{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T17:13:37Z","timestamp":1793898817225,"version":"4.8.0"},"reference-count":121,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T00:00:00Z","timestamp":1787616000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T00:00:00Z","timestamp":1787616000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Aging"],"DOI":"10.1038\/s43587-026-01181-4","type":"journal-article","created":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T09:03:05Z","timestamp":1787648585000},"page":"1946-1966","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["A geroprotective probiotic and its functional metabolite counteract inflammaging to extend healthspan"],"prefix":"10.1038","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-6084-7376","authenticated-orcid":false,"given":"Xiaoyong","family":"Lu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Ping","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zichu","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lixiao","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muzhao","family":"Xiong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanling","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2712-0064","authenticated-orcid":false,"given":"Jiaming","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyan","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kejie","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zheng-Kai","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiale","family":"Ping","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Xiong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuesheng","family":"Zuo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3126-7889","authenticated-orcid":false,"given":"Jingyi","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1886-4854","authenticated-orcid":false,"given":"Qiaoran","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan-Dan","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beier","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuhui","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8858-4383","authenticated-orcid":false,"given":"Shuai","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2431-0612","authenticated-orcid":false,"given":"Si","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3988-5067","authenticated-orcid":false,"given":"Jing","family":"Qu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2821-8541","authenticated-orcid":false,"given":"Yun-Gui","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6751-0377","authenticated-orcid":false,"given":"Feng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9289-8177","authenticated-orcid":false,"given":"Guang-Hui","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8885-5104","authenticated-orcid":false,"given":"Weiqi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,25]]},"reference":[{"key":"1181_CR1","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nature08821","volume":"464","author":"J Qin","year":"2010","unstructured":"Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59\u201365 (2010).","journal-title":"Nature"},{"key":"1181_CR2","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1038\/s41586-019-1238-8","volume":"569","author":"The Integrative HMP (iHMP) Research Network Consortium.","year":"2019","unstructured":"The Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project. Nature 569, 641\u2013648 (2019).","journal-title":"Nature"},{"key":"1181_CR3","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/nm.4517","volume":"24","author":"JA Gilbert","year":"2018","unstructured":"Gilbert, J. A. et al. Current understanding of the human microbiome. Nat. Med. 24, 392\u2013400 (2018).","journal-title":"Nat. Med."},{"key":"1181_CR4","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-022-01092-0","volume":"14","author":"TO Cox","year":"2022","unstructured":"Cox, T. O., Lundgren, P., Nath, K. & Thaiss, C. A. Metabolic control by the microbiome. Genome Med. 14, 80 (2022).","journal-title":"Genome Med."},{"key":"1181_CR5","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1038\/s43587-022-00306-9","volume":"2","author":"TS Ghosh","year":"2022","unstructured":"Ghosh, T. S., Shanahan, F. & O\u2019Toole, P. W. Toward an improved definition of a healthy microbiome for healthy aging. Nat. Aging 2, 1054\u20131069 (2022).","journal-title":"Nat. Aging"},{"key":"1181_CR6","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","volume":"569","author":"J Lloyd-Price","year":"2019","unstructured":"Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655\u2013662 (2019).","journal-title":"Nature"},{"key":"1181_CR7","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1016\/j.chom.2017.03.002","volume":"21","author":"N Thevaranjan","year":"2017","unstructured":"Thevaranjan, N. et al. Age-associated microbial dysbiosis promotes intestinal permeability, systemic inflammation, and macrophage dysfunction. Cell Host Microbe 21, 455\u2013466 (2017).","journal-title":"Cell Host Microbe"},{"key":"1181_CR8","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1016\/j.cell.2016.10.020","volume":"167","author":"M Schirmer","year":"2016","unstructured":"Schirmer, M. et al. Linking the human gut microbiome to inflammatory cytokine production capacity. Cell 167, 1125\u20131136 (2016).","journal-title":"Cell"},{"key":"1181_CR9","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","volume":"11","author":"D Hyatt","year":"2010","unstructured":"Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).","journal-title":"BMC Bioinformatics"},{"key":"1181_CR10","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/s41522-022-00338-4","volume":"8","author":"Y Luo","year":"2022","unstructured":"Luo, Y. et al. Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges. NPJ Biofilms Microbiomes 8, 81 (2022).","journal-title":"NPJ Biofilms Microbiomes"},{"key":"1181_CR11","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/s12866-016-0625-7","volume":"16","author":"KA Kim","year":"2016","unstructured":"Kim, K. A., Jeong, J. J., Yoo, S. Y. & Kim, D. H. Gut microbiota lipopolysaccharide accelerates inflamm-aging in mice. BMC Microbiol. 16, 9 (2016).","journal-title":"BMC Microbiol."},{"key":"1181_CR12","doi-asserted-by":"publisher","first-page":"1214","DOI":"10.1126\/science.aac8469","volume":"350","author":"PW O\u2019Toole","year":"2015","unstructured":"O\u2019Toole, P. W. & Jeffery, I. B. Gut microbiota and aging. Science 350, 1214\u20131215 (2015).","journal-title":"Science"},{"key":"1181_CR13","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1038\/s41575-022-00605-x","volume":"19","author":"TS Ghosh","year":"2022","unstructured":"Ghosh, T. S., Shanahan, F. & O\u2019Toole, P. W. The gut microbiome as a modulator of healthy ageing. Nat. Rev. Gastroenterol. Hepatol. 19, 565\u2013584 (2022).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"1181_CR14","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34667-x","volume":"13","author":"ZD Wallen","year":"2022","unstructured":"Wallen, Z. D. et al. Metagenomics of Parkinson\u2019s disease implicates the gut microbiome in multiple disease mechanisms. Nat. Commun. 13, 6958 (2022).","journal-title":"Nat. Commun."},{"key":"1181_CR15","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10430-7","volume":"10","author":"M Stebegg","year":"2019","unstructured":"Stebegg, M. et al. Heterochronic faecal transplantation boosts gut germinal centres in aged mice. Nat. Commun. 10, 2443 (2019).","journal-title":"Nat. Commun."},{"key":"1181_CR16","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-022-01243-w","volume":"10","author":"A Parker","year":"2022","unstructured":"Parker, A. et al. Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain. Microbiome 10, 68 (2022).","journal-title":"Microbiome"},{"key":"1181_CR17","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-022-01386-w","volume":"10","author":"KH Kim","year":"2022","unstructured":"Kim, K. H. et al. Gut microbiota of the young ameliorates physical fitness of the aged in mice. Microbiome 10, 238 (2022).","journal-title":"Microbiome"},{"key":"1181_CR18","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1038\/s43587-021-00093-9","volume":"1","author":"M Boehme","year":"2021","unstructured":"Boehme, M. et al. Microbiota from young mice counteracts selective age-associated behavioral deficits. Nat. Aging 1, 666\u2013676 (2021).","journal-title":"Nat. Aging"},{"key":"1181_CR19","doi-asserted-by":"publisher","first-page":"1234","DOI":"10.1038\/s41591-019-0504-5","volume":"25","author":"C Barcena","year":"2019","unstructured":"Barcena, C. et al. Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice. Nat. Med. 25, 1234\u20131242 (2019).","journal-title":"Nat. Med."},{"key":"1181_CR20","doi-asserted-by":"publisher","first-page":"4095","DOI":"10.1039\/D3FO04575G","volume":"15","author":"Q Zeng","year":"2024","unstructured":"Zeng, Q. et al. Bifidobacterium pseudocatenulatum NCU-08 ameliorated senescence via modulation of the AMPK\/Sirt1 signaling pathway and gut microbiota in mice. Food Funct. 15, 4095\u20134108 (2024).","journal-title":"Food Funct."},{"key":"1181_CR21","doi-asserted-by":"publisher","unstructured":"Haibo, S. et al. Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications. Sci. China Life Sci. 69, 2230\u20132248 https:\/\/doi.org\/10.1007\/s11427-025-3163-6 (2026).","DOI":"10.1007\/s11427-025-3163-6"},{"key":"1181_CR22","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/nature09944","volume":"473","author":"M Arumugam","year":"2011","unstructured":"Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174\u2013180 (2011).","journal-title":"Nature"},{"key":"1181_CR23","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1038\/s43587-022-00286-w","volume":"2","author":"J Si","year":"2022","unstructured":"Si, J. et al. Long-term life history predicts current gut microbiome in a population-based cohort study. Nat. Aging 2, 885\u2013895 (2022).","journal-title":"Nat. Aging"},{"key":"1181_CR24","doi-asserted-by":"publisher","DOI":"10.1186\/s13099-025-00730-3","volume":"17","author":"YR Bah","year":"2025","unstructured":"Bah, Y. R. et al. Bacteroides- and Prevotella-enriched gut microbial clusters associate with metabolic risks. Gut Pathog. 17, 55 (2025).","journal-title":"Gut Pathog."},{"key":"1181_CR25","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-016-0160-7","volume":"4","author":"A Gorvitovskaia","year":"2016","unstructured":"Gorvitovskaia, A., Holmes, S. P. & Huse, S. M. Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome 4, 15 (2016).","journal-title":"Microbiome"},{"key":"1181_CR26","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1038\/s41586-022-04567-7","volume":"604","author":"R Gacesa","year":"2022","unstructured":"Gacesa, R. et al. Environmental factors shaping the gut microbiome in a Dutch population. Nature 604, 732\u2013739 (2022).","journal-title":"Nature"},{"key":"1181_CR27","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1126\/science.1208344","volume":"334","author":"GD Wu","year":"2011","unstructured":"Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105\u2013108 (2011).","journal-title":"Science"},{"key":"1181_CR28","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1038\/s43587-020-00014-2","volume":"1","author":"X Zhang","year":"2021","unstructured":"Zhang, X. et al. Sex- and age-related trajectories of the adult human gut microbiota shared across populations of different ethnicities. Nat. Aging 1, 87\u2013100 (2021).","journal-title":"Nat. Aging"},{"key":"1181_CR29","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/s41579-021-00559-y","volume":"19","author":"A Tett","year":"2021","unstructured":"Tett, A., Pasolli, E., Masetti, G., Ercolini, D. & Segata, N. Prevotella diversity, niches and interactions with the human host. Nat. Rev. Microbiol. 19, 585\u2013599 (2021).","journal-title":"Nat. Rev. Microbiol."},{"key":"1181_CR30","first-page":"mgen000926","volume":"9","author":"R Denise","year":"2023","unstructured":"Denise, R., Babor, J., Gerlt, J. A. & de Crecy-Lagard, V. Pyridoxal 5\u2032-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes. Microb. Genom. 9, mgen000926 (2023).","journal-title":"Microb. Genom."},{"key":"1181_CR31","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1038\/s41589-019-0276-8","volume":"15","author":"L Doyle","year":"2019","unstructured":"Doyle, L. et al. Biosynthesis of a conserved glycolipid anchor for Gram-negative bacterial capsules. Nat. Chem. Biol. 15, 632\u2013640 (2019).","journal-title":"Nat. Chem. Biol."},{"key":"1181_CR32","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1016\/j.chom.2023.05.024","volume":"31","author":"C Frioux","year":"2023","unstructured":"Frioux, C. et al. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe 31, 1111\u20131125 (2023).","journal-title":"Cell Host Microbe"},{"key":"1181_CR33","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.copbio.2021.07.012","volume":"73","author":"F Turroni","year":"2022","unstructured":"Turroni, F., Milani, C., Ventura, M. & van Sinderen, D. The human gut microbiota during the initial stages of life: insights from bifidobacteria. Curr. Opin. Biotechnol. 73, 81\u201387 (2022).","journal-title":"Curr. Opin. Biotechnol."},{"key":"1181_CR34","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2021.1875796","volume":"13","author":"X Liu","year":"2021","unstructured":"Liu, X. et al. Blautia\u2014a new functional genus with potential probiotic properties? Gut Microbes 13, 1875796 (2021).","journal-title":"Gut Microbes"},{"key":"1181_CR35","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1016\/j.cell.2024.01.004","volume":"187","author":"K Fu","year":"2024","unstructured":"Fu, K. et al. Streptococcus anginosus promotes gastric inflammation, atrophy, and tumorigenesis in mice. Cell 187, 882\u2013896 (2024).","journal-title":"Cell"},{"key":"1181_CR36","doi-asserted-by":"publisher","first-page":"1852","DOI":"10.3390\/microorganisms8121852","volume":"8","author":"OJ Park","year":"2020","unstructured":"Park, O. J. et al. Streptococcus gordonii: pathogenesis and host response to its cell wall components. Microorganisms 8, 1852 (2020).","journal-title":"Microorganisms"},{"key":"1181_CR37","doi-asserted-by":"publisher","first-page":"2463","DOI":"10.1136\/gutjnl-2021-325753","volume":"71","author":"E Belda","year":"2022","unstructured":"Belda, E. et al. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism. Gut 71, 2463\u20132480 (2022).","journal-title":"Gut"},{"key":"1181_CR38","doi-asserted-by":"publisher","first-page":"1513","DOI":"10.1016\/j.celrep.2017.07.057","volume":"20","author":"A Hayashi","year":"2017","unstructured":"Hayashi, A. et al. Intestinal dysbiosis and biotin deprivation induce alopecia through overgrowth of Lactobacillus murinus in mice. Cell Rep. 20, 1513\u20131524 (2017).","journal-title":"Cell Rep."},{"key":"1181_CR39","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1007\/s11684-024-1055-9","volume":"18","author":"Y Song","year":"2024","unstructured":"Song, Y. et al. Gut microbiota-dependent phenylacetylglutamine in cardiovascular disease: current knowledge and new insights. Front. Med. 18, 31\u201345 (2024).","journal-title":"Front. Med."},{"key":"1181_CR40","doi-asserted-by":"publisher","unstructured":"Jian, Y. et al. A framework of biomarkers for adipose tissue aging: a consensus statement by the Aging Biomarker Consortium. Life Med. 4, lnaf027 https:\/\/doi.org\/10.1093\/lifemedi\/lnaf027 (2025).","DOI":"10.1093\/lifemedi\/lnaf027"},{"key":"1181_CR41","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1002\/9780470942390.mo110165","volume":"2","author":"SP Brooks","year":"2012","unstructured":"Brooks, S. P., Trueman, R. C. & Dunnett, S. B. Assessment of motor coordination and balance in mice using the rotarod, elevated bridge, and footprint tests. Curr. Protoc. Mouse Biol. 2, 37\u201353 (2012).","journal-title":"Curr. Protoc. Mouse Biol."},{"key":"1181_CR42","doi-asserted-by":"publisher","first-page":"5403","DOI":"10.1016\/j.cell.2025.06.001","volume":"188","author":"L Geng","year":"2025","unstructured":"Geng, L. et al. Systematic profiling reveals betaine as an exercise mimetic for geroprotection. Cell 188, 5403\u20135425 (2025).","journal-title":"Cell"},{"key":"1181_CR43","doi-asserted-by":"publisher","first-page":"1011","DOI":"10.3390\/foods13071011","volume":"13","author":"Y Wu","year":"2024","unstructured":"Wu, Y. et al. Bifidobacterium relieved fluoride-induced hepatic and ileal toxicity via inflammatory response and bile acid transporters in mice. Foods 13, 1011 (2024).","journal-title":"Foods"},{"key":"1181_CR44","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1016\/j.jare.2024.07.034","volume":"72","author":"C Liang","year":"2025","unstructured":"Liang, C. et al. Fluoride induces hepatointestinal damage and vitamin B(2) mitigation by regulating IL-17A and Bifidobacterium in ileum. J. Adv. Res. 72, 671\u2013684 (2025).","journal-title":"J. Adv. Res."},{"key":"1181_CR45","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1038\/ismej.2007.69","volume":"2","author":"R Wall","year":"2008","unstructured":"Wall, R. et al. Presence of two Lactobacillus and Bifidobacterium probiotic strains in the neonatal ileum. ISME J. 2, 83\u201391 (2008).","journal-title":"ISME J."},{"key":"1181_CR46","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1016\/j.exger.2003.07.001","volume":"38","author":"MP Muehlenbein","year":"2003","unstructured":"Muehlenbein, M. P. et al. Dehydroepiandrosterone-sulfate as a biomarker of senescence in male non-human primates. Exp. Gerontol. 38, 1077\u20131085 (2003).","journal-title":"Exp. Gerontol."},{"key":"1181_CR47","doi-asserted-by":"publisher","first-page":"e13472","DOI":"10.1111\/eci.13472","volume":"51","author":"MC Mokhaneli","year":"2021","unstructured":"Mokhaneli, M. C. et al. L-homoarginine is associated with decreased cardiovascular- and all-cause mortality. Eur. J. Clin. Invest. 51, e13472 (2021).","journal-title":"Eur. J. Clin. Invest."},{"key":"1181_CR48","first-page":"R779","volume":"311","author":"DM Sepa-Kishi","year":"2016","unstructured":"Sepa-Kishi, D. M., Wu, M. V., Uthayakumar, A., Mohasses, A. & Ceddia, R. B. Antilipolytic and antilipogenic effects of the CPT-1b inhibitor oxfenicine in the white adipose tissue of rats. Am. J. Physiol. 311, R779\u2013R787 (2016).","journal-title":"Am. J. Physiol."},{"key":"1181_CR49","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1016\/j.tem.2022.04.004","volume":"33","author":"R Haikonen","year":"2022","unstructured":"Haikonen, R., Karkkainen, O., Koistinen, V. & Hanhineva, K. Diet- and microbiota-related metabolite, 5-aminovaleric acid betaine (5-AVAB), in health and disease. Trends Endocrinol. Metab. 33, 463\u2013480 (2022).","journal-title":"Trends Endocrinol. Metab."},{"key":"1181_CR50","doi-asserted-by":"publisher","first-page":"994930","DOI":"10.3389\/fendo.2022.994930","volume":"13","author":"S Zhang","year":"2022","unstructured":"Zhang, S. & Dang, Y. Roles of gut microbiota and metabolites in overweight and obesity of children. Front. Endocrinol. 13, 994930 (2022).","journal-title":"Front. Endocrinol."},{"key":"1181_CR51","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1038\/s43587-022-00294-w","volume":"2","author":"T Wilmanski","year":"2022","unstructured":"Wilmanski, T., Gibbons, S. M. & Price, N. D. Healthy aging and the human gut microbiome: why we cannot just turn back the clock. Nat. Aging 2, 869\u2013871 (2022).","journal-title":"Nat. Aging"},{"key":"1181_CR52","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1038\/s43587-022-00287-9","volume":"2","author":"PJ Larson","year":"2022","unstructured":"Larson, P. J. et al. Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults. Nat. Aging 2, 941\u2013955 (2022).","journal-title":"Nat. Aging"},{"key":"1181_CR53","doi-asserted-by":"publisher","first-page":"lnag020","DOI":"10.1093\/lifemedi\/lnag020","volume":"5","author":"Z Wu","year":"2026","unstructured":"Wu, Z. et al. The entropic view of aging: from thermodynamics to biology. Life Med. 5, lnag020 (2026).","journal-title":"Life Med."},{"key":"1181_CR54","doi-asserted-by":"publisher","unstructured":"Cohen, H. Y. et al. Perspectives on the essence and drivers of aging. Life Med. 4, lnaf006 https:\/\/doi.org\/10.1093\/lifemedi\/lnaf006 (2025).","DOI":"10.1093\/lifemedi\/lnaf006"},{"key":"1181_CR55","doi-asserted-by":"publisher","first-page":"4586","DOI":"10.1073\/pnas.1000097107","volume":"108","author":"MJ Claesson","year":"2011","unstructured":"Claesson, M. J. et al. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc. Natl Acad. Sci. USA 108, 4586\u20134591 (2011).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1181_CR56","doi-asserted-by":"publisher","first-page":"127832","DOI":"10.1016\/j.micres.2024.127832","volume":"286","author":"N Tewari","year":"2024","unstructured":"Tewari, N. & Dey, P. Navigating commensal dysbiosis: gastrointestinal host\u2013pathogen interplay orchestrating opportunistic infections. Microbiol. Res. 286, 127832 (2024).","journal-title":"Microbiol. Res."},{"key":"1181_CR57","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-025-02127-5","volume":"13","author":"A Jan","year":"2025","unstructured":"Jan, A. et al. A consortium of seven commensal bacteria promotes gut microbiota recovery and strengthens ecological barrier against vancomycin-resistant enterococci. Microbiome 13, 129 (2025).","journal-title":"Microbiome"},{"key":"1181_CR58","doi-asserted-by":"publisher","first-page":"wrae133","DOI":"10.1093\/ismejo\/wrae133","volume":"18","author":"CE Williams","year":"2024","unstructured":"Williams, C. E., Hammer, T. J. & Williams, C. L. Diversity alone does not reliably indicate the healthiness of an animal microbiome. ISME J. 18, wrae133 (2024).","journal-title":"ISME J."},{"key":"1181_CR59","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-01973-8","volume":"8","author":"C Duvallet","year":"2017","unstructured":"Duvallet, C., Gibbons, S. M., Gurry, T., Irizarry, R. A. & Alm, E. J. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat. Commun. 8, 1784 (2017).","journal-title":"Nat. Commun."},{"key":"1181_CR60","doi-asserted-by":"publisher","DOI":"10.1111\/acel.70166","volume":"24","author":"T Xu","year":"2025","unstructured":"Xu, T. et al. L-Tryptophan produced by Bifidobacterium pseudocatenulatum NCU-08 delays aging in SAMP8 mice by activating the Sirt1\/P53\/P21\/Rb signaling pathway. Aging Cell 24, e70166 (2025).","journal-title":"Aging Cell"},{"key":"1181_CR61","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1038\/s41522-026-00913-z","volume":"12","author":"Y Li","year":"2026","unstructured":"Li, Y. et al. Restoration of ethanol-induced Bifidobacterium pseudocatenulatum depletion ameliorates alcohol-associated liver disease. NPJ Biofilms Microbiomes 12, 47 (2026).","journal-title":"NPJ Biofilms Microbiomes"},{"key":"1181_CR62","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2025.2464945","volume":"17","author":"Y Chen","year":"2025","unstructured":"Chen, Y. et al. Bifidobacterium inhibits the progression of colorectal tumorigenesis in mice through fatty acid isomerization and gut microbiota modulation. Gut Microbes 17, 2464945 (2025).","journal-title":"Gut Microbes"},{"key":"1181_CR63","doi-asserted-by":"publisher","first-page":"e0126976","DOI":"10.1371\/journal.pone.0126976","volume":"10","author":"A Moya-Perez","year":"2015","unstructured":"Moya-Perez, A., Neef, A. & Sanz, Y. Bifidobacterium pseudocatenulatum CECT 7765 reduces obesity-associated inflammation by restoring the lymphocyte\u2013macrophage balance and gut microbiota structure in high-fat diet-fed mice. PLoS ONE 10, e0126976 (2015).","journal-title":"PLoS ONE"},{"key":"1181_CR64","doi-asserted-by":"publisher","first-page":"5337","DOI":"10.1007\/s12035-017-0768-z","volume":"55","author":"A Agusti","year":"2018","unstructured":"Agusti, A. et al. Bifidobacterium pseudocatenulatum CECT 7765 ameliorates neuroendocrine alterations associated with an exaggerated stress response and anhedonia in obese mice. Mol. Neurobiol. 55, 5337\u20135352 (2018).","journal-title":"Mol. Neurobiol."},{"key":"1181_CR65","doi-asserted-by":"publisher","DOI":"10.1038\/s41522-023-00448-7","volume":"9","author":"J Tang","year":"2023","unstructured":"Tang, J. et al. The therapeutic value of bifidobacteria in cardiovascular disease. NPJ Biofilms Microbiomes 9, 82 (2023).","journal-title":"NPJ Biofilms Microbiomes"},{"key":"1181_CR66","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/s41586-020-2745-3","volume":"586","author":"HE Vuong","year":"2020","unstructured":"Vuong, H. E. et al. The maternal microbiome modulates fetal neurodevelopment in mice. Nature 586, 281\u2013286 (2020).","journal-title":"Nature"},{"key":"1181_CR67","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s12866-022-02457-6","volume":"22","author":"T Pessa-Morikawa","year":"2022","unstructured":"Pessa-Morikawa, T. et al. Maternal microbiota-derived metabolic profile in fetal murine intestine, brain and placenta. BMC Microbiol. 22, 46 (2022).","journal-title":"BMC Microbiol."},{"key":"1181_CR68","doi-asserted-by":"publisher","first-page":"2468","DOI":"10.3390\/cancers12092468","volume":"12","author":"N D\u2019Onofrio","year":"2020","unstructured":"D\u2019Onofrio, N. et al. Synergistic effect of dietary betaines on SIRT1-mediated apoptosis in human oral squamous cell carcinoma Cal 27. Cancers 12, 2468 (2020).","journal-title":"Cancers"},{"key":"1181_CR69","doi-asserted-by":"publisher","first-page":"971","DOI":"10.1093\/ajcn\/nqy169","volume":"108","author":"O Karkkainen","year":"2018","unstructured":"Karkkainen, O. et al. Diets rich in whole grains increase betainized compounds associated with glucose metabolism. Am. J. Clin. Nutr. 108, 971\u2013979 (2018).","journal-title":"Am. J. Clin. Nutr."},{"key":"1181_CR70","doi-asserted-by":"publisher","first-page":"2266","DOI":"10.1053\/j.gastro.2020.02.033","volume":"158","author":"M Zhao","year":"2020","unstructured":"Zhao, M. et al. TMAVA, a metabolite of intestinal microbes, is increased in plasma from patients with liver steatosis, inhibits gamma-butyrobetaine hydroxylase, and exacerbates fatty liver in mice. Gastroenterology 158, 2266\u20132281 (2020).","journal-title":"Gastroenterology"},{"key":"1181_CR71","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-31484-5","volume":"8","author":"O Karkkainen","year":"2018","unstructured":"Karkkainen, O. et al. Whole grain intake associated molecule 5-aminovaleric acid betaine decreases beta-oxidation of fatty acids in mouse cardiomyocytes. Sci. Rep. 8, 13036 (2018).","journal-title":"Sci. Rep."},{"key":"1181_CR72","doi-asserted-by":"publisher","first-page":"1694","DOI":"10.1038\/s42255-021-00502-8","volume":"3","author":"KH Liu","year":"2021","unstructured":"Liu, K. H. et al. Microbial metabolite delta-valerobetaine is a diet-dependent obesogen. Nat. Metab. 3, 1694\u20131705 (2021).","journal-title":"Nat. Metab."},{"key":"1181_CR73","doi-asserted-by":"publisher","first-page":"4489","DOI":"10.1016\/j.cell.2026.04.025","volume":"189","author":"J Li","year":"2026","unstructured":"Li, J. et al. Multimodal clocks of human aging. Cell 189, 4489\u20134511 (2026).","journal-title":"Cell"},{"key":"1181_CR74","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1016\/j.medj.2023.06.010","volume":"4","author":"J Li","year":"2023","unstructured":"Li, J. et al. Determining a multimodal aging clock in a cohort of Chinese women. Med 4, 825\u2013848 (2023).","journal-title":"Med"},{"key":"1181_CR75","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1093\/procel\/pwae011","volume":"15","author":"Z Zheng","year":"2024","unstructured":"Zheng, Z. et al. DNA methylation clocks for estimating biological age in Chinese cohorts. Protein Cell 15, 575\u2013593 (2024).","journal-title":"Protein Cell"},{"key":"1181_CR76","doi-asserted-by":"publisher","first-page":"1669","DOI":"10.1038\/s43587-025-00935-w","volume":"5","author":"J Li","year":"2025","unstructured":"Li, J. et al. The X-Age Project to construct a Chinese aging clock. Nat. Aging 5, 1669\u20131685 (2025).","journal-title":"Nat. Aging"},{"key":"1181_CR77","doi-asserted-by":"publisher","unstructured":"Ren, J. et al. The Aging Biomarker Consortium represents a new era for aging research in China. Nat. Med. 29, 2162\u20132165 https:\/\/doi.org\/10.1038\/s41591-023-02444-y (2023).","DOI":"10.1038\/s41591-023-02444-y"},{"key":"1181_CR78","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.jbiotec.2015.06.416","volume":"210","author":"H Morita","year":"2015","unstructured":"Morita, H. et al. Complete genome sequence of Bifidobacterium pseudocatenulatum JCM 1200T isolated from infant feces. J. Biotechnol. 210, 68\u201369 (2015).","journal-title":"J. Biotechnol."},{"key":"1181_CR79","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1093\/procel\/pwad027","volume":"15","author":"J Lei","year":"2024","unstructured":"Lei, J. et al. Human ESC-derived vascular cells promote vascular regeneration in a HIF-1alpha dependent manner. Protein Cell 15, 36\u201351 (2024).","journal-title":"Protein Cell"},{"key":"1181_CR80","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1101\/pdb.prot073411","volume":"2014","author":"RD Cardiff","year":"2014","unstructured":"Cardiff, R. D., Miller, C. H. & Munn, R. J. Manual hematoxylin and eosin staining of mouse tissue sections. Cold Spring Harb. Protoc. 2014, 655\u2013658 (2014).","journal-title":"Cold Spring Harb. Protoc."},{"key":"1181_CR81","doi-asserted-by":"publisher","first-page":"1798","DOI":"10.1038\/nprot.2009.191","volume":"4","author":"F Debacq-Chainiaux","year":"2009","unstructured":"Debacq-Chainiaux, F., Erusalimsky, J. D., Campisi, J. & Toussaint, O. Protocols to detect senescence-associated beta-galactosidase (SA-betagal) activity, a biomarker of senescent cells in culture and in vivo. Nat. Protoc. 4, 1798\u20131806 (2009).","journal-title":"Nat. Protoc."},{"key":"1181_CR82","doi-asserted-by":"publisher","first-page":"e1000255","DOI":"10.1371\/journal.pgen.1000255","volume":"4","author":"SM Huse","year":"2008","unstructured":"Huse, S. M. et al. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4, e1000255 (2008).","journal-title":"PLoS Genet."},{"key":"1181_CR83","doi-asserted-by":"publisher","first-page":"4516","DOI":"10.1073\/pnas.1000080107","volume":"108","author":"JG Caporaso","year":"2011","unstructured":"Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. USA 108, 4516\u20134522 (2011).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1181_CR84","doi-asserted-by":"publisher","first-page":"eabd0695","DOI":"10.1126\/science.abd0695","volume":"371","author":"I Salas-Gonzalez","year":"2021","unstructured":"Salas-Gonzalez, I. et al. Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis. Science 371, eabd0695 (2021).","journal-title":"Science"},{"key":"1181_CR85","doi-asserted-by":"publisher","first-page":"6358","DOI":"10.1016\/j.cell.2024.08.021","volume":"187","author":"Y Yang","year":"2024","unstructured":"Yang, Y. et al. Metformin decelerates aging clock in male monkeys. Cell 187, 6358\u20136378 (2024).","journal-title":"Cell"},{"key":"1181_CR86","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1038\/nbt.2377","volume":"30","author":"MC Chambers","year":"2012","unstructured":"Chambers, M. C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918\u2013920 (2012).","journal-title":"Nat. Biotechnol."},{"key":"1181_CR87","doi-asserted-by":"publisher","first-page":"6382","DOI":"10.1021\/ac800795f","volume":"80","author":"HP Benton","year":"2008","unstructured":"Benton, H. P., Wong, D. M., Trauger, S. A. & Siuzdak, G. XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal. Chem. 80, 6382\u20136389 (2008).","journal-title":"Anal. Chem."},{"key":"1181_CR88","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1021\/ac202450g","volume":"84","author":"C Kuhl","year":"2012","unstructured":"Kuhl, C., Tautenhahn, R., Bottcher, C., Larson, T. R. & Neumann, S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography\/mass spectrometry data sets. Anal. Chem. 84, 283\u2013289 (2012).","journal-title":"Anal. Chem."},{"key":"1181_CR89","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1093\/bioinformatics\/btx754","volume":"34","author":"LJ McIver","year":"2018","unstructured":"McIver, L. J. et al. bioBakery: a meta\u2019omic analysis environment. Bioinformatics 34, 1235\u20131237 (2018).","journal-title":"Bioinformatics"},{"key":"1181_CR90","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"1181_CR91","doi-asserted-by":"publisher","first-page":"e65088","DOI":"10.7554\/eLife.65088","volume":"10","author":"F Beghini","year":"2021","unstructured":"Beghini, F. et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 10, e65088 (2021).","journal-title":"eLife"},{"key":"1181_CR92","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1111\/j.1654-1103.2003.tb02228.x","volume":"14","author":"P Dixon","year":"2003","unstructured":"Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927\u2013930 (2003).","journal-title":"J. Veg. Sci."},{"key":"1181_CR93","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","volume":"50","author":"B Liu","year":"2022","unstructured":"Liu, B., Zheng, D., Zhou, S., Chen, L. & Yang, J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 50, D912\u2013D917 (2022).","journal-title":"Nucleic Acids Res."},{"key":"1181_CR94","doi-asserted-by":"crossref","first-page":"D517","DOI":"10.1093\/nar\/gkz1136","volume":"48","author":"BP Alcock","year":"2020","unstructured":"Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48, D517\u2013D525 (2020).","journal-title":"Nucleic Acids Res."},{"key":"1181_CR95","doi-asserted-by":"publisher","first-page":"e1004557","DOI":"10.1371\/journal.pcbi.1004557","volume":"11","author":"J Kaminski","year":"2015","unstructured":"Kaminski, J. et al. High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS Comput. Biol. 11, e1004557 (2015).","journal-title":"PLoS Comput. Biol."},{"key":"1181_CR96","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/s41564-017-0072-8","volume":"3","author":"PI Costea","year":"2018","unstructured":"Costea, P. I. et al. Enterotypes in the landscape of gut microbial community composition. Nat. Microbiol. 3, 8\u201316 (2018).","journal-title":"Nat. Microbiol."},{"key":"1181_CR97","doi-asserted-by":"publisher","first-page":"e1009442","DOI":"10.1371\/journal.pcbi.1009442","volume":"17","author":"H Mallick","year":"2021","unstructured":"Mallick, H. et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput. Biol. 17, e1009442 (2021).","journal-title":"PLoS Comput. Biol."},{"key":"1181_CR98","doi-asserted-by":"publisher","first-page":"2416","DOI":"10.1038\/s41591-025-03693-9","volume":"31","author":"G Piccinno","year":"2025","unstructured":"Piccinno, G. et al. Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer. Nat. Med. 31, 2416\u20132429 (2025).","journal-title":"Nat. Med."},{"key":"1181_CR99","doi-asserted-by":"publisher","first-page":"1834","DOI":"10.1016\/j.cell.2024.03.014","volume":"187","author":"C Li","year":"2024","unstructured":"Li, C. et al. Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria. Cell 187, 1834\u20131852 (2024).","journal-title":"Cell"},{"key":"1181_CR100","doi-asserted-by":"publisher","first-page":"1619","DOI":"10.1038\/s43587-024-00692-2","volume":"4","author":"X Shen","year":"2024","unstructured":"Shen, X. et al. Nonlinear dynamics of multi-omics profiles during human aging. Nat. Aging 4, 1619\u20131634 (2024).","journal-title":"Nat. Aging"},{"key":"1181_CR101","doi-asserted-by":"publisher","first-page":"igz036","DOI":"10.1093\/geroni\/igz036","volume":"3","author":"CR Brydges","year":"2019","unstructured":"Brydges, C. R. Effect size guidelines, sample size calculations, and statistical power in gerontology. Innov. Aging 3, igz036 (2019).","journal-title":"Innov. Aging"},{"key":"1181_CR102","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1038\/s41576-022-00511-7","volume":"23","author":"J Rutledge","year":"2022","unstructured":"Rutledge, J., Oh, H. & Wyss-Coray, T. Measuring biological age using omics data. Nat. Rev. Genet. 23, 715\u2013727 (2022).","journal-title":"Nat. Rev. Genet."},{"key":"1181_CR103","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1038\/s43587-021-00044-4","volume":"1","author":"ML Elliott","year":"2021","unstructured":"Elliott, M. L. et al. Disparities in the pace of biological aging among midlife adults of the same chronological age have implications for future frailty risk and policy. Nat. Aging 1, 295\u2013308 (2021).","journal-title":"Nat. Aging"},{"key":"1181_CR104","doi-asserted-by":"publisher","first-page":"1482","DOI":"10.1016\/j.cmet.2024.05.012","volume":"36","author":"Z Yu","year":"2024","unstructured":"Yu, Z. et al. Thermal facial image analyses reveal quantitative hallmarks of aging and metabolic diseases. Cell Metab. 36, 1482\u20131493 (2024).","journal-title":"Cell Metab."},{"key":"1181_CR105","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v039.i05","volume":"39","author":"N Simon","year":"2011","unstructured":"Simon, N., Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for Cox\u2019s proportional hazards model via coordinate descent. J. Stat. Softw. 39, 1\u201313 (2011).","journal-title":"J. Stat. Softw."},{"key":"1181_CR106","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852\u2013857 (2019).","journal-title":"Nat. Biotechnol."},{"key":"1181_CR107","doi-asserted-by":"publisher","first-page":"D334","DOI":"10.1093\/nar\/gkaf1247","volume":"54","author":"M Chuvochina","year":"2026","unstructured":"Chuvochina, M. et al. SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity. Nucleic Acids Res. 54, D334\u2013D341 (2026).","journal-title":"Nucleic Acids Res."},{"key":"1181_CR108","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"1181_CR109","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","volume":"33","author":"M Pertea","year":"2015","unstructured":"Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290\u2013295 (2015).","journal-title":"Nat. Biotechnol."},{"key":"1181_CR110","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol"},{"key":"1181_CR111","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284\u2013287 (2012).","journal-title":"OMICS"},{"key":"1181_CR112","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09234-6","volume":"10","author":"Y Zhou","year":"2019","unstructured":"Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).","journal-title":"Nat. Commun."},{"key":"1181_CR113","doi-asserted-by":"publisher","first-page":"D611","DOI":"10.1093\/nar\/gkac868","volume":"51","author":"DS Wishart","year":"2023","unstructured":"Wishart, D. S. et al. MiMeDB: the Human Microbial Metabolome Database. Nucleic Acids Res. 51, D611\u2013D620 (2023).","journal-title":"Nucleic Acids Res."},{"key":"1181_CR114","first-page":"e10","volume":"1","author":"G Yu","year":"2022","unstructured":"Yu, G., Xu, C., Zhang, D., Ju, F. & Ni, Y. MetOrigin: discriminating the origins of microbial metabolites for integrative analysis of the gut microbiome and metabolome. iM eta 1, e10 (2022).","journal-title":"iM eta"},{"key":"1181_CR115","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674\u20131676 (2015).","journal-title":"Bioinformatics"},{"key":"1181_CR116","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0541-1","volume":"6","author":"GV Uritskiy","year":"2018","unstructured":"Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP\u2013a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 158 (2018).","journal-title":"Microbiome"},{"key":"1181_CR117","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","volume":"11","author":"MR Olm","year":"2017","unstructured":"Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864\u20132868 (2017).","journal-title":"ISME J."},{"key":"1181_CR118","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043\u20131055 (2015).","journal-title":"Genome Res."},{"key":"1181_CR119","doi-asserted-by":"publisher","first-page":"D785","DOI":"10.1093\/nar\/gkab776","volume":"50","author":"DH Parks","year":"2022","unstructured":"Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 50, D785\u2013D794 (2022).","journal-title":"Nucleic Acids Res."},{"key":"1181_CR120","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293\u2013W296 (2021).","journal-title":"Nucleic Acids Res."},{"key":"1181_CR121","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389\u20133402 (1997).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature Aging"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s43587-026-01181-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43587-026-01181-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43587-026-01181-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T10:06:02Z","timestamp":1789466762000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s43587-026-01181-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,25]]},"references-count":121,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["1181"],"URL":"https:\/\/doi.org\/10.1038\/s43587-026-01181-4","relation":{},"ISSN":["2662-8465"],"issn-type":[{"value":"2662-8465","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,25]]},"assertion":[{"value":"9 August 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}