{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T06:18:41Z","timestamp":1783491521450,"version":"3.55.0"},"reference-count":48,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["No. 82204050"],"award-info":[{"award-number":["No. 82204050"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017610","name":"Shenzhen Science and Technology Innovation Program","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100017610","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012151","name":"Sanming Project of Medicine in Shenzen Municipality","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012151","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Early infancy is critical for gut microbiome assembly and the establishment of colonization resistance against pathobionts. Whether age-associated microbiome maturation is accompanied by changes in colonization-resistance proxies and relative antimicrobial resistance gene profiles under low infant antibiotic exposure remains unclear.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We analyzed shotgun metagenomes from 82 fecal samples collected from 54 healthy infants (54 at 1 month and 28 at 6 months). Taxonomic and functional profiles were generated using MetaPhlAn 4 and HUMAnN3, and AMR genes were annotated using RGI\/CARD. Age-associated taxa were screened by LEfSe and tested using MaAsLin2 with adjustment for key perinatal covariates.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Age group was associated with modest but statistically significant differences in community structure (Bray\u2013Curtis PERMANOVA\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sup>2<\/jats:sup>\n                      = 0.03,\n                      <jats:italic>p<\/jats:italic>\n                      = 0.005) and higher species richness at 6 months (\n                      <jats:italic>p<\/jats:italic>\n                      &amp;lt; 0.001), with no statistically significant difference in Shannon or Simpson indices. In adjusted models, skin-associated pioneer taxa, including\n                      <jats:italic>Staphylococcus epidermidis<\/jats:italic>\n                      , were lower at 6 months, whereas several anaerobic or oral-associated taxa were higher, including\n                      <jats:italic>Flavonifractor plautii<\/jats:italic>\n                      .\n                      <jats:italic>Enterobacteriaceae<\/jats:italic>\n                      relative abundance was lower at 6 months than at 1 month (median 16.64 vs. 1.86%,\n                      <jats:italic>p<\/jats:italic>\n                      &amp;lt; 0.001), and\n                      <jats:italic>Bifidobacterium<\/jats:italic>\n                      \u2013\n                      <jats:italic>Enterobacteriaceae<\/jats:italic>\n                      antagonism indices were higher. However,\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      and\n                      <jats:italic>Klebsiella<\/jats:italic>\n                      spp. did not show significant genus-level reductions. Copies per million (CPM)-normalized \u03b2-lactamase (\n                      <jats:italic>bla<\/jats:italic>\n                      ) relative abundance showed no statistically significant timepoint difference and was positively correlated with selected\n                      <jats:italic>Bifidobacterium<\/jats:italic>\n                      species.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      In this infant antibiotic-restricted cohort, microbiome profiles at 6 months were associated with lower relative abundance of potential pathobionts and higher colonization-resistance proxy indices. CPM-normalized\n                      <jats:italic>bla<\/jats:italic>\n                      relative abundance showed no statistically significant timepoint difference. These observational findings do not establish the genomic host or mobility of\n                      <jats:italic>bla<\/jats:italic>\n                      genes. Quantitative and host-resolved studies are needed to distinguish compositional shifts from absolute resistome trajectories.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1862116","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:56:41Z","timestamp":1783490201000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Age-associated gut microbiome succession, colonization resistance, and relative resistome patterns in an antibiotic-restricted infant cohort"],"prefix":"10.3389","volume":"17","author":[{"given":"Manting","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital","place":["Shenzhen, China"]},{"name":"Centre for Big Data Research in Health, Faculty of Medicine and Health, UNSW Sydney","place":["Kensington, NSW, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shutong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Medical Research Institute, Shenzhen Baoan Women's and Children's Hospital","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meiying","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Biobank, Shenzhen Baoan Women's and Children's Hospital","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongyan","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Shenzhen Baoan Women's and Children's Hospital","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meiqun","family":"Xiao","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Shenzhen Baoan Women's and Children's Hospital","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Liao","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Shenzhen Baoan Women's and Children's Hospital","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Shenzhen Baoan Women's and Children's Hospital","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, School of Public Health (Shenzhen), Sun Yat-sen University","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengying","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Food Hygiene, School of Public Health, Peking University","place":["Beijing, China"]},{"name":"Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiying","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital","place":["Shenzhen, China"]},{"name":"Health Science Center, Shenzhen University","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,8]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1111\/j.1651-2227.2008.01060.x","article-title":"Establishment of the gut microbiota in Western infants","volume":"98","author":"Adlerberth","year":"2009","journal-title":"Acta Paediatr"},{"key":"B2","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1053\/j.gastro.2014.07.020","article-title":"Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota","volume":"147","author":"Albenberg","year":"2014","journal-title":"Gastroenterology"},{"key":"B3","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"B4","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1111\/j.1442-9993.2001.01070.pp.x","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","author":"Anderson","year":"2001","journal-title":"Austral. 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