{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,9]],"date-time":"2026-11-09T00:44:49Z","timestamp":1794185089806,"version":"4.8.0"},"reference-count":69,"publisher":"Springer Science and Business Media LLC","issue":"8062","license":[{"start":{"date-parts":[[2025,4,2]],"date-time":"2025-04-02T00:00:00Z","timestamp":1743552000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,4,2]],"date-time":"2025-04-02T00:00:00Z","timestamp":1743552000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2025,5,8]]},"DOI":"10.1038\/s41586-025-08796-4","type":"journal-article","created":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T14:03:43Z","timestamp":1743775423000},"page":"456-464","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":60,"title":["Bifidobacteria support optimal infant vaccine responses"],"prefix":"10.1038","volume":"641","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1565-4598","authenticated-orcid":false,"given":"Feargal J.","family":"Ryan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9635-8784","authenticated-orcid":false,"given":"Michelle","family":"Clarke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam A.","family":"Lynn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saoirse C.","family":"Benson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia","family":"McAlister","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynne C.","family":"Giles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jocelyn M.","family":"Choo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charn\u00e9","family":"Rossouw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan Yung","family":"Ng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5188-7946","authenticated-orcid":false,"given":"Evgeny A.","family":"Semchenko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alyson","family":"Richard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lex E. X.","family":"Leong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven L.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J.","family":"Blake","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8168-1976","authenticated-orcid":false,"given":"Joyce I.","family":"Mugabushaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary","family":"Walker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steve L.","family":"Wesselingh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6086-6285","authenticated-orcid":false,"given":"Paul V.","family":"Licciardi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7094-3528","authenticated-orcid":false,"given":"Kate L.","family":"Seib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5709-857X","authenticated-orcid":false,"given":"Damon J.","family":"Tumes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7562-7228","authenticated-orcid":false,"given":"Peter","family":"Richmond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geraint B.","family":"Rogers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen S.","family":"Marshall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4664-1404","authenticated-orcid":false,"given":"David J.","family":"Lynn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,4,2]]},"reference":[{"key":"8796_CR1","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1016\/j.chom.2018.04.009","volume":"23","author":"MA Lynn","year":"2018","unstructured":"Lynn, M. A. et al. Early-life antibiotic-driven dysbiosis leads to dysregulated vaccine immune responses in mice. Cell Host Microbe 23, 653\u2013660 (2018).","journal-title":"Cell Host Microbe"},{"key":"8796_CR2","doi-asserted-by":"publisher","DOI":"10.1542\/peds.2021-052061","volume":"149","author":"TJ Chapman","year":"2022","unstructured":"Chapman, T. J., Pham, M., Bajorski, P. & Pichichero, M. E. Antibiotic use and vaccine antibody levels. Pediatrics 149, e2021052061 (2022).","journal-title":"Pediatrics"},{"key":"8796_CR3","doi-asserted-by":"publisher","first-page":"e0066123","DOI":"10.1128\/msystems.00661-23","volume":"8","author":"M Shaffer","year":"2023","unstructured":"Shaffer, M. et al. Very early life microbiome and metabolome correlates with primary vaccination variability in children. mSystems 8, e0066123 (2023).","journal-title":"mSystems"},{"key":"8796_CR4","doi-asserted-by":"publisher","first-page":"1856","DOI":"10.1093\/infdis\/jiad524","volume":"229","author":"ME Pichichero","year":"2024","unstructured":"Pichichero, M. E., Xu, L., Gonzalez, E., Pham, M. & Kaur, R. Variability of vaccine responsiveness in young children. J. Infect. Dis. 229, 1856\u20131865 (2024).","journal-title":"J. Infect. Dis."},{"key":"8796_CR5","doi-asserted-by":"publisher","first-page":"140","DOI":"10.2471\/BLT.07.040089","volume":"86","author":"FE Andre","year":"2008","unstructured":"Andre, F. E. et al. Vaccination greatly reduces disease, disability, death and inequity worldwide. Bull. World Health Organ. 86, 140\u2013146 (2008).","journal-title":"Bull. World Health Organ."},{"key":"8796_CR6","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1016\/S1473-3099(22)00320-6","volume":"22","author":"OJ Watson","year":"2022","unstructured":"Watson, O. J. et al. Global impact of the first year of COVID-19 vaccination: a mathematical modelling study. Lancet Infect. Dis. 22, 1293\u20131302 (2022).","journal-title":"Lancet Infect. Dis."},{"key":"8796_CR7","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1038\/s41577-021-00554-7","volume":"22","author":"DJ Lynn","year":"2022","unstructured":"Lynn, D. J., Benson, S. C., Lynn, M. A. & Pulendran, B. Modulation of immune responses to vaccination by the microbiota: implications and potential mechanisms. Nat. Rev. Immunol. 22, 33\u201346 (2022).","journal-title":"Nat. Rev. Immunol."},{"key":"8796_CR8","doi-asserted-by":"publisher","DOI":"10.1111\/febs.17241","author":"C Rossouw","year":"2024","unstructured":"Rossouw, C., Ryan, F. J. & Lynn, D. J. The role of the gut microbiota in regulating responses to vaccination: current knowledge and future directions. FEBS J. https:\/\/doi.org\/10.1111\/febs.17241 (2024).","journal-title":"FEBS J."},{"key":"8796_CR9","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.immuni.2014.08.009","volume":"41","author":"JZ Oh","year":"2014","unstructured":"Oh, J. Z. et al. TLR5-mediated sensing of gut microbiota is necessary for antibody responses to seasonal influenza vaccination. Immunity 41, 478\u2013492 (2014).","journal-title":"Immunity"},{"issue":"7","key":"8796_CR10","doi-asserted-by":"publisher","first-page":"1222","DOI":"10.1136\/gutjnl-2023-329810","volume":"73","author":"T Norton","year":"2024","unstructured":"Norton, T. et al. B and T cell responses to the BNT162b2 COVID-19 mRNA vaccine are not impaired in germ-free or antibiotic-treated mice. Gut\u00a073, 1222\u20131224\u00a0(2024).","journal-title":"Gut"},{"key":"8796_CR11","doi-asserted-by":"publisher","first-page":"1313","DOI":"10.1016\/j.cell.2019.08.010","volume":"178","author":"T Hagan","year":"2019","unstructured":"Hagan, T. et al. Antibiotics-driven gut microbiome perturbation alters immunity to vaccines in humans. Cell 178, 1313\u20131328 (2019).","journal-title":"Cell"},{"key":"8796_CR12","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/j.chom.2018.07.005","volume":"24","author":"VC Harris","year":"2018","unstructured":"Harris, V. C. et al. Effect of antibiotic-mediated microbiome modulation on rotavirus vaccine immunogenicity: a human, randomized-control proof-of-concept trial. Cell Host Microbe 24, 197\u2013207.e194 (2018).","journal-title":"Cell Host Microbe"},{"key":"8796_CR13","doi-asserted-by":"publisher","first-page":"674","DOI":"10.1128\/CVI.00408-09","volume":"17","author":"KE Elberse","year":"2010","unstructured":"Elberse, K. E., Tcherniaeva, I., Berbers, G. A. & Schouls, L. M. Optimization and application of a multiplex bead-based assay to quantify serotype-specific IgG against Streptococcus pneumoniae polysaccharides: response to the booster vaccine after immunization with the pneumococcal 7-valent conjugate vaccine. Clin. Vaccine Immunol. 17, 674\u2013682 (2010).","journal-title":"Clin. Vaccine Immunol."},{"key":"8796_CR14","doi-asserted-by":"publisher","first-page":"101360","DOI":"10.1016\/j.mex.2021.101360","volume":"8","author":"SM McAlister","year":"2021","unstructured":"McAlister, S. M., van den Biggelaar, A. H. J., Thornton, R. B. & Richmond, P. C. Optimising a 6-plex tetanus-diphtheria-pertussis fluorescent bead-based immunoassay. MethodsX 8, 101360 (2021).","journal-title":"MethodsX"},{"key":"8796_CR15","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00128-18","volume":"3","author":"D Pavliakova","year":"2018","unstructured":"Pavliakova, D. et al. Development and validation of 13-plex Luminex-based assay for measuring human serum antibodies to Streptococcus pneumoniae capsular polysaccharides. mSphere 3, e00128-18 (2018).","journal-title":"mSphere"},{"key":"8796_CR16","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1309\/LMCH-C4Q2-VFL9-3T1A","volume":"117","author":"JW Pickering","year":"2002","unstructured":"Pickering, J. W. et al. A multiplexed fluorescent microsphere immunoassay for antibodies to pneumococcal capsular polysaccharides. Am. J. Clin. Pathol. 117, 589\u2013596 (2002).","journal-title":"Am. J. Clin. Pathol."},{"key":"8796_CR17","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/S0264-410X(97)00210-7","volume":"16","author":"DI Bernstein","year":"1998","unstructured":"Bernstein, D. I. et al. Safety and immunogenicity of live, attenuated human rotavirus vaccine 89-12. Vaccine 16, 381\u2013387 (1998).","journal-title":"Vaccine"},{"key":"8796_CR18","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.vaccine.2019.09.088","volume":"38","author":"B Lee","year":"2020","unstructured":"Lee, B. et al. The effect of increased inoculum on oral rotavirus vaccine take among infants in Dhaka, Bangladesh: a double-blind, parallel group, randomized, controlled trial. Vaccine 38, 90\u201399 (2020).","journal-title":"Vaccine"},{"key":"8796_CR19","doi-asserted-by":"publisher","first-page":"1773","DOI":"10.1016\/j.celrep.2019.07.047","volume":"28","author":"M Vono","year":"2019","unstructured":"Vono, M. et al. Maternal antibodies inhibit neonatal and infant responses to vaccination by shaping the early-life B cell repertoire within germinal centers. Cell Rep. 28, 1773\u20131784.e1775 (2019).","journal-title":"Cell Rep."},{"key":"8796_CR20","doi-asserted-by":"publisher","first-page":"1737","DOI":"10.1016\/S1473-3099(22)00438-8","volume":"22","author":"TD Swarthout","year":"2022","unstructured":"Swarthout, T. D. et al. Waning of antibody levels induced by a 13-valent pneumococcal conjugate vaccine, using a 3+0 schedule, within the first year of life among children younger than 5 years in Blantyre, Malawi: an observational, population-level, serosurveillance study. Lancet Infect. Dis. 22, 1737\u20131747 (2022).","journal-title":"Lancet Infect. Dis."},{"key":"8796_CR21","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1016\/S1473-3099(14)70822-9","volume":"14","author":"NJ Andrews","year":"2014","unstructured":"Andrews, N. J. et al. Serotype-specific effectiveness and correlates of protection for the 13-valent pneumococcal conjugate vaccine: a postlicensure indirect cohort study. Lancet Infect. Dis. 14, 839\u2013846 (2014).","journal-title":"Lancet Infect. Dis."},{"key":"8796_CR22","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1080\/14760584.2021.1940144","volume":"21","author":"J Findlow","year":"2022","unstructured":"Findlow, J., Lucidarme, J., Taha, M. K., Burman, C. & Balmer, P. Correlates of protection for meningococcal surface protein vaccines: lessons from the past. Expert Rev. Vaccines 21, 739\u2013751 (2022).","journal-title":"Expert Rev. Vaccines"},{"key":"8796_CR23","doi-asserted-by":"publisher","first-page":"1788","DOI":"10.1038\/s41590-022-01328-6","volume":"23","author":"T Hagan","year":"2022","unstructured":"Hagan, T. et al. Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses. Nat. Immunol. 23, 1788\u20131798 (2022).","journal-title":"Nat. Immunol."},{"key":"8796_CR24","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/ni.2789","volume":"15","author":"S Li","year":"2014","unstructured":"Li, S. et al. Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nat. Immunol. 15, 195\u2013204 (2014).","journal-title":"Nat. Immunol."},{"key":"8796_CR25","doi-asserted-by":"publisher","first-page":"100971","DOI":"10.1016\/j.xcrm.2023.100971","volume":"4","author":"FJ Ryan","year":"2023","unstructured":"Ryan, F. J. et al. A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccines. Cell Rep. Med. 4, 100971 (2023).","journal-title":"Cell Rep. Med."},{"key":"8796_CR26","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1016\/j.tim.2019.08.001","volume":"27","author":"M Derrien","year":"2019","unstructured":"Derrien, M., Alvarez, A. S. & de Vos, W. M. The gut microbiota in the first decade of life. Trends Microbiol. 27, 997\u20131010 (2019).","journal-title":"Trends Microbiol."},{"issue":"1","key":"8796_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/19490976.2020.1870402","volume":"13","author":"L McDonnell","year":"2021","unstructured":"McDonnell, L. et al. Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis. Gut Microbes 13, 1870402 (2021).","journal-title":"Gut Microbes"},{"key":"8796_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v059.i05","volume":"59","author":"D Tingley","year":"2014","unstructured":"Tingley, D., Yamamoto, T., Hirose, K., Keele, L. & Imai, K. Mediation: R package for causal mediation analysis. J. Stat. Softw. 59, 1\u201338 (2014).","journal-title":"J. Stat. Softw."},{"key":"8796_CR29","unstructured":"Imai, K., Keele, L., Tingley, D. & Yamamoto, T. in Advances in Social Science Research Using R. (ed. Vinod, H. D.) Ch. 8 (Springer, 2010)."},{"key":"8796_CR30","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/S1201-9712(99)90024-3","volume":"3","author":"AB Hoyos","year":"1999","unstructured":"Hoyos, A. B. Reduced incidence of necrotizing enterocolitis associated with enteral administration of Lactobacillus acidophilus and Bifidobacterium infantis to neonates in an intensive care unit. Int. J. Infect. Dis. 3, 197\u2013202 (1999).","journal-title":"Int. J. Infect. Dis."},{"key":"8796_CR31","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1111\/jpc.16390","volume":"59","author":"EK Cripps","year":"2023","unstructured":"Cripps, E. K., Dargaville, P. A. & De Paoli, A. G. Impact of probiotic administration on the incidence of necrotising enterocolitis: a single-centre cohort study. J. Paediatr. Child Health 59, 760\u2013765 (2023).","journal-title":"J. Paediatr. Child Health"},{"key":"8796_CR32","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1016\/j.tim.2017.10.001","volume":"26","author":"F Turroni","year":"2018","unstructured":"Turroni, F. et al. Glycan utilization and cross-feeding activities by Bifidobacteria. Trends Microbiol. 26, 339\u2013350 (2018).","journal-title":"Trends Microbiol."},{"key":"8796_CR33","doi-asserted-by":"publisher","first-page":"e20181489","DOI":"10.1542\/peds.2018-1489","volume":"143","author":"MN Huda","year":"2019","unstructured":"Huda, M. N. et al. Bifidobacterium abundance in early infancy and vaccine response at 2 years of age. Pediatrics 143, e20181489 (2019).","journal-title":"Pediatrics"},{"key":"8796_CR34","doi-asserted-by":"publisher","first-page":"e362","DOI":"10.1542\/peds.2013-3937","volume":"134","author":"MN Huda","year":"2014","unstructured":"Huda, M. N. et al. Stool microbiota and vaccine responses of infants. Pediatrics 134, e362\u2013e372 (2014).","journal-title":"Pediatrics"},{"key":"8796_CR35","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.ade1370","volume":"9","author":"DD Nyangahu","year":"2023","unstructured":"Nyangahu, D. D. et al. Bifidobacterium infantis associates with T cell immunity in human infants and is sufficient to enhance antigen-specific T cells in mice. Sci. Adv. 9, eade1370 (2023).","journal-title":"Sci. Adv."},{"key":"8796_CR36","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0490-8","volume":"6","author":"SN Lundgren","year":"2018","unstructured":"Lundgren, S. N. et al. Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Microbiome 6, 109 (2018).","journal-title":"Microbiome"},{"key":"8796_CR37","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34155-2","volume":"13","author":"EM de Koff","year":"2022","unstructured":"de Koff, E. M. et al. Mode of delivery modulates the intestinal microbiota and impacts the response to vaccination. Nat. Commun. 13, 6638 (2022).","journal-title":"Nat. Commun."},{"key":"8796_CR38","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku864","volume":"42","author":"JT Leek","year":"2014","unstructured":"Leek, J. T. svaseq: removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res. 42, e161 (2014).","journal-title":"Nucleic Acids Res."},{"key":"8796_CR39","doi-asserted-by":"publisher","unstructured":"Korotkevich, G. et al. Fast gene set enrichment analysis. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/060012 (2016).","DOI":"10.1101\/060012"},{"key":"8796_CR40","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2010).","journal-title":"Bioinformatics"},{"key":"8796_CR41","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.jim.2005.11.019","volume":"309","author":"SA Schlottmann","year":"2006","unstructured":"Schlottmann, S. A., Jain, N., Chirmule, N. & Esser, M. T. A novel chemistry for conjugating pneumococcal polysaccharides to Luminex microspheres. J. Immunol. Methods 309, 75\u201385 (2006).","journal-title":"J. Immunol. Methods"},{"key":"8796_CR42","doi-asserted-by":"publisher","first-page":"1642","DOI":"10.1016\/j.vaccine.2021.01.041","volume":"39","author":"SM McAlister","year":"2021","unstructured":"McAlister, S. M. et al. An observational study of antibody responses to a primary or subsequent pertussis booster vaccination in Australian healthcare workers. Vaccine 39, 1642\u20131651 (2021).","journal-title":"Vaccine"},{"key":"8796_CR43","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00070-18","volume":"3","author":"A Balloch","year":"2018","unstructured":"Balloch, A. et al. Interlaboratory comparison of the pneumococcal multiplex opsonophagocytic assays and their level of agreement for determination of antibody function in pediatric sera. mSphere 3, e00070-18 (2018).","journal-title":"mSphere"},{"key":"8796_CR44","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1016\/S1473-3099(23)00061-0","volume":"23","author":"B Temple","year":"2023","unstructured":"Temple, B. et al. Efficacy against pneumococcal carriage and the immunogenicity of reduced-dose (0+1 and 1+1) PCV10 and PCV13 schedules in Ho Chi Minh City, Viet Nam: a parallel, single-blind, randomised controlled trial. Lancet Infect. Dis. 23, 933\u2013944 (2023).","journal-title":"Lancet Infect. Dis."},{"key":"8796_CR45","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1007\/978-1-4939-9202-7_12","volume":"1969","author":"J Lucidarme","year":"2019","unstructured":"Lucidarme, J., Louth, J., Townsend-Payne, K. & Borrow, R. Meningococcal serogroup A, B, C, W, X, and Y serum bactericidal antibody assays. Methods Mol. Biol. 1969, 169\u2013179 (2019).","journal-title":"Methods Mol. Biol."},{"key":"8796_CR46","unstructured":"Andrews, S. FastQC: a quality control tool for high throughput sequence data. Babraham Institute www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/ (2010)."},{"key":"8796_CR47","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels, P., Magnusson, M., Lundin, S. & Kaller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047\u20133048 (2016).","journal-title":"Bioinformatics"},{"key":"8796_CR48","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"8796_CR49","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","volume":"12","author":"D Kim","year":"2015","unstructured":"Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357\u2013360 (2015).","journal-title":"Nat. Methods"},{"key":"8796_CR50","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923\u2013930 (2014).","journal-title":"Bioinformatics"},{"key":"8796_CR51","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-14-7","volume":"14","author":"S H\u00e4nzelmann","year":"2013","unstructured":"H\u00e4nzelmann, S., Castelo, R. & Guinney, J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 14, 7 (2013).","journal-title":"BMC Bioinformatics"},{"key":"8796_CR52","doi-asserted-by":"publisher","DOI":"10.1038\/srep16350","volume":"5","author":"JM Choo","year":"2015","unstructured":"Choo, J. M., Leong, L. E. & Rogers, G. B. Sample storage conditions significantly influence faecal microbiome profiles. Sci. Rep. 5, 16350 (2015).","journal-title":"Sci. Rep."},{"key":"8796_CR53","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00103-18","volume":"3","author":"JM Choo","year":"2018","unstructured":"Choo, J. M. et al. Impact of long-term erythromycin therapy on the oropharyngeal microbiome and resistance gene reservoir in non-cystic fibrosis bronchiectasis. mSphere 3, e00103-18 (2018).","journal-title":"mSphere"},{"key":"8796_CR54","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.58407","volume":"9","author":"FM Mobegi","year":"2020","unstructured":"Mobegi, F. M. et al. Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities. eLife 9, e58407 (2020).","journal-title":"eLife"},{"key":"8796_CR55","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019).","journal-title":"Genome Biol."},{"key":"8796_CR56","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1101\/gr.213959.116","volume":"27","author":"S Nurk","year":"2017","unstructured":"Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824\u2013834 (2017).","journal-title":"Genome Res."},{"key":"8796_CR57","doi-asserted-by":"publisher","first-page":"e7359","DOI":"10.7717\/peerj.7359","volume":"7","author":"DD Kang","year":"2019","unstructured":"Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).","journal-title":"PeerJ"},{"key":"8796_CR58","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","volume":"36","author":"P-A Chaumeil","year":"2019","unstructured":"Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925\u20131927 (2019).","journal-title":"Bioinformatics"},{"key":"8796_CR59","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02655-5","volume":"23","author":"H Zhou","year":"2022","unstructured":"Zhou, H., He, K., Chen, J. & Zhang, X. LinDA: linear models for differential abundance analysis of microbiome compositional data. Genome Biol. 23, 95 (2022).","journal-title":"Genome Biol."},{"key":"8796_CR60","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).","journal-title":"PLoS ONE"},{"key":"8796_CR61","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1038\/s41592-018-0176-y","volume":"15","author":"EA Franzosa","year":"2018","unstructured":"Franzosa, E. A. et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods 15, 962\u2013968 (2018).","journal-title":"Nat. Methods"},{"key":"8796_CR62","doi-asserted-by":"publisher","first-page":"D593","DOI":"10.1093\/nar\/gku1201","volume":"43","author":"SF Stoddard","year":"2015","unstructured":"Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. & Schmidt, T. M. rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res. 43, D593\u2013D598 (2015).","journal-title":"Nucleic Acids Res."},{"key":"8796_CR63","doi-asserted-by":"publisher","first-page":"101914","DOI":"10.1016\/j.xpro.2022.101914","volume":"3","author":"MA Lynn","year":"2022","unstructured":"Lynn, M. A., Ryan, F. J., Tee, Y. C. & Lynn, D. J. Protocol to colonize gnotobiotic mice in early life and assess the impact on early life immune programming. STAR Protoc. 3, 101914 (2022).","journal-title":"STAR Protoc."},{"key":"8796_CR64","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":"8796_CR65","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581\u2013583 (2016).","journal-title":"Nat. Methods"},{"key":"8796_CR66","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590\u2013D596 (2013).","journal-title":"Nucleic Acids Res."},{"key":"8796_CR67","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1099\/00221287-148-1-257","volume":"148","author":"MA Nadkarni","year":"2002","unstructured":"Nadkarni, M. A., Martin, F. E., Jacques, N. A. & Hunter, N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148, 257\u2013266 (2002).","journal-title":"Microbiology"},{"key":"8796_CR68","doi-asserted-by":"publisher","first-page":"100499","DOI":"10.1016\/j.xpro.2021.100499","volume":"2","author":"S Fra-Bido","year":"2021","unstructured":"Fra-Bido, S., Walker, S. A., Innocentin, S. & Linterman, M. A. Optimized immunofluorescence staining protocol for imaging germinal centers in secondary lymphoid tissues of vaccinated mice. STAR Protoc. 2, 100499 (2021).","journal-title":"STAR Protoc."},{"key":"8796_CR69","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-08796-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-08796-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-08796-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T20:02:32Z","timestamp":1747166552000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-08796-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,2]]},"references-count":69,"journal-issue":{"issue":"8062","published-print":{"date-parts":[[2025,5,8]]}},"alternative-id":["8796"],"URL":"https:\/\/doi.org\/10.1038\/s41586-025-08796-4","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,2]]},"assertion":[{"value":"21 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 April 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"D.J.L., S.J.B., F.J.R. and M.A.L. have received funding from GSK related to this area of research. D.J.L. and H.S.M. are consultants for GPN Vaccines (Australia). H.S.M. is an investigator on sponsored vaccine trials funded by Iliad and Pfizer. H.S.M. has received institutional funding for investigator-led studies from Pfizer, Sanofi-Aventis and Seqiris. P.R. has received institutional funding for investigator-led grants from Merck and Sanofi outside this work. His institution receives funding for his participation in vaccine scientific advisory boards from Pfizer, Merck, GSK, GPN Vaccines (Australia) and Sanofi-Aventis unrelated to this work. He is an investigator on sponsored vaccine trials funded by Iliad, GSK, Merck, Sanofi, Dynavax and Pfizer. He is coinventor on a patent for a new bacteriotherapy for treating or preventing respiratory infection unrelated to this work. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}