schult, Pieter Verschaffelt, Paul Wilmes, Jean Armengaud, Benoit J Kunath","doi":"10.1186/s40168-026-02463-0","DOIUrl":"10.1186/s40168-026-02463-0","url":null,"abstract":"<p><p>The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape ( https://metaproteomics.org/ ). We outline the Initiative's organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13393725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148579195","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 need for standardization and improved open (meta)data practices in metaproteomics.","authors":"Tim Van Den Bossche, Maximilian Wolf, Jean Armengaud, Magnus Ø Arntzen, Dirk Benndorf, Daniel Figeys, Lucia Grenga, Robert L Hettich, Nithu Sara John, Pratik Jagtap, Nico Jehmlich, Manuel Kleiner, Benoit J Kunath, Leyuan Li, Mary Lipton, Bart Mesuere, Benjamin A Neely, Zhibin Ning, Ane Laura Pedersen, Yasset Perez-Riverol, Jeena Rajan, Kay Schallert, Jana Seifert, Sergio Uzzau, Pieter Verschaffelt, Paul Wilmes, Juan Antonio Vizcaíno, Lennart Martens, Robert Heyer","doi":"10.1186/s40168-026-02455-0","DOIUrl":"10.1186/s40168-026-02455-0","url":null,"abstract":"<p><p>Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13393928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148579241","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}