MicrobiomePub Date : 2026-08-28DOI: 10.1186/s40168-026-02501-x
Benjamin Seethaler, Maryam Basrai, Nathalie M Delzenne, Jens Walter, Nguyen K Nguyen, Stephan C Bischoff
{"title":"Baseline gut microbiome and metabolome profiles predict weight loss after a structured lifestyle intervention.","authors":"Benjamin Seethaler, Maryam Basrai, Nathalie M Delzenne, Jens Walter, Nguyen K Nguyen, Stephan C Bischoff","doi":"10.1186/s40168-026-02501-x","DOIUrl":"10.1186/s40168-026-02501-x","url":null,"abstract":"<p><strong>Background: </strong>Obesity remains a global health challenge, and responses to lifestyle-based weight-loss interventions are heterogeneous. Here, we evaluate a one-year structured lifestyle program in 50 adults with obesity (mean BMI 42 ± 7.0 kg/m<sup>2</sup>), integrating clinical, microbiome, and metabolomic profiling, to identify predictors of weight-loss success and metabolic improvement (ClinicalTrials.gov: NCT01344525). The intervention included a 3-month very low-calorie formula diet (approximately 850 kcal/day), a 3-month transition phase from a formula diet to a balanced diet (approximately 1000 kcal/day), and a 6-month maintenance period in which the participants followed a balanced diet (gradually increasing to a maximum of 2000 kcal/day).</p><p><strong>Results: </strong>Following the intervention, the participants exhibited marked reductions in body weight, body fat percentage, C-reactive protein, and glycated hemoglobin. Longitudinal analyses revealed that shifts in the gut microbiota composition were associated with changes in clinical and anthropometric data, as well as gut barrier function. An increased abundance of Lachnospiraceae was associated with improved gut barrier function; the relationship was mediated by fecal butyrate and propionate. Multivariate analyses revealed that serum baseline levels of diacylphosphatidylcholine C40:1 predicted postintervention BMI, indicating that this metabolite could serve as a biomarker of weight loss success. A random forest model incorporating baseline microbial and clinical features was used to predict weight loss and clinical improvements with high accuracy.</p><p><strong>Conclusions: </strong>Our findings elucidate the interplay between the gut microbiota and host metabolism during weight loss and highlight the potential utility of baseline profiling to achieve a high success rate in personalized obesity treatment. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13525661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148857542","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}
MicrobiomePub Date : 2026-08-26DOI: 10.1186/s40168-026-02473-y
Marta Turon, Cristina Díez-Vives, Tyler J Carrier, Laura de la Cruz-Castillejo, Maria Conejero, Leon Steiner, Sabrina Jung, Lucía Pita, Vasiliki Koutsouveli, Sören Franzenburg, Ute Hentschel, Ana Riesgo
{"title":"Phagocytosis of microbial symbionts supports embryonic nutrition in the sponge Halichondria panicea.","authors":"Marta Turon, Cristina Díez-Vives, Tyler J Carrier, Laura de la Cruz-Castillejo, Maria Conejero, Leon Steiner, Sabrina Jung, Lucía Pita, Vasiliki Koutsouveli, Sören Franzenburg, Ute Hentschel, Ana Riesgo","doi":"10.1186/s40168-026-02473-y","DOIUrl":"10.1186/s40168-026-02473-y","url":null,"abstract":"<p><strong>Background: </strong>Animal development is frequently supported by microbial symbionts that contribute to host nutrition, metabolism, and physiology. While the functional importance of microbiomes in adult hosts is increasingly recognized, the role of symbiotic microbes during gametogenesis and embryogenesis remains poorly understood, particularly in early-diverging metazoans. Sponges represent an ideal system to investigate these processes due to their dense and diverse microbial communities. Here, we examined host-symbiont dynamics across the reproductive cycle of the marine sponge Halichondria panicea to assess how microbial communities contribute to reproduction and early development.</p><p><strong>Results: </strong>Specimens were collected monthly from February to July and classified by reproductive stage using histological analyses. We combined ultrastructural imaging, dual RNA sequencing of host and symbionts, 16S rRNA gene amplicon sequencing, and quantitative PCR to characterize microbial and transcriptional dynamics throughout reproduction. Pronounced shifts in both host gene expression and microbial community composition occurred during early embryogenesis, particularly in May. Transmission electron microscopy revealed nurse cells phagocytosing bacterial aggregates in close proximity to late oocytes, presumably converting them into yolk precursors. This coincided with a significant decline in the abundance of the dominant obligate symbiont, Candidatus Halichondribacter symbioticus. Host transcriptomic analyses showed upregulation of immune and phagocytic pathways, including pattern recognition receptors, lectins, and vesicle trafficking components, specifically in females undergoing embryogenesis in May. Concurrently, symbiont gene expression profiles indicated responses to acidic conditions, consistent with exposure to phagosomal environments.</p><p><strong>Conclusions: </strong>Our results are consistent with intracellular digestion of microbial symbionts during early embryogenesis, potentially to supplement the nutritional requirements of embryogenesis. These findings reveal symbiont phagocytosis as a previously underappreciated nutritional strategy during animal development and highlight the dynamic functional integration of microbiomes into reproductive physiology in basal metazoans. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13543439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148891922","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}
MicrobiomePub Date : 2026-08-19DOI: 10.1186/s40168-026-02458-x
Feng Xue, Xiaoxiu Tan, Chenhong Zhang, Hongyu Zhao, Tao Wang
{"title":"Deciphering microbial community dynamics using cross-sectional data-informed NeuralODE.","authors":"Feng Xue, Xiaoxiu Tan, Chenhong Zhang, Hongyu Zhao, Tao Wang","doi":"10.1186/s40168-026-02458-x","DOIUrl":"10.1186/s40168-026-02458-x","url":null,"abstract":"<p><strong>Background: </strong>Understanding the ecological mechanisms of host-associated microbial ecosystems typically relies on either cross-sectional or time-series data. Cross-sectional analyses are limited in their ability to assess intervention effects, whereas time-series models require dense and informative sampling that is often impractical.</p><p><strong>Results: </strong>Here, we present an enhanced Neural Ordinary Differential Equations (NeuralODE) framework that, for the first time, integrates cross-sectional data into the dynamic modeling of sparse and weakly informative temporal data. We develop two instantiations of this framework, tailored to relative and absolute abundances, and introduce a dynamic keystoneness metric to quantify species importance over time. Across simulated and real-data benchmarks, incorporating cross-sectional data improved performance over competing methods, particularly in data-scarce settings. Moreover, biological validation demonstrated that the framework recovers experimentally supported interactions and prioritizes identified influential species.</p><p><strong>Conclusions: </strong>Together, these results establish our method as a reliable framework for mechanistic modeling of microbial ecosystems, offering new insights into their dynamic behavior. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13523204/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148840864","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}
MicrobiomePub Date : 2026-08-19DOI: 10.1186/s40168-026-02488-5
Hans Hoenicka, Kristina Ulrich, Charlotte Haffner, Marta Starczak, Daniel Gackowski, Ben Bubner, Andreas Ulrich
{"title":"Microbiome analysis and epigenetic patterns revealed distinct differences between two elm species with contrasting Dutch elm disease resistance.","authors":"Hans Hoenicka, Kristina Ulrich, Charlotte Haffner, Marta Starczak, Daniel Gackowski, Ben Bubner, Andreas Ulrich","doi":"10.1186/s40168-026-02488-5","DOIUrl":"10.1186/s40168-026-02488-5","url":null,"abstract":"<p><strong>Background: </strong>Dutch elm disease (DED), caused by the fungus Ophiostoma novo-ulmi, has devastated elm species in Europe and North America for over a century. While the Chinese elm (Ulmus parvifolia) frequently displays notable resistance to DED, the European wych elm (Ulmus glabra) remains highly susceptible. Understanding microbiome interaction and epigenetic factors might help to explain this contrasting resilience and subsequently improve disease management.</p><p><strong>Results: </strong>Seedlings of both elm species were germinated and maintained under identical environmental conditions. Comparative metabarcoding revealed distinct differences in bacterial and eukaryotic microbiomes, as well as in their associations with lichenized fungi and their photobiont algae. In U. parvifolia, 24 eukaryotic and 14 bacterial taxa were identified as the most differentially abundant microbiome components, and exhibited significantly different levels compared to U. glabra. In particular, Leotiomycetes fungi and Rhizobiales bacteria, both previously implicated in resistance to pathogens, were strongly enriched in U. parvifolia. Lichenized fungi and chlorophyte algae were likewise more abundant in U. parvifolia. In U. glabra, 11 eukaryotic and 16 bacterial taxa were significantly more abundant, including Nocardioides bacteria and Leptospora fungi. Ultra-performance liquid chromatography coupled with mass spectrometry revealed that, compared to U. glabra, U. parvifolia exhibited higher levels of 5-(hydroxymethyl)-2'-deoxycytidine and lower levels of 5-methyl-2'-deoxycytidine and N6-methyl-2'-deoxyadenosine in DNA, as well as increased amounts of 5-methylcytidine, N6-methyladenosine, and 5-hydroxymethyluridine in RNA. The elevated levels of well-established epigenetic markers in DNA and RNA are remarkable. However, it remains unclear what part of the holobiont may be responsible for this effect.</p><p><strong>Conclusions: </strong>The contrasting susceptibility of Chinese and European elms to DED correlates with pronounced differences in their associated microbial communities and lichens, as well as in patterns of epigenetic nucleoside modifications. In particular, the enrichment of specific stress-associated microbiome components, together with lichen associations and elevated levels of modified DNA and RNA nucleosides in U. parvifolia, may underlie its increased tolerance to DED. Although this study did not identify the factors responsible for DED resistance, it provides valuable insights into microbiomic and epigenetic features that could contribute to the development of new approaches to combat DED. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13488114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795201","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}
MicrobiomePub Date : 2026-08-04DOI: 10.1186/s40168-026-02457-y
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
{"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}
MicrobiomePub Date : 2026-07-23DOI: 10.1186/s40168-026-02463-0
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
{"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}
MicrobiomePub Date : 2026-07-23DOI: 10.1186/s40168-026-02455-0
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
{"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}