{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T19:06:54Z","timestamp":1793387214720,"version":"4.5.0"},"reference-count":223,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T00:00:00Z","timestamp":1757980800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The human microbiome, once regarded as a passive passenger, is now recognized as a dynamic and essential determinant of human physiology, shaping immunity, metabolism, neurodevelopment, and therapeutic responsiveness across the lifespan. Advances in multi-omic technologies, experimental models, and computational approaches have revealed mechanistic insights into how microbial communities modulate host systems across diverse body sites, including the gut, skin, lungs, oral cavity, and reproductive tract. The clinical translation of this knowledge has begun to redefine early-life programming, cardiometabolic regulation, immune homeostasis, neuropsychiatric resilience, and cancer therapy response. Innovative strategies such as phage therapy, live biotherapeutics, precision nutrition, and microbiota transplantation illustrate the therapeutic potential of harnessing microbial functions to prevent or treat disease. In parallel, large-scale initiatives cataloging the microbiome of underexplored niches, such as the vagina and skin, are advancing health equity by broadening representation in microbial reference datasets. Yet significant challenges persist, including interindividual variability, incomplete functional annotation of microbial \u201cdark matter,\u201d and the absence of validated biomarkers. Addressing these gaps requires standardized methodologies, harmonized regulatory frameworks, and longitudinal studies across diverse populations. This review outlines the progress and remaining hurdles in translating microbiome science into clinical practice and concludes that the microbiome now stands at the forefront of a paradigm shift, transforming concepts of disease etiology, therapeutic design, and the future of individualized medicine.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1632435","type":"journal-article","created":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T05:34:38Z","timestamp":1758000878000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":58,"title":["The human microbiome in clinical translation: from bench to bedside"],"prefix":"10.3389","volume":"16","author":[{"given":"Jhommara","family":"Bautista","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina E.","family":"Echeverr\u00eda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iv\u00e1n","family":"Maldonado-Noboa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sof\u00eda","family":"Ojeda-Mosquera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camila","family":"Hidalgo-Tinoco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9s","family":"L\u00f3pez-Cort\u00e9s","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,9,16]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"2249152","DOI":"10.1080\/19490976.2023.2249152","article-title":"The curious case of Prevotella copri","volume":"15","author":"Abdelsalam","year":"2023","journal-title":"Gut Microbes"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"999001","DOI":"10.3389\/fmicb.2022.999001","article-title":"Human gut microbiota in health and disease: unveiling the relationship","volume":"13","author":"Afzaal","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"2524","DOI":"10.1016\/j.cell.2021.03.022","article-title":"SnapShot: the microbiota-gut-brain axis","volume":"184","author":"Agirman","year":"2021","journal-title":"Cell"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/j.chom.2017.04.010","article-title":"Gut microbiome function predicts response to anti-integrin biologic therapy in inflammatory bowel diseases","volume":"21","author":"Ananthakrishnan","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"3942","DOI":"10.1016\/j.cell.2025.04.014","article-title":"Global genetic diversity of human gut microbiome species is related to geographic location and host health","volume":"188","author":"Andreu-S\u00e1nchez","year":"2025","journal-title":"Cell"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1186\/s13059-020-02015-1","article-title":"MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data","volume":"21","author":"Argelaguet","year":"2020","journal-title":"Genome Biol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1038\/s41522-023-00459-4","article-title":"The microbiome: from the beginning to the end","volume":"121","author":"Aurora","year":"2024","journal-title":"Mo. Med."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"7937","DOI":"10.1038\/s41467-023-43455-0","article-title":"Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics","volume":"14","author":"Baig","year":"2023","journal-title":"Nat. Commun."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"1379","DOI":"10.1016\/j.jhep.2021.12.003","article-title":"Promises of microbiome-based therapies","volume":"76","author":"Bajaj","year":"2022","journal-title":"J. Hepatol."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"eabk1107","DOI":"10.1126\/scitranslmed.abk1107","article-title":"Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition","volume":"14","author":"Barratt","year":"2022","journal-title":"Sci. Transl. Med."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1272955","DOI":"10.3389\/fnins.2023.1272955","article-title":"Enteroendocrine cell regulation of the gut-brain axis","volume":"17","author":"Barton","year":"2023","journal-title":"Front. Neurosci."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1126\/science.abb5920","article-title":"Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients","volume":"371","author":"Baruch","year":"2021","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"e70504","DOI":"10.1002\/jmv.70504","article-title":"Unraveling the gut-brain-immune interplay in herpes simplex virus-associated neurodegeneration","volume":"97","author":"Bautista","year":"","journal-title":"J. Med. Virol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"242","DOI":"10.3389\/fendo.2025.1606242","article-title":"Peripheral clocks and systemic zeitgeber interactions: from molecular mechanisms to circadian precision medicine","volume":"16","author":"Bautista","year":"","journal-title":"Front. Endocrinol. (Lausanne)"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"100065","DOI":"10.1016\/j.crimmu.2023.100065","article-title":"Lung microbiome and origins of the respiratory diseases","volume":"4","author":"Beliz\u00e1rio","year":"2023","journal-title":"Curr. Res. Immunol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1486","DOI":"10.1136\/gutjnl-2022-329201","article-title":"Gut microbiome modulates the effects of a personalised postprandial-targeting (PPT) diet on cardiometabolic markers: a diet intervention in pre-diabetes","volume":"72","author":"Ben-Yacov","year":"2023","journal-title":"Gut"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1038\/s41591-024-02803-3","article-title":"Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma","volume":"30","author":"Bj\u00f6rk","year":"2024","journal-title":"Nat. Med."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1172\/JCI183884","article-title":"Missing microbiomes: global underrepresentation restricts who research will benefit","volume":"134","author":"Blake","year":"2024","journal-title":"J. Clin. Invest."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"4048","DOI":"10.1016\/j.csbj.2020.11.049","article-title":"Measuring the microbiome: best practices for developing and benchmarking microbiomics methods","volume":"18","author":"Bokulich","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1001\/jamaoncol.2022.7753","article-title":"Association of a mediterranean diet with outcomes for patients treated with immune checkpoint blockade for advanced melanoma","volume":"9","author":"Bolte","year":"2023","journal-title":"JAMA Oncol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"102326","DOI":"10.1016\/j.pbi.2022.102326","article-title":"Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies","volume":"71","author":"Busato","year":"2023","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/nrmicro.2017.157","article-title":"The human skin microbiome","volume":"16","author":"Byrd","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"101557","DOI":"10.1016\/j.molmet.2022.101557","article-title":"Role of gut microbe-derived metabolites in cardiometabolic diseases: systems based approach","volume":"64","author":"Cao","year":"2022","journal-title":"Mol. Metab."},{"key":"ref24","first-page":"203","article-title":"The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems","volume":"28","author":"Carabotti","year":"2015","journal-title":"Ann. Gastroenterol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"400","DOI":"10.3390\/nu16030400","article-title":"The role of diet and nutritional interventions for the infant gut microbiome","volume":"16","author":"Catassi","year":"2024","journal-title":"Nutrients"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1979882","DOI":"10.1080\/19490976.2021.1979882","article-title":"Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile","volume":"13","author":"Chandra","year":"2021","journal-title":"Gut Microbes"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"10394","DOI":"10.1038\/s41598-024-60730-2","article-title":"Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users","volume":"14","author":"Chattopadhyay","year":"2024","journal-title":"Sci. Rep."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"D1205","DOI":"10.1093\/nar\/gkac891","article-title":"BIC: a database for the transcriptional landscape of bacteria in cancer","volume":"51","author":"Chen","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1166022","DOI":"10.3389\/fphar.2023.1166022","article-title":"Effects of Litsea cubeba essential oil on growth performance, blood antioxidation, immune function, apparent digestibility of nutrients, and fecal microflora of pigs","volume":"14","author":"Chen","year":"2023","journal-title":"Front. Pharmacol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1007\/s43657-022-00073-y","article-title":"Skin microbiome, metabolome and skin phenome, from the perspectives of skin as an ecosystem","volume":"2","author":"Chen","year":"2022","journal-title":"Phenomics"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1186\/s12888-020-02654-5","article-title":"Effect of fecal microbiota transplant on symptoms of psychiatric disorders: a systematic review","volume":"20","author":"Chinna Meyyappan","year":"2020","journal-title":"BMC Psychiatry"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1016\/j.coi.2011.07.010","article-title":"Pathobionts of the gastrointestinal microbiota and inflammatory disease","volume":"23","author":"Chow","year":"2011","journal-title":"Curr. Opin. Immunol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1007\/s00125-023-06019-x","article-title":"The metabolomic signature of weight loss and remission in the diabetes remission clinical trial (DiRECT)","volume":"67","author":"Corbin","year":"2024","journal-title":"Diabetologia"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1016\/j.cell.2014.05.052","article-title":"Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences","volume":"158","author":"Cox","year":"2014","journal-title":"Cell"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1126\/science.abf3363","article-title":"Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients","volume":"371","author":"Davar","year":"2021","journal-title":"Science"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1020","DOI":"10.1136\/gutjnl-2021-326789","article-title":"Gut microbiome and health: mechanistic insights","volume":"71","author":"de Vos","year":"2022","journal-title":"Gut"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e0207524","DOI":"10.1128\/mbio.02075-24","article-title":"From microbes to mind: germ-free models in neuropsychiatric research","volume":"15","author":"Delgado-Oca\u00f1a","year":"2024","journal-title":"MBio"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"122","DOI":"10.4103\/jomfp.JOMFP_304_18","article-title":"Oral microbiome: unveiling the fundamentals","volume":"23","author":"Deo","year":"2019","journal-title":"J. Oral Maxillofac. Pathol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/s41591-021-01655-5","article-title":"Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer","volume":"28","author":"Derosa","year":"2022","journal-title":"Nat. Med."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"301","DOI":"10.3390\/microorganisms7090301","article-title":"Staphylococcus aureus and the cutaneous microbiota biofilms in the pathogenesis of atopic dermatitis","volume":"7","author":"Di Domenico","year":"2019","journal-title":"Microorganisms"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"e00964-21","DOI":"10.1128\/mSystems.00964-21","article-title":"Baseline gut metagenomic functional gene signature associated with variable weight loss responses following a healthy lifestyle intervention in humans","volume":"6","author":"Diener","year":"2021","journal-title":"mSystems"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"11971","DOI":"10.1073\/pnas.1002601107","article-title":"Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns","volume":"107","author":"Dominguez-Bello","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1434804","DOI":"10.3389\/fimmu.2024.1434804","article-title":"From bench to bedside: an interdisciplinary journey through the gut-lung axis with insights into lung cancer and immunotherapy","volume":"15","author":"Dora","year":"2024","journal-title":"Front. Immunol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"31647","DOI":"10.1038\/s41598-024-80281-w","article-title":"Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study","volume":"14","author":"Ecklu-Mensah","year":"2024","journal-title":"Sci. Rep."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"eadh1469","DOI":"10.1126\/scitranslmed.adh1469","article-title":"Multiomic profiling of cutaneous leishmaniasis infections reveals microbiota-driven mechanisms underlying disease severity","volume":"15","author":"Farias Amorim","year":"2023","journal-title":"Sci. Transl. Med."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/s13311-017-0600-5","article-title":"Gut microbiota and the neuroendocrine system","volume":"15","author":"Farzi","year":"2018","journal-title":"Neurotherapeutics"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/s41591-021-01672-4","article-title":"A roadmap to increase diversity in genomic studies","volume":"28","author":"Fatumo","year":"2022","journal-title":"Nat. Med."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"2879","DOI":"10.1016\/j.cell.2022.07.003","article-title":"Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation","volume":"185","author":"Federici","year":"2022","journal-title":"Cell"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1056\/NEJMoa2106516","article-title":"SER-109, an oral microbiome therapy for recurrent Clostridioides difficile infection","volume":"386","author":"Feuerstadt","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"e0115121","DOI":"10.1128\/mSystems.01151-21","article-title":"Advancing equity and inclusion in microbiome research and training","volume":"6","author":"Foxx","year":"2021","journal-title":"mSystems"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1970","DOI":"10.1038\/s41591-021-01520-5","article-title":"IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies","volume":"27","author":"Friedrich","year":"2021","journal-title":"Nat. Med."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"eaaz0108","DOI":"10.1126\/sciadv.aaz0108","article-title":"Adverse effects of electronic cigarettes on the disease-naive oral microbiome","volume":"6","author":"Ganesan","year":"2020","journal-title":"Sci. Adv."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1007\/s13238-018-0548-1","article-title":"Oral microbiomes: more and more importance in oral cavity and whole body","volume":"9","author":"Gao","year":"2018","journal-title":"Protein Cell"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.chom.2022.02.007","article-title":"Debugging the gut-brain axis in depression","volume":"30","author":"Gheorghe","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"1450","DOI":"10.1093\/advances\/nmac075","article-title":"Perspective: leveraging the gut microbiota to predict personalized responses to dietary, prebiotic, and probiotic interventions","volume":"13","author":"Gibbons","year":"2022","journal-title":"Adv. Nutr."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1038\/s41591-025-03615-9","article-title":"Clinical translation of microbiome research","volume":"31","author":"Gilbert","year":"2025","journal-title":"Nat. Med."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/nm.4517","article-title":"Current understanding of the human microbiome","volume":"24","author":"Gilbert","year":"2018","journal-title":"Nat. Med."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/nature18850","article-title":"Microbiome-wide association studies link dynamic microbial consortia to disease","volume":"535","author":"Gilbert","year":"2016","journal-title":"Nature"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/j.chom.2017.08.013","article-title":"Host genetic control of the oral microbiome in health and disease","volume":"22","author":"Gomez","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1038\/nrmicro2537","article-title":"The skin microbiome","volume":"9","author":"Grice","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/j.tem.2024.05.002","article-title":"Neuroendocrine gut-brain signaling in obesity","volume":"36","author":"Gruber","year":"2025","journal-title":"Trends Endocrinol. Metab."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"13978","DOI":"10.1038\/s41598-018-32264-x","article-title":"Analysis of racial\/ethnic representation in select basic and applied cancer research studies","volume":"8","author":"Guerrero","year":"2018","journal-title":"Sci. Rep."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"105130","DOI":"10.1016\/j.tifs.2025.105130","article-title":"Commercial and regulatory frameworks for postbiotics: an industry-oriented scientific perspective for non-viable microbial ingredients conferring beneficial physiological effects","volume":"163","author":"Guglielmetti","year":"2025","journal-title":"Trends Food Sci. Technol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1111\/apt.17049","article-title":"Review article: the future of microbiome-based therapeutics","volume":"56","author":"Gulliver","year":"2022","journal-title":"Aliment. Pharmacol. Ther."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1038\/s42003-024-07158-6","article-title":"Cross-comparison of gut metagenomic profiling strategies","volume":"7","author":"Guly\u00e1s","year":"2024","journal-title":"Commun. Biol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/s41467-024-44776-4","article-title":"Engineering tumor-colonizing E. coli Nissle 1917 for detection and treatment of colorectal neoplasia","volume":"15","author":"Gurbatri","year":"2024","journal-title":"Nat. Commun."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1016\/j.chom.2023.02.009","article-title":"Oral polymicrobial communities: assembly, function, and impact on diseases","volume":"31","author":"Hajishengallis","year":"2023","journal-title":"Cell Host Microbe"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1158\/2159-8290.CD-21-1059","article-title":"Hallmarks of cancer: new dimensions","volume":"12","author":"Hanahan","year":"2022","journal-title":"Cancer Discov."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"5464","DOI":"10.1038\/s41598-024-54285-5","article-title":"Gut dysbiosis is linked to metabolic syndrome in obese Egyptian women: potential treatment by probiotics and high fiber diets regimen","volume":"14","author":"Hassan","year":"2024","journal-title":"Sci. Rep."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/s13046-025-03313-x","article-title":"Dysbiosis and extraintestinal cancers","volume":"44","author":"He","year":"2025","journal-title":"J. Exp. Clin. Cancer Res."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"541","DOI":"10.3390\/nu13124541","article-title":"Infant formula with added bovine Milk fat globule membrane and modified Iron supports growth and Normal Iron status at one year of age: a randomized controlled trial","volume":"13","author":"Hedrick","year":"2021","journal-title":"Nutrients"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"3884","DOI":"10.1016\/j.cell.2021.05.030","article-title":"Bifidobacteria-mediated immune system imprinting early in life","volume":"184","author":"Henrick","year":"2021","journal-title":"Cell"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1093\/aje\/kwv254","article-title":"Using big data to emulate a target trial when a randomized trial is not available","volume":"183","author":"Hern\u00e1n","year":"2016","journal-title":"Am. J. Epidemiol."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1038\/s41385-022-00564-1","article-title":"Microbiome-based interventions to modulate gut ecology and the immune system","volume":"15","author":"Hitch","year":"2022","journal-title":"Mucosal Immunol."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"4169","DOI":"10.1038\/s41467-018-06473-x","article-title":"Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations","volume":"9","author":"Ho","year":"2018","journal-title":"Nat. Commun."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1038\/s41392-022-00974-4","article-title":"Microbiota in health and diseases","volume":"7","author":"Hou","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.chom.2022.02.014","article-title":"Can maternal-child microbial seeding interventions improve the health of infants delivered by Cesarean section?","volume":"30","author":"Hourigan","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref78","doi-asserted-by":"publisher","first-page":"2185","DOI":"10.1038\/s41564-024-01751-5","article-title":"A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome","volume":"9","author":"Huang","year":"2024","journal-title":"Nat. Microbiol."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/mi.2016.108","article-title":"The respiratory tract microbiome and lung inflammation: a two-way street","volume":"10","author":"Huffnagle","year":"2017","journal-title":"Mucosal Immunol."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/s41385-020-00368-1","article-title":"The intestinal neuro-immune axis: crosstalk between neurons, immune cells, and microbes","volume":"14","author":"Jacobson","year":"2021","journal-title":"Mucosal Immunol."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"6289","DOI":"10.1038\/s41467-021-26634-9","article-title":"The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model","volume":"12","author":"Ja\u0161arevi\u0107","year":"2021","journal-title":"Nat. Commun."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/s41593-018-0182-5","article-title":"The maternal vaginal microbiome partially mediates the effects of prenatal stress on offspring gut and hypothalamus","volume":"21","author":"Ja\u0161arevi\u0107","year":"2018","journal-title":"Nat. Neurosci."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"580","DOI":"10.3389\/frmbi.2024.1359580","article-title":"A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome","volume":"3","author":"John","year":"2024","journal-title":"Front. Microbiomes"},{"key":"ref85","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/s44184-025-00123-z","article-title":"Probiotics reduce negative mood over time: the value of daily self-reports in detecting effects","volume":"4","author":"Johnson","year":"2025","journal-title":"NPJ Ment. Health Res."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/s44324-025-00066-1","article-title":"Mechanisms and implications of the gut microbial modulation of intestinal metabolic processes","volume":"3","author":"Jyoti","year":"2025","journal-title":"NPJ Metab. Health Dis."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"5821","DOI":"10.1038\/s41598-019-42183-0","article-title":"Long-term benefit of microbiota transfer therapy on autism symptoms and gut microbiota","volume":"9","author":"Kang","year":"2019","journal-title":"Sci. Rep."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/s40168-016-0225-7","article-title":"Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study","volume":"5","author":"Kang","year":"2017","journal-title":"Microbiome"},{"key":"ref89","doi-asserted-by":"publisher","first-page":"101478","DOI":"10.1016\/j.xcrm.2024.101478","article-title":"Modulating gut microbiome in cancer immunotherapy: harnessing microbes to enhance treatment efficacy","volume":"5","author":"Kang","year":"2024","journal-title":"Cell Rep. Med."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"e2306020120","DOI":"10.1073\/pnas.2306020120","article-title":"Localized microbially induced inflammation influences distant healthy tissues in the human oral cavity","volume":"120","author":"Kerns","year":"2023","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"102156","DOI":"10.1016\/j.mib.2022.102156","article-title":"Human milk oligosaccharides and the infant gut microbiome from an eco-evolutionary perspective","volume":"68","author":"Kijner","year":"2022","journal-title":"Curr. Opin. Microbiol."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1186\/s12864-019-6288-7","article-title":"A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships","volume":"20","author":"Kim","year":"2019","journal-title":"BMC Genomics"},{"key":"ref93","doi-asserted-by":"publisher","first-page":"111787","DOI":"10.1016\/j.mad.2023.111787","article-title":"Gut-brain axis through the lens of gut microbiota and their relationships with Alzheimer\u2019s disease pathology: review and recommendations","volume":"211","author":"Krishaa","year":"2023","journal-title":"Mech. Ageing Dev."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"919728","DOI":"10.3389\/fimmu.2022.919728","article-title":"Host and microbiome interplay shapes the vaginal microenvironment","volume":"13","author":"Kwon","year":"2022","journal-title":"Front. Immunol."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1038\/s41579-018-0089-x","article-title":"The oral microbiota: dynamic communities and host interactions","volume":"16","author":"Lamont","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"2183","DOI":"10.1038\/s41564-023-01500-0","article-title":"A citizen-science-enabled catalogue of the vaginal microbiome and associated factors","volume":"8","author":"Lebeer","year":"2023","journal-title":"Nat. Microbiol."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1200\/JCO.2024.42.3_suppl.368","article-title":"Phase II study of GEN-001 in combination with avelumab in patients with PD-L1\u2013positive locally advanced, or metastatic gastric cancer (GC) or gastroesophageal junction cancer (GEJC) who have progressed after second-line (2L) and beyond (GEN001-201 study)","volume":"42","author":"Lee","year":"2024","journal-title":"J. Clin. Oncol."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"1294","DOI":"10.1016\/j.chom.2021.06.019","article-title":"Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease","volume":"29","author":"Lee","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref99","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1101\/gr.278637.123","article-title":"Global compositional and functional states of the human gut microbiome in health and disease","volume":"34","author":"Lee","year":"2024","journal-title":"Genome Res."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1038\/s41591-022-01695-5","article-title":"Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma","volume":"28","author":"Lee","year":"2022","journal-title":"Nat. Med."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1016\/j.cell.2024.01.029","article-title":"High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota","volume":"187","author":"Lee","year":"2024","journal-title":"Cell"},{"key":"ref102","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/s41522-025-00786-8","article-title":"Gut microbiota shapes cancer immunotherapy responses","volume":"11","author":"Lei","year":"2025","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref103","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1038\/s41564-019-0498-2","article-title":"Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance","volume":"4","author":"Levan","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref104","doi-asserted-by":"publisher","first-page":"1500","DOI":"10.1038\/s41591-019-0600-6","article-title":"Vaginal microbiome transplantation in women with intractable bacterial vaginosis","volume":"25","author":"Lev-Sagie","year":"2019","journal-title":"Nat. Med."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/s41392-023-01722-y","article-title":"Lung microbiome: new insights into the pathogenesis of respiratory diseases","volume":"9","author":"Li","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"1369823","DOI":"10.3389\/fped.2024.1369823","article-title":"Effects and microbiota changes following oral lyophilized fecal microbiota transplantation in children with autism spectrum disorder","volume":"12","author":"Li","year":"2024","journal-title":"Front. Pediatr."},{"key":"ref107","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s13045-024-01541-w","article-title":"Critical role of the gut microbiota in immune responses and cancer immunotherapy","volume":"17","author":"Li","year":"2024","journal-title":"J. Hematol. Oncol."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"104163","DOI":"10.1016\/j.ebiom.2022.104163","article-title":"Gut microbiome in modulating immune checkpoint inhibitors","volume":"82","author":"Li","year":"2022","journal-title":"EBioMedicine"},{"key":"ref109","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/s42255-024-00988-y","article-title":"Resistant starch intake facilitates weight loss in humans by reshaping the gut microbiota","volume":"6","author":"Li","year":"2024","journal-title":"Nat. Metab."},{"key":"ref110","doi-asserted-by":"publisher","first-page":"1022567","DOI":"10.3389\/fphar.2022.1022567","article-title":"Pharmacokinetics effects of chuanxiong rhizoma on warfarin in pseudo germ-free rats","volume":"13","author":"Li","year":"2022","journal-title":"Front. Pharmacol."},{"key":"ref111","doi-asserted-by":"publisher","first-page":"4530","DOI":"10.1016\/j.cell.2025.05.010","article-title":"A microbial amino-acid-conjugated bile acid, tryptophan-cholic acid, improves glucose homeostasis via the orphan receptor MRGPRE","volume":"188","author":"Lin","year":"2025","journal-title":"Cell"},{"key":"ref112","doi-asserted-by":"publisher","first-page":"103908","DOI":"10.1016\/j.ebiom.2022.103908","article-title":"Microbiota and the gut-brain-axis: implications for new therapeutic design in the CNS","volume":"77","author":"Liu","year":"2022","journal-title":"EBioMedicine"},{"key":"ref113","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1038\/s41590-023-01500-6","article-title":"Crosstalk between skin microbiota and immune system in health and disease","volume":"24","author":"Liu","year":"2023","journal-title":"Nat. Immunol."},{"key":"ref114","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1186\/s13073-016-0307-y","article-title":"The healthy human microbiome","volume":"8","author":"Lloyd-Price","year":"2016","journal-title":"Genome Med."},{"key":"ref115","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"ref116","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1038\/s41392-024-01743-1","article-title":"Microbiota-gut-brain axis and its therapeutic applications in neurodegenerative diseases","volume":"9","author":"Loh","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref117","doi-asserted-by":"publisher","first-page":"598925","DOI":"10.3389\/fphar.2021.598925","article-title":"In silico analyses of immune system protein interactome network, single-cell RNA sequencing of human tissues, and artificial neural networks reveal potential therapeutic targets for drug repurposing against COVID-19","volume":"12","author":"L\u00f3pez-Cort\u00e9s","year":"2021","journal-title":"Front. Pharmacol."},{"key":"ref118","doi-asserted-by":"publisher","first-page":"pyw020","DOI":"10.1093\/ijnp\/pyw020","article-title":"Growing up in a bubble: using germ-free animals to assess the influence of the gut microbiota on brain and behavior","volume":"19","author":"Luczynski","year":"2016","journal-title":"Int. J. Neuropsychopharmacol."},{"key":"ref119","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/s41392-024-01946-6","article-title":"A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation","volume":"9","author":"Ma","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref120","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.1016\/j.immuni.2023.07.011","article-title":"Boundaries and integration between microbiota, the nervous system, and immunity","volume":"56","author":"Macpherson","year":"2023","journal-title":"Immunity"},{"key":"ref121","doi-asserted-by":"publisher","first-page":"1970","DOI":"10.1038\/s41467-021-22097-0","article-title":"Fasting alters the gut microbiome reducing blood pressure and body weight in metabolic syndrome patients","volume":"12","author":"Maifeld","year":"2021","journal-title":"Nat. Commun."},{"key":"ref122","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1038\/s42003-025-08515-9","article-title":"A systematic benchmark of integrative strategies for microbiome-metabolome data","volume":"8","author":"Mangnier","year":"2025","journal-title":"Commun. Biol."},{"key":"ref123","doi-asserted-by":"publisher","first-page":"1399","DOI":"10.1038\/s41390-025-04021-0","article-title":"Genomics and multiomics in the age of precision medicine","volume":"97","author":"Mani","year":"2025","journal-title":"Pediatr. Res."},{"key":"ref124","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1016\/j.chom.2020.07.009","article-title":"Oral microbiome geography: Micron-scale habitat and niche","volume":"28","author":"Mark Welch","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref125","doi-asserted-by":"publisher","first-page":"100141","DOI":"10.1016\/j.medmic.2025.100141","article-title":"Microbiota during pregnancy, childbirth, and postpartum, and its relationship with health and disease states","volume":"25","author":"M\u00e1rquez Ibarra","year":"2025","journal-title":"Med. Microecol."},{"key":"ref126","doi-asserted-by":"publisher","first-page":"e21","DOI":"10.1016\/j.amjmed.2014.06.020","article-title":"Fecal microbiota transplantation: the case of immunocompromised patients","volume":"128","author":"Matuchansky","year":"2015","journal-title":"Am. J. Med."},{"key":"ref127","doi-asserted-by":"publisher","first-page":"100713","DOI":"10.1016\/j.xcrm.2022.100713","article-title":"Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy","volume":"3","author":"McCauley","year":"2022","journal-title":"Cell Rep. Med."},{"key":"ref128","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1038\/s41467-024-45665-6","article-title":"Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis","volume":"15","author":"Mennillo","year":"2024","journal-title":"Nat. Commun."},{"key":"ref129","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1099\/mgen.0.001405","article-title":"Assessing the safety of microbiome perturbations","volume":"11","author":"Metris","year":"2025","journal-title":"Microb. Genom."},{"key":"ref130","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1128\/MMBR.00036-17","article-title":"The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota","volume":"81","author":"Milani","year":"2017","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref131","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.addr.2016.04.032","article-title":"Microbiome therapeutics - advances and challenges","volume":"105","author":"Mimee","year":"2016","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref132","doi-asserted-by":"publisher","first-page":"e0049123","DOI":"10.1128\/mbio.00491-23","article-title":"Maternal bacterial engraftment in multiple body sites of Cesarean section born neonates after vaginal seeding-a randomized controlled trial","volume":"14","author":"Mueller","year":"2023","journal-title":"MBio"},{"key":"ref133","doi-asserted-by":"publisher","first-page":"2621","DOI":"10.1038\/s41467-024-46888-3","article-title":"Multi-omic integration of microbiome data for identifying disease-associated modules","volume":"15","author":"Muller","year":"2024","journal-title":"Nat. Commun."},{"key":"ref134","doi-asserted-by":"publisher","first-page":"17724","DOI":"10.1177\/17562848211017725","article-title":"The contribution of bile acid metabolism to the pathogenesis of Clostridioides difficile infection","volume":"14","author":"Mullish","year":"2021","journal-title":"Ther. Adv. Gastroenterol."},{"key":"ref135","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1186\/s40168-021-01061-6","article-title":"Gut microbiome variation modulates the effects of dietary fiber on host metabolism","volume":"9","author":"Murga-Garrido","year":"2021","journal-title":"Microbiome"},{"key":"ref136","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1126\/scitranslmed.aaz8631","article-title":"Therapeutic responses to Roseomonas mucosa in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair","volume":"12","author":"Myles","year":"2020","journal-title":"Sci. Transl. Med."},{"key":"ref137","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1016\/j.coi.2021.09.001","article-title":"Mechanisms for control of skin immune function by the microbiome","volume":"72","author":"Nakatsuji","year":"","journal-title":"Curr. Opin. Immunol."},{"key":"ref138","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1038\/s41591-021-01256-2","article-title":"Development of a human skin commensal microbe for bacteriotherapy of atopic dermatitis and use in a phase 1 randomized clinical trial","volume":"27","author":"Nakatsuji","year":"","journal-title":"Nat. Med."},{"key":"ref139","doi-asserted-by":"publisher","first-page":"e003964","DOI":"10.1136\/bmjdrc-2023-003964","article-title":"Unveiling contrasts in microbiota response: A1c control improves dysbiosis in low-A1c T2DM, but fails in high-A1c cases-a key to metabolic memory?","volume":"12","author":"Napoli","year":"2024","journal-title":"BMJ Open Diabetes Res. Care"},{"key":"ref140","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/s41579-022-00821-x","article-title":"The dynamic lung microbiome in health and disease","volume":"21","author":"Natalini","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref141","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/19490976.2021.1897212","article-title":"The role of short-chain fatty acids in the interplay between gut microbiota and diet in cardio-metabolic health","volume":"13","author":"Nogal","year":"2021","journal-title":"Gut Microbes"},{"key":"ref142","doi-asserted-by":"publisher","first-page":"101982","DOI":"10.1016\/j.xcrm.2025.101982","article-title":"The gut microbiota-immune-brain axis: therapeutic implications","volume":"6","author":"O\u2019Riordan","year":"2025","journal-title":"Cell Rep. Med."},{"key":"ref143","doi-asserted-by":"publisher","first-page":"1381168","DOI":"10.3389\/fphar.2024.1381168","article-title":"The pharmacoepigenetic paradigm in cancer treatment","volume":"15","author":"Oca\u00f1a-Paredes","year":"2024","journal-title":"Front. Pharmacol."},{"key":"ref144","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1016\/j.cell.2019.01.001","article-title":"Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle","volume":"176","author":"Pasolli","year":"2019","journal-title":"Cell"},{"key":"ref145","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1542\/peds.2005-2824","article-title":"Factors influencing the composition of the intestinal microbiota in early infancy","volume":"118","author":"Penders","year":"2006","journal-title":"Pediatrics"},{"key":"ref146","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1038\/s41368-022-00163-7","article-title":"Oral microbiota in human systematic diseases","volume":"14","author":"Peng","year":"2022","journal-title":"Int. J. Oral Sci."},{"key":"ref147","doi-asserted-by":"publisher","first-page":"14198","DOI":"10.1038\/s41598-023-39401-1","article-title":"Integrated multi-omics analysis reveals the molecular interplay between circadian clocks and cancer pathogenesis","volume":"13","author":"P\u00e9rez-Villa","year":"2023","journal-title":"Sci. Rep."},{"key":"ref148","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1016\/j.chom.2024.11.001","article-title":"Prenatal antibiotics reduce breast milk IgA and induce dysbiosis in mouse offspring, increasing neonatal susceptibility to bacterial sepsis","volume":"32","author":"Pietrasanta","year":"2024","journal-title":"Cell Host Microbe"},{"key":"ref149","doi-asserted-by":"publisher","first-page":"2836","DOI":"10.1016\/j.cell.2025.04.016","article-title":"The microbiome for clinicians","volume":"188","author":"Porcari","year":"2025","journal-title":"Cell"},{"key":"ref150","doi-asserted-by":"publisher","first-page":"103599","DOI":"10.1016\/j.micpath.2019.103599","article-title":"Vaginal microbiota of asymptomatic bacterial vaginosis and vulvovaginal candidiasis: are they different from normal microbiota?","volume":"134","author":"Pramanick","year":"2019","journal-title":"Microb. Pathog."},{"key":"ref151","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1097\/MPG.0000000000001520","article-title":"Effects of infant formula with human milk oligosaccharides on growth and morbidity: a randomized multicenter trial","volume":"64","author":"Puccio","year":"2017","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"ref152","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1038\/s41588-021-00991-z","article-title":"Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort","volume":"54","author":"Qin","year":"2022","journal-title":"Nat. Genet."},{"key":"ref153","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"},{"key":"ref154","doi-asserted-by":"publisher","first-page":"114128","DOI":"10.1016\/j.celrep.2024.114128","article-title":"Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer\u2019s disease","volume":"43","author":"Qiu","year":"2024","journal-title":"Cell Rep."},{"key":"ref155","doi-asserted-by":"publisher","first-page":"204","DOI":"10.12688\/f1000research.20204.1","article-title":"Recent advances in modulating the microbiome","volume":"9","author":"Quigley","year":"2020","journal-title":"F1000Res"},{"key":"ref156","doi-asserted-by":"publisher","first-page":"572912","DOI":"10.3389\/fcimb.2020.572912","article-title":"Antibiotics as major disruptors of gut microbiota","volume":"10","author":"Ramirez","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref157","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/j.trecan.2019.12.007","article-title":"The influence of lung microbiota on lung carcinogenesis, immunity, and immunotherapy","volume":"6","author":"Ram\u00edrez-Labrada","year":"2020","journal-title":"Trends Cancer"},{"key":"ref158","doi-asserted-by":"publisher","first-page":"v67","DOI":"10.1093\/neuonc\/noad179.0265","article-title":"Ctim-25. eo2401 peptide immunotherapy + nivolumab +\/\u2212 bevacizumab in first recurrent glioblastoma: the phase 1\/2 eogbm1-18\/rosalie study (nct04116658)","volume":"25","author":"Reardon","year":"2023","journal-title":"Neuro-Oncology"},{"key":"ref159","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1111\/j.1574-695X.2001.tb00531.x","article-title":"Probiotic Lactobacillus dose required to restore and maintain a normal vaginal flora","volume":"32","author":"Reid","year":"2001","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref160","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1016\/j.jhin.2019.12.022","article-title":"Faecal microbiota transplantation for recurrent Clostridioides difficile infection: experience with lyophilized oral capsules","volume":"105","author":"Reigadas","year":"2020","journal-title":"J. Hosp. Infect."},{"key":"ref161","doi-asserted-by":"publisher","first-page":"4997","DOI":"10.1038\/s41467-019-13014-7","article-title":"Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life","volume":"10","author":"Reyman","year":"2019","journal-title":"Nat. Commun."},{"key":"ref162","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1007\/s10238-025-01691-2","article-title":"Oncolytic virotherapy and tumor microenvironment modulation","volume":"25","author":"Rivera-Orellana","year":"2025","journal-title":"Clin. Exp. Med."},{"key":"ref163","doi-asserted-by":"publisher","first-page":"1154","DOI":"10.1016\/j.csbj.2024.02.018","article-title":"Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: a review","volume":"23","author":"Rosati","year":"2024","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref164","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1038\/nature25973","article-title":"Environment dominates over host genetics in shaping human gut microbiota","volume":"555","author":"Rothschild","year":"2018","journal-title":"Nature"},{"key":"ref165","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1053\/j.gastro.2025.02.035","article-title":"Machine learning and artificial intelligence in the multi-omics approach to gut microbiota","volume":"169","author":"Rozera","year":"2025","journal-title":"Gastroenterology"},{"key":"ref166","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1038\/s41586-025-08796-4","article-title":"Bifidobacteria support optimal infant vaccine responses","volume":"641","author":"Ryan","year":"2025","journal-title":"Nature"},{"key":"ref167","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s13059-023-02858-4","article-title":"Leveraging explainable AI for gut microbiome-based colorectal cancer classification","volume":"24","author":"Rynazal","year":"2023","journal-title":"Genome Biol."},{"key":"ref168","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1093\/bib\/bbaf323","article-title":"Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions","volume":"26","author":"Sabih Ur Rehman","year":"2025","journal-title":"Brief. Bioinform."},{"key":"ref169","doi-asserted-by":"publisher","first-page":"e0010723","DOI":"10.1128\/mbio.00107-23","article-title":"A new phenotype in Candida-epithelial cell interaction distinguishes colonization- versus vulvovaginal candidiasis-associated strains","volume":"14","author":"Sala","year":"2023","journal-title":"MBio"},{"key":"ref170","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.4049\/jimmunol.1800893","article-title":"Short-chain fatty acids from Cutibacterium acnes activate both a canonical and epigenetic inflammatory response in human Sebocytes","volume":"202","author":"Sanford","year":"2019","journal-title":"J. Immunol."},{"key":"ref171","doi-asserted-by":"publisher","first-page":"1487641","DOI":"10.3389\/fmicb.2024.1487641","article-title":"A comprehensive review of probiotics and human health-current prospective and applications","volume":"15","author":"Sarita","year":"2024","journal-title":"Front. Microbiol."},{"key":"ref172","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1038\/s41575-021-00499-1","article-title":"The promise of the gut microbiome as part of individualized treatment strategies","volume":"19","author":"Schupack","year":"2022","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref173","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1111\/prd.12393","article-title":"The oral microbiome: role of key organisms and complex networks in oral health and disease","volume":"87","author":"Sedghi","year":"2021","journal-title":"Periodontol."},{"key":"ref174","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1038\/s41586-019-1560-1","article-title":"Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth","volume":"574","author":"Shao","year":"2019","journal-title":"Nature"},{"key":"ref175","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1186\/s13059-023-03090-w","article-title":"A genome catalog of the early-life human skin microbiome","volume":"24","author":"Shen","year":"2023","journal-title":"Genome Biol."},{"key":"ref176","doi-asserted-by":"publisher","first-page":"3055","DOI":"10.1093\/bioinformatics\/bty1054","article-title":"DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays","volume":"35","author":"Singh","year":"2019","journal-title":"Bioinformatics"},{"key":"ref177","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1038\/nbt.3981","article-title":"Assessment of variation in microbial community amplicon sequencing by the microbiome quality control (MBQC) project consortium","volume":"35","author":"Sinha","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"ref178","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1016\/j.chom.2020.01.021","article-title":"Dysbiosis-induced secondary bile acid deficiency promotes intestinal inflammation","volume":"27","author":"Sinha","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref179","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1126\/science.aac4255","article-title":"Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy","volume":"350","author":"Sivan","year":"2015","journal-title":"Science"},{"key":"ref180","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1111\/mmi.15115","article-title":"Heterogeneity of the group B streptococcal type VII secretion system and influence on colonization of the female genital tract","volume":"120","author":"Spencer","year":"2023","journal-title":"Mol. Microbiol."},{"key":"ref181","doi-asserted-by":"publisher","first-page":"1632","DOI":"10.1126\/science.aaz7015","article-title":"Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response","volume":"374","author":"Spencer","year":"2021","journal-title":"Science"},{"key":"ref182","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.1001\/jamaoncol.2016.1854","article-title":"Racial\/ethnic disparities in genomic sequencing","volume":"2","author":"Spratt","year":"2016","journal-title":"JAMA Oncol."},{"key":"ref183","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-018-0617-x","article-title":"Temporal development of the gut microbiome in early childhood from the TEDDY study","volume":"562","author":"Stewart","year":"2018","journal-title":"Nature"},{"key":"ref184","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1038\/nature13793","article-title":"Artificial sweeteners induce glucose intolerance by altering the gut microbiota","volume":"514","author":"Suez","year":"2014","journal-title":"Nature"},{"key":"ref185","doi-asserted-by":"publisher","first-page":"7416","DOI":"10.1038\/s41467-024-51062-w","article-title":"Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes","volume":"15","author":"Sulaiman","year":"2024","journal-title":"Nat. Commun."},{"key":"ref186","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1038\/s41522-024-00610-9","article-title":"Unlocking gut-liver-brain axis communication metabolites: energy metabolism, immunity and barriers","volume":"10","author":"Sun","year":"2024","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref187","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1093\/lifemeta\/load022","article-title":"Neural innervation in adipose tissue, gut, pancreas, and liver","volume":"2","author":"Sun","year":"2023","journal-title":"Life Metab."},{"key":"ref188","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1038\/s41522-024-00567-9","article-title":"A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases","volume":"10","author":"Sun","year":"2024","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref189","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1038\/nm.4142","article-title":"The microbiome in early life: implications for health outcomes","volume":"22","author":"Tamburini","year":"2016","journal-title":"Nat. Med."},{"key":"ref190","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1161\/CIRCRESAHA.117.309715","article-title":"Gut microbiota in cardiovascular health and disease","volume":"120","author":"Tang","year":"2017","journal-title":"Circ. Res."},{"key":"ref191","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1038\/s41597-021-00981-0","article-title":"Data sharing practices and data availability upon request differ across scientific disciplines","volume":"8","author":"Tedersoo","year":"2021","journal-title":"Sci Data"},{"key":"ref192","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1038\/nature20796","article-title":"Persistent microbiome alterations modulate the rate of post-dieting weight regain","volume":"540","author":"Thaiss","year":"2016","journal-title":"Nature"},{"key":"ref193","doi-asserted-by":"publisher","first-page":"e70018","DOI":"10.1002\/mco2.70018","article-title":"Influence of gut and lung dysbiosis on lung cancer progression and their modulation as promising therapeutic targets: a comprehensive review","volume":"5","author":"Thapa","year":"2024","journal-title":"MedComm"},{"key":"ref194","doi-asserted-by":"publisher","first-page":"e0191521","DOI":"10.1128\/spectrum.01915-21","article-title":"Characterization and demonstration of mock communities as control reagents for accurate human microbiome community measurements","volume":"10","author":"Tourlousse","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref195","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1016\/j.cell.2018.10.029","article-title":"US immigration westernizes the human gut microbiome","volume":"175","author":"Vangay","year":"2018","journal-title":"Cell"},{"key":"ref196","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1126\/science.aad1329","article-title":"Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota","volume":"350","author":"V\u00e9tizou","year":"2015","journal-title":"Science"},{"key":"ref197","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1093\/femsre\/fuaf005","article-title":"Bile acids as germinants for Clostridioides difficile spores, evidence of adaptation to the gut?","volume":"49","author":"Vinay","year":"2025","journal-title":"FEMS Microbiol. Rev."},{"key":"ref198","doi-asserted-by":"publisher","first-page":"1158","DOI":"10.1001\/jamapediatrics.2023.3849","article-title":"Probiotics, prebiotics, lactoferrin, and combination products for prevention of mortality and morbidity in preterm infants: a systematic review and network meta-analysis","volume":"177","author":"Wang","year":"2023","journal-title":"JAMA Pediatr."},{"key":"ref199","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1186\/s12964-025-02275-z","article-title":"Combination strategies of gut microbiota in cancer therapy through metabolic reprogramming and immune remodeling","volume":"23","author":"Wang","year":"2025","journal-title":"Cell Commun. Signal"},{"key":"ref200","doi-asserted-by":"publisher","first-page":"15425","DOI":"10.1038\/s41598-022-19019-5","article-title":"Network-based integration of multi-omics data for clinical outcome prediction in neuroblastoma","volume":"12","author":"Wang","year":"2022","journal-title":"Sci. Rep."},{"key":"ref201","doi-asserted-by":"publisher","first-page":"166","DOI":"10.3390\/microorganisms13010166","article-title":"Fecal microbiome and metabolomic profiles of mixed-fed infants are more similar to formula-fed than breastfed infants","volume":"13","author":"Wang","year":"2025","journal-title":"Microorganisms"},{"key":"ref202","doi-asserted-by":"publisher","first-page":"754401","DOI":"10.3389\/fendo.2022.754401","article-title":"Adjuvant probiotics of Lactobacillus salivarius subsp. salicinius AP-32, L. johnsonii MH-68, and Bifidobacterium animalis subsp. lactis CP-9 attenuate glycemic levels and inflammatory cytokines in patients with type 1 diabetes mellitus","volume":"13","author":"Wang","year":"2022","journal-title":"Front. Endocrinol. (Lausanne)"},{"key":"ref203","doi-asserted-by":"publisher","first-page":"e0226722","DOI":"10.1128\/spectrum.02267-22","article-title":"Infant mode of delivery shapes the skin mycobiome of prepubescent children","volume":"10","author":"Wang","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref204","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1172\/JCI154944","article-title":"Next-generation sequencing: insights to advance clinical investigations of the microbiome","volume":"132","author":"Wensel","year":"2022","journal-title":"J. Clin. Invest."},{"key":"ref205","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.jaci.2014.11.012","article-title":"The gut microbiota and inflammatory noncommunicable diseases: associations and potentials for gut microbiota therapies","volume":"135","author":"West","year":"2015","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref206","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1038\/s41522-022-00279-y","article-title":"Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors","volume":"8","author":"Willis","year":"2022","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref300","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/j.csbj.2024.12.030","article-title":"AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships","volume":"27","author":"Wu","year":"2025","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref207","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1038\/s41423-025-01326-2","article-title":"The gut microbiota in cancer immunity and immunotherapy","volume":"22","author":"Xie","year":"2025","journal-title":"Cell. Mol. Immunol."},{"key":"ref208","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1016\/j.cell.2023.12.019","article-title":"Complement in breast milk modifies offspring gut microbiota to promote infant health","volume":"187","author":"Xu","year":"2024","journal-title":"Cell"},{"key":"ref209","doi-asserted-by":"publisher","first-page":"5715","DOI":"10.1038\/s41598-023-32901-0","article-title":"Lung microbiome and cytokine profiles in different disease states of COPD: a cohort study","volume":"13","author":"Xue","year":"2023","journal-title":"Sci. Rep."},{"key":"ref210","doi-asserted-by":"publisher","first-page":"2441356","DOI":"10.1080\/19490976.2024.2441356","article-title":"Faecal metaproteomics analysis reveals a high cardiovascular risk profile across healthy individuals and heart failure patients","volume":"17","author":"Yang","year":"2025","journal-title":"Gut Microbes"},{"key":"ref211","doi-asserted-by":"publisher","first-page":"e2412001","DOI":"10.4014\/jmb.2412.12001","article-title":"Advancing gut microbiome research: the shift from metagenomics to multi-omics and future perspectives","volume":"35","author":"Yang","year":"2025","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref212","doi-asserted-by":"publisher","first-page":"1875","DOI":"10.1111\/odi.14186","article-title":"Oral microbiome of electronic cigarette users: a cross-sectional exploration","volume":"29","author":"Yang","year":"2023","journal-title":"Oral Dis."},{"key":"ref213","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature"},{"key":"ref214","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1186\/s13059-024-03401-9","article-title":"Assessing and mitigating batch effects in large-scale omics studies","volume":"25","author":"Yu","year":"2024","journal-title":"Genome Biol."},{"key":"ref215","doi-asserted-by":"publisher","first-page":"e162385","DOI":"10.1001\/jamapediatrics.2016.2385","article-title":"Association between cesarean birth and risk of obesity in offspring in childhood, adolescence, and early adulthood","volume":"170","author":"Yuan","year":"2016","journal-title":"JAMA Pediatr."},{"key":"ref216","doi-asserted-by":"publisher","first-page":"e33684","DOI":"10.1016\/j.heliyon.2024.e33684","article-title":"Impact of antibiotics, corticosteroids, and microbiota on immunotherapy efficacy in patients with non-small cell lung cancer","volume":"10","author":"Zapata-Garc\u00eda","year":"2024","journal-title":"Heliyon"},{"key":"ref217","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1038\/s41564-024-01902-8","article-title":"Free fatty acid receptor 4 modulates dietary sugar preference via the gut microbiota","volume":"10","author":"Zhang","year":"2025","journal-title":"Nat. Microbiol."},{"key":"ref218","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.cmet.2021.12.011","article-title":"Emerging targetome and signalome landscape of gut microbial metabolites","volume":"34","author":"Zheng","year":"2022","journal-title":"Cell Metab."},{"key":"ref219","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1038\/s41422-020-0332-7","article-title":"Interaction between microbiota and immunity in health and disease","volume":"30","author":"Zheng","year":"2020","journal-title":"Cell Res."},{"key":"ref220","doi-asserted-by":"publisher","first-page":"1431367","DOI":"10.3389\/fmicb.2024.1431367","article-title":"Mendelian randomization identifies causal associations between GWAS-associated bacteria and their metabolites and rheumatoid arthritis","volume":"15","author":"Zhou","year":"2024","journal-title":"Front. Microbiol."},{"key":"ref221","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1016\/j.chom.2024.02.012","article-title":"Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease","volume":"32","author":"Zhou","year":"2024","journal-title":"Cell Host Microbe"},{"key":"ref222","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1038\/s41467-025-56237-7","article-title":"A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment","volume":"16","author":"Zhu","year":"2025","journal-title":"Nat. Commun."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1632435\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T05:34:40Z","timestamp":1758000880000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1632435\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,16]]},"references-count":223,"alternative-id":["10.3389\/fmicb.2025.1632435"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1632435","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,16]]},"article-number":"1632435"}}