{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T16:17:01Z","timestamp":1762273021813,"version":"3.41.2"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["2018YFC0910502","31671374","31871334","32071465"],"award-info":[{"award-number":["2018YFC0910502","31671374","31871334","32071465"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The gut microbial communities are highly plastic throughout life, and the human gut microbial communities show spatial-temporal dynamic patterns at different life stages. However, the underlying association between gut microbial communities and time-related factors remains unclear. The lack of context-awareness, insufficient data, and the existence of batch effect are the three major issues, making the life trajection of the host based on gut microbial communities problematic. Here, we used a novel computational approach (microDELTA, microbial-based deep life trajectory) to track longitudinal human gut microbial communities\u2019 alterations, which employs transfer learning for context-aware mining of gut microbial community dynamics at different life stages. Using an infant cohort, we demonstrated that microDELTA outperformed Neural Network for accurately predicting the age of infant with different delivery mode, especially for newborn infants of vaginal delivery with the area under the receiver operating characteristic curve of microDELTA and Neural Network at 0.811 and 0.436, respectively. In this context, we have discovered the influence of delivery mode on infant gut microbial communities. Along the human lifespan, we also applied microDELTA to a Chinese traveler cohort, a Hadza hunter-gatherer cohort and an elderly cohort. Results revealed the association between long-term dietary shifts during travel and adult gut microbial communities, the seasonal cycling of gut microbial communities for the Hadza hunter-gatherers, and the distinctive microbial pattern of elderly gut microbial communities. In summary, microDELTA can largely solve the issues in tracing the life trajectory of the human microbial communities and generate accurate and flexible models for a broad spectrum of microbial-based longitudinal researches.<\/jats:p>","DOI":"10.1093\/bib\/bbac629","type":"journal-article","created":{"date-parts":[[2023,1,12]],"date-time":"2023-01-12T03:06:36Z","timestamp":1673492796000},"source":"Crossref","is-referenced-by-count":6,"title":["Tracing human life trajectory using gut microbial communities by context-aware deep learning"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6267-4244","authenticated-orcid":false,"given":"Haohong","family":"Zhang","sequence":"first","affiliation":[{"name":"Huazhong University of Science and Technology Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Wuhan 430074, Hubei , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7676-7975","authenticated-orcid":false,"given":"Hui","family":"Chong","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Wuhan 430074, Hubei , China"}]},{"given":"Qingyang","family":"Yu","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Wuhan 430074, Hubei , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3702-9416","authenticated-orcid":false,"given":"Yuguo","family":"Zha","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Wuhan 430074, Hubei , China"}]},{"given":"Mingyue","family":"Cheng","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Wuhan 430074, Hubei , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3325-5387","authenticated-orcid":false,"given":"Kang","family":"Ning","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Wuhan 430074, Hubei , China"}]}],"member":"286","published-online":{"date-parts":[[2023,1,11]]},"reference":[{"key":"2023011917093722000_ref1","doi-asserted-by":"crossref","first-page":"4799","DOI":"10.1128\/AEM.65.11.4799-4807.1999","article-title":"Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut","volume":"65","author":"Suau","year":"1999","journal-title":"Appl Environ Microbiol"},{"key":"2023011917093722000_ref2","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nature11550","article-title":"Diversity, stability and resilience of the human gut microbiota","volume":"489","author":"Lozupone","year":"2012","journal-title":"Nature"},{"key":"2023011917093722000_ref3","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.cca.2015.01.003","article-title":"The role of the gut microbiome in the healthy adult status","volume":"451","author":"D\u2019Argenio","year":"2015","journal-title":"Clin Chim Acta"},{"key":"2023011917093722000_ref4","first-page":"e00261","article-title":"Age- and sex-dependent patterns of gut microbial diversity in human adults","volume":"4","author":"Jdl","year":"2019","journal-title":"mSystems"},{"key":"2023011917093722000_ref5","doi-asserted-by":"crossref","DOI":"10.1038\/s41579-022-00768-z","article-title":"Microbiota succession throughout life from the cradle to the grave","volume":"20","author":"Martino","year":"2022","journal-title":"Nat Rev Microbiol"},{"key":"2023011917093722000_ref6","doi-asserted-by":"crossref","first-page":"4578","DOI":"10.1073\/pnas.1000081107","article-title":"Succession of microbial consortia in the developing infant gut microbiome","volume":"108","author":"Koenig","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"2023011917093722000_ref7","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/nature10213","article-title":"Human nutrition, the gut microbiome and the immune system","volume":"474","author":"Kau","year":"2011","journal-title":"Nature"},{"key":"2023011917093722000_ref8","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1007\/s13277-013-0684-4","article-title":"The role of gut microbiota in the pathogenesis of colorectal cancer","volume":"34","author":"Zhu","year":"2013","journal-title":"Tumour Biol"},{"key":"2023011917093722000_ref9","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1038\/nature12820","article-title":"Diet rapidly and reproducibly alters the human gut microbiome","volume":"505","author":"David","year":"2014","journal-title":"Nature"},{"key":"2023011917093722000_ref10","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.0050177","article-title":"Development of the human infant intestinal microbiota","volume":"5","author":"Palmer","year":"2007","journal-title":"PLoS Biol"},{"key":"2023011917093722000_ref11","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1016\/j.cmet.2014.11.008","article-title":"Diet and feeding pattern affect the diurnal dynamics of the gut microbiome","volume":"20","author":"Zarrinpar","year":"2014","journal-title":"Cell Metab"},{"key":"2023011917093722000_ref12","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.1126\/science.aac8469","article-title":"Gut microbiota and aging","volume":"350","author":"O'Toole","year":"2015","journal-title":"Science"},{"key":"2023011917093722000_ref13","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.01857-21","article-title":"Successional stages in infant gut microbiota maturation","volume":"12","author":"Beller","year":"2021","journal-title":"MBio"},{"key":"2023011917093722000_ref14","article-title":"Microbiome resilience and health implications for people in half-year travel","volume":"13","author":"Cheng","year":"2022","journal-title":"Front Immunol"},{"key":"2023011917093722000_ref15","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1017\/S0029665112002807","article-title":"Ageing and the gut","volume":"72","author":"Britton","year":"2013","journal-title":"Proc Nutr Soc"},{"key":"2023011917093722000_ref16","doi-asserted-by":"crossref","first-page":"E4485","DOI":"10.1073\/pnas.1415174111","article-title":"Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity","volume":"111","author":"Leclercq","year":"2014","journal-title":"Proc Natl Acad Sci USA"},{"key":"2023011917093722000_ref17","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1038\/s41598-018-36430-z","article-title":"Altered gut microbiota and short chain fatty acids in Chinese children with autism spectrum disorder","volume":"9","author":"Liu","year":"2019","journal-title":"Sci Rep"},{"key":"2023011917093722000_ref18","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/S1474-4422(19)30356-4","article-title":"The gut microbiome in neurological disorders","volume":"19","author":"Cryan","year":"2020","journal-title":"Lancet Neurol"},{"key":"2023011917093722000_ref19","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1080\/19490976.2020.1758010","article-title":"Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity","volume":"11","author":"Ames","year":"2020","journal-title":"Gut Microbes"},{"key":"2023011917093722000_ref20","first-page":"71","article-title":"Longitudinal analysis of the impact of oral contraceptive use on the gut microbiome","author":"Hua","year":"2022","journal-title":"J Med Microbiol"},{"key":"2023011917093722000_ref21","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.1016\/j.cub.2016.04.016","article-title":"Gut microbiota and extreme longevity","volume":"26","author":"Biagi","year":"2016","journal-title":"Curr Biol"},{"key":"2023011917093722000_ref22","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.chom.2015.05.012","article-title":"Dynamics and stabilization of the human gut microbiome during the first year of life","volume":"17","author":"Backhed","year":"2015","journal-title":"Cell Host Microbe"},{"key":"2023011917093722000_ref23","doi-asserted-by":"crossref","first-page":"2254","DOI":"10.1136\/gutjnl-2018-317298","article-title":"Resilience of human gut microbial communities for the long stay with multiple dietary shifts","volume":"68","author":"Liu","year":"2019","journal-title":"Gut"},{"key":"2023011917093722000_ref24","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1038\/s42255-021-00377-9","article-title":"Gut microbiome pattern reflects healthy ageing and predicts survival in humans","volume":"3","author":"Wilmanski","year":"2021","journal-title":"Nat Metab"},{"key":"2023011917093722000_ref25","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00630-19","article-title":"Human skin, oral, and gut microbiomes predict chronological age","volume":"5","author":"Huang","year":"2020","journal-title":"mSystems"},{"key":"2023011917093722000_ref26","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.642439","article-title":"Microbiome sample comparison and search: from pair-wise calculations to model-based matching","volume":"12","author":"Zha","year":"2021","journal-title":"Front Microbiol"},{"key":"2023011917093722000_ref27","doi-asserted-by":"crossref","first-page":"1724","DOI":"10.1371\/journal.pgen.0030161","article-title":"Capturing heterogeneity in gene expression studies by surrogate variable analysis","volume":"3","author":"Leek","year":"2007","journal-title":"PLoS Genet"},{"key":"2023011917093722000_ref28","article-title":"How transferable are features in deep neural networks?","volume":"27","author":"Yosinski","year":"2014","journal-title":"NIPS"},{"key":"2023011917093722000_ref29","article-title":"Very deep convolutional networks for large-scale image recognition","author":"Simonyan","year":"2015","journal-title":"ICLR"},{"key":"2023011917093722000_ref30","doi-asserted-by":"crossref","first-page":"3386","DOI":"10.1109\/BIBM52615.2021.9669640","volume-title":"IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","author":"Ito","year":"2021"},{"key":"2023011917093722000_ref31","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac396","article-title":"EXPERT: transfer learning-enabled context-aware microbial community classification","volume":"23","author":"Chong","year":"2022","journal-title":"Brief Bioinform"},{"key":"2023011917093722000_ref32","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1001\/jamapediatrics.2015.3732","article-title":"Association of Cesarean delivery and formula supplementation with the intestinal microbiome of 6-week-old infants","volume":"170","author":"Madan","year":"2016","journal-title":"JAMA Pediatr"},{"key":"2023011917093722000_ref33","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1126\/science.aan4834","article-title":"Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania","volume":"357","author":"Smits","year":"2017","journal-title":"Science"},{"key":"2023011917093722000_ref34","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1016\/j.chom.2021.02.021","article-title":"Developmental trajectory of the healthy human gut microbiota during the first 5 years of life","volume":"29","author":"Roswall","year":"2021","journal-title":"Cell Host Microbe"},{"key":"2023011917093722000_ref35","doi-asserted-by":"crossref","first-page":"343ra382","DOI":"10.1126\/scitranslmed.aad7121","article-title":"Antibiotics, birth mode, and diet shape microbiome maturation during early life","volume":"8","author":"Bokulich","year":"2016","journal-title":"Sci Transl Med"},{"key":"2023011917093722000_ref36","doi-asserted-by":"crossref","DOI":"10.1016\/j.tmaid.2021.102199","article-title":"Changes to human faecal microbiota after international travel","volume":"44","author":"Kampmann","year":"2021","journal-title":"Travel Med Infect Dis"},{"volume-title":"The Hadza: hunter-gatherers of Tanzania","year":"2010","author":"Marlowe","key":"2023011917093722000_ref37"},{"key":"2023011917093722000_ref38","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/nature11319","article-title":"Gut microbiota composition correlates with diet and health in the elderly","volume":"488","author":"Claesson","year":"2012","journal-title":"Nature"},{"key":"2023011917093722000_ref39","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13073-016-0275-2","article-title":"Erratum to: signatures of early frailty in the gut microbiota","volume":"8","author":"Jackson","year":"2016","journal-title":"Genome Med"},{"key":"2023011917093722000_ref40","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/s13042-016-0634-8","article-title":"Negative transfer detection in transductive transfer learning","volume":"9","author":"Gui","year":"2018","journal-title":"Int J Mach Learn Cybern"},{"key":"2023011917093722000_ref41","doi-asserted-by":"crossref","DOI":"10.1002\/9780471729259.mc01e05s27","article-title":"Using QIIME to analyze 16S rRNA gene sequences from microbial communities","author":"Kuczynski","year":"2012","journal-title":"Curr Protoc Microbiol"},{"key":"2023011917093722000_ref42","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1038\/s41587-019-0252-6","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (vol 37, pg 852, 2019)","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2023011917093722000_ref43","first-page":"807","article-title":"Rectified linear units improve restricted Boltzmann machines","volume":"27","author":"Vinod","year":"2010","journal-title":"ICML"},{"volume-title":"Proceedings of the IEEE International Conference on Computer Vision (ICCV)","year":"2015","author":"He","key":"2023011917093722000_ref44"},{"key":"2023011917093722000_ref45","first-page":"249","volume-title":"Understanding the difficulty of training deep feedforward neural networks","author":"Glorot","year":"2010"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/1\/bbac629\/48783090\/bbac629.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/1\/bbac629\/48783090\/bbac629.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T17:21:34Z","timestamp":1674148894000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac629\/6984796"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1]]},"references-count":45,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac629","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2023,1]]},"published":{"date-parts":[[2023,1]]},"article-number":"bbac629"}}