{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T20:28:20Z","timestamp":1790886500276,"version":"4.1.0"},"reference-count":80,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T00:00:00Z","timestamp":1725580800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T00:00:00Z","timestamp":1725580800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100014188","name":"Ministry of Science and ICT, South Korea","doi-asserted-by":"publisher","award":["NRF-2021M3E5D1A01015187"],"award-info":[{"award-number":["NRF-2021M3E5D1A01015187"]}],"id":[{"id":"10.13039\/501100014188","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002701","name":"Ministry of Education","doi-asserted-by":"publisher","award":["NRF-2021R1I1A1A01050391"],"award-info":[{"award-number":["NRF-2021R1I1A1A01050391"]}],"id":[{"id":"10.13039\/501100002701","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002701","name":"Ministry of Education","doi-asserted-by":"publisher","award":["NRF-2018R1D1A1B07045711"],"award-info":[{"award-number":["NRF-2018R1D1A1B07045711"]}],"id":[{"id":"10.13039\/501100002701","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003669","name":"Korea Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["2021ER260300"],"award-info":[{"award-number":["2021ER260300"]}],"id":[{"id":"10.13039\/501100003669","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Transl Med"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are pivotal in combating coronavirus disease 2019 (COVID-19); however, the declining antibody titers postvaccination pose challenges for sustained protection and herd immunity. Although gut microbiome is reported to affect the early antibody response after vaccination, its impact on the longevity of vaccine-induced antibodies remains unexplored.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>A prospective cohort study was conducted involving 44 healthy adults who received two doses of either the BNT162b2 or ChAdOx1 vaccine, followed by a BNT162b2 booster at six months. The gut microbiome was serially analyzed using 16S rRNA and shotgun sequencing, while humoral immune response was assessed using a SARS-CoV-2 spike protein immunoassay.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p><jats:italic>Faecalibacterium prausnitzii<\/jats:italic> was associated with robust and persistent antibody responses post-BNT162b2 vaccination. In comparison, <jats:italic>Escherichia coli<\/jats:italic> was associated with a slower antibody decay following ChAdOx1 vaccination. The booster immune response was correlated with metabolic pathways involving cellular functions and aromatic amino acid synthesis.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The findings of this study underscored the potential interaction between the gut microbiome and the longevity\/boosting effect of antibodies following vaccination against SARS-CoV-2. The identification of specific microbial associations suggests the prospect of microbiome-based strategies for enhancing vaccine efficacy.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12967-024-05637-2","type":"journal-article","created":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T17:02:16Z","timestamp":1725642136000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["The gut microbiota modifies antibody durability and booster responses after SARS-CoV-2 vaccination"],"prefix":"10.1186","volume":"22","author":[{"given":"Hye","family":"Seong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin Gu","family":"Yoon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eliel","family":"Nham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu Jung","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji Yun","family":"Noh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hee Jin","family":"Cheong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Woo Joo","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eui Ho","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chulwoo","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Young-Hee","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sooyeon","family":"Lim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0148-7194","authenticated-orcid":false,"given":"Joon Young","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,9,6]]},"reference":[{"key":"5637_CR1","doi-asserted-by":"publisher","first-page":"2439","DOI":"10.1056\/NEJMoa2027906","volume":"383","author":"EE Walsh","year":"2020","unstructured":"Walsh EE, Frenck RW Jr, Falsey AR, Kitchin N, Absalon J, Gurtman A, Lockhart S, Neuzil K, Mulligan MJ, Bailey R, et al. Safety and immunogenicity of two RNA-based COVID-19 vaccine candidates. N Engl J Med. 2020;383:2439\u201350.","journal-title":"N Engl J Med"},{"key":"5637_CR2","doi-asserted-by":"publisher","DOI":"10.1016\/j.eclinm.2023.102140","volume":"64","author":"JY Song","year":"2023","unstructured":"Song JY, Choi WS, Heo JY, Kim EJ, Lee JS, Jung DS, Kim SW, Park KH, Eom JS, Jeong SJ, et al. Immunogenicity and safety of SARS-CoV-2 recombinant protein nanoparticle vaccine GBP510 adjuvanted with AS03: interim results of a randomised, active-controlled, observer-blinded, phase 3 trial. EClinicalMedicine. 2023;64: 102140.","journal-title":"EClinicalMedicine"},{"key":"5637_CR3","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1016\/S1473-3099(20)30987-7","volume":"21","author":"Z Wu","year":"2021","unstructured":"Wu Z, Hu Y, Xu M, Chen Z, Yang W, Jiang Z, Li M, Jin H, Cui G, Chen P, et al. Safety, tolerability, and immunogenicity of an inactivated SARS-CoV-2 vaccine (CoronaVac) in healthy adults aged 60 years and older: a randomised, double-blind, placebo-controlled, phase 1\/2 clinical trial. Lancet Infect Dis. 2021;21:803\u201312.","journal-title":"Lancet Infect Dis"},{"key":"5637_CR4","doi-asserted-by":"publisher","first-page":"1979","DOI":"10.1016\/S0140-6736(20)32466-1","volume":"396","author":"MN Ramasamy","year":"2021","unstructured":"Ramasamy MN, Minassian AM, Ewer KJ, Flaxman AL, Folegatti PM, Owens DR, Voysey M, Aley PK, Angus B, Babbage G, et al. Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2\/3 trial. Lancet. 2021;396:1979\u201393.","journal-title":"Lancet"},{"key":"5637_CR5","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41467-022-28527-x","volume":"13","author":"H Ward","year":"2022","unstructured":"Ward H, Whitaker M, Flower B, Tang SN, Atchison C, Darzi A, Donnelly CA, Cann A, Diggle PJ, Ashby D, et al. Population antibody responses following COVID-19 vaccination in 212,102 individuals. Nat Commun. 2022;13:907.","journal-title":"Nat Commun"},{"key":"5637_CR6","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1111\/j.1600-065X.2010.00938.x","volume":"237","author":"T Yoshida","year":"2010","unstructured":"Yoshida T, Mei H, D\u00f6rner T, Hiepe F, Radbruch A, Fillatreau S, Hoyer BF. Memory B and memory plasma cells. Immunol Rev. 2010;237:117\u201339.","journal-title":"Immunol Rev"},{"key":"5637_CR7","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1038\/40540","volume":"388","author":"RA Manz","year":"1997","unstructured":"Manz RA, Thiel A, Radbruch A. Lifetime of plasma cells in the bone marrow. Nature. 1997;388:133\u20134.","journal-title":"Nature"},{"key":"5637_CR8","doi-asserted-by":"publisher","first-page":"2138","DOI":"10.3389\/fimmu.2019.02138","volume":"10","author":"DC Nguyen","year":"2019","unstructured":"Nguyen DC, Joyner CJ, Sanz I, Lee FE. Factors affecting early antibody secreting cell maturation into long-lived plasma cells. Front Immunol. 2019;10:2138.","journal-title":"Front Immunol"},{"issue":"374","key":"5637_CR9","first-page":"abm0829","volume":"2021","author":"RR Goel","year":"1979","unstructured":"Goel RR, Painter MM, Apostolidis SA, Mathew D, Meng W, Rosenfeld AM, Lundgreen KA, Reynaldi A, Khoury DS, Pattekar A, et al. mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science. 1979;2021(374):abm0829.","journal-title":"Science"},{"key":"5637_CR10","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1016\/j.chom.2022.01.003","volume":"30","author":"S Terreri","year":"2022","unstructured":"Terreri S, Piano Mortari E, Vinci MR, Russo C, Alteri C, Albano C, Colavita F, Gramigna G, Agrati C, Linardos G, et al. Persistent B cell memory after SARS-CoV-2 vaccination is functional during breakthrough infections. Cell Host Microbe. 2022;30:400-408.e404.","journal-title":"Cell Host Microbe"},{"key":"5637_CR11","doi-asserted-by":"publisher","first-page":"20140144","DOI":"10.1098\/rstb.2014.0144","volume":"370","author":"I Praharaj","year":"2015","unstructured":"Praharaj I, John SM, Bandyopadhyay R, Kang G. Probiotics, antibiotics and the immune responses to vaccines. Philos Trans R Soc Lond B Biol Sci. 2015;370:20140144.","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"5637_CR12","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-021-00554-7","author":"DJ Lynn","year":"2021","unstructured":"Lynn DJ, Benson SC, Lynn MA, Pulendran B. Modulation of immune responses to vaccination by the microbiota: implications and potential mechanisms. Nat Rev Immunol. 2021. https:\/\/doi.org\/10.1038\/s41577-021-00554-7.","journal-title":"Nat Rev Immunol"},{"key":"5637_CR13","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.3389\/fimmu.2018.02640","volume":"9","author":"S Hanada","year":"2018","unstructured":"Hanada S, Pirzadeh M, Carver KY, Deng JC. Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. Front Immunol. 2018;9:2640.","journal-title":"Front Immunol"},{"key":"5637_CR14","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1038\/s41422-020-0332-7","volume":"30","author":"D Zheng","year":"2020","unstructured":"Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res. 2020;30:492\u2013506.","journal-title":"Cell Res"},{"key":"5637_CR15","doi-asserted-by":"publisher","first-page":"844335","DOI":"10.3389\/fimmu.2022.844335","volume":"13","author":"Y Li","year":"2022","unstructured":"Li Y, Ye Z, Zhu J, Fang S, Meng L, Zhou C. Effects of gut microbiota on host adaptive immunity under immune homeostasis and tumor pathology state. Front Immunol. 2022;13:844335.","journal-title":"Front Immunol"},{"key":"5637_CR16","doi-asserted-by":"publisher","first-page":"1587","DOI":"10.3390\/microorganisms8101587","volume":"8","author":"JY Yoo","year":"2020","unstructured":"Yoo JY, Groer M, Dutra SVO, Sarkar A, McSkimming DI. Gut microbiota and immune system interactions. Microorganisms. 2020;8:1587.","journal-title":"Microorganisms"},{"key":"5637_CR17","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.cell.2014.03.011","volume":"157","author":"Y Belkaid","year":"2014","unstructured":"Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157:121\u201341.","journal-title":"Cell"},{"key":"5637_CR18","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1136\/gutjnl-2021-326563","volume":"71","author":"SC Ng","year":"2022","unstructured":"Ng SC, Peng Y, Zhang L, Mok CK, Zhao S, Li A, Ching JY, Liu Y, Yan S, Chan DLS, et al. Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events. Gut. 2022;71:1106\u201316.","journal-title":"Gut"},{"key":"5637_CR19","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1038\/s41392-023-01445-0","volume":"8","author":"H Seong","year":"2023","unstructured":"Seong H, Choi BK, Han YH, Kim JH, Gim JA, Lim S, Noh JY, Cheong HJ, Kim WJ, Song JY. Gut microbiota as a potential key to modulating humoral immunogenicity of new platform COVID-19 vaccines. Signal Transduct Target Ther. 2023;8:178.","journal-title":"Signal Transduct Target Ther"},{"key":"5637_CR20","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2022.104430","volume":"88","author":"JL Alexander","year":"2023","unstructured":"Alexander JL, Mullish BH, Danckert NP, Liu Z, Olbei ML, Saifuddin A, Torkizadeh M, Ibraheim H, Blanco JM, Roberts LA, et al. The gut microbiota and metabolome are associated with diminished COVID-19 vaccine-induced antibody responses in immunosuppressed inflammatory bowel disease patients. EBioMedicine. 2023;88: 104430.","journal-title":"EBioMedicine"},{"key":"5637_CR21","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1080\/01621459.1992.10475194","volume":"87","author":"A Chao","year":"1992","unstructured":"Chao A, Lee S-M. Estimating the number of classes via sample coverage. J Am Stat Assoc. 1992;87:210\u20137.","journal-title":"J Am Stat Assoc"},{"key":"5637_CR22","doi-asserted-by":"publisher","first-page":"783","DOI":"10.2307\/2531532","volume":"43","author":"A Chao","year":"1987","unstructured":"Chao A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics. 1987;43:783\u201391.","journal-title":"Biometrics"},{"key":"5637_CR23","doi-asserted-by":"publisher","first-page":"927","DOI":"10.2307\/1936861","volume":"60","author":"KP Burnham","year":"1979","unstructured":"Burnham KP, Overton WS. Robust estimation of population size when capture probabilities vary among animals. Ecology. 1979;60:927\u201336.","journal-title":"Ecology"},{"key":"5637_CR24","volume-title":"Measuring biological diversity","author":"AE Magurran","year":"2013","unstructured":"Magurran AE. Measuring biological diversity. Hoboken: Wiley; 2013."},{"key":"5637_CR25","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1023\/A:1026096204727","volume":"10","author":"A Chao","year":"2003","unstructured":"Chao A, Shen T-J. Nonparametric estimation of Shannon\u2019s index of diversity when there are unseen species in sample. Environ Ecol Stat. 2003;10:429\u201343.","journal-title":"Environ Ecol Stat"},{"key":"5637_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0006-3207(92)91201-3","volume":"61","author":"DP Faith","year":"1992","unstructured":"Faith DP. Conservation evaluation and phylogenetic diversity. Biol Cons. 1992;61:1\u201310.","journal-title":"Biol Cons"},{"key":"5637_CR27","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1109\/18.61115","volume":"37","author":"J Lin","year":"1991","unstructured":"Lin J. Divergence measures based on the Shannon entropy. IEEE Trans Inf Theory. 1991;37:145\u201351.","journal-title":"IEEE Trans Inf Theory"},{"key":"5637_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0065-2504(08)60168-3","volume":"14","author":"EW Beals","year":"1984","unstructured":"Beals EW. Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data. Adv Ecol Res. 1984;14:1\u201355.","journal-title":"Adv Ecol Res"},{"key":"5637_CR29","doi-asserted-by":"publisher","first-page":"2106","DOI":"10.1093\/bioinformatics\/bts342","volume":"28","author":"J Chen","year":"2012","unstructured":"Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics. 2012;28:2106\u201313.","journal-title":"Bioinformatics"},{"key":"5637_CR30","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1038\/ismej.2009.97","volume":"4","author":"M Hamady","year":"2010","unstructured":"Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010;4:17\u201327.","journal-title":"ISME J"},{"key":"5637_CR31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2011-12-6-r60","volume":"12","author":"N Segata","year":"2011","unstructured":"Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:1\u201318.","journal-title":"Genome Biol"},{"key":"5637_CR32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000465","volume":"5","author":"Y Ye","year":"2009","unstructured":"Ye Y, Doak TG. A parsimony approach to biological pathway reconstruction\/inference for genomes and metagenomes. PLoS Comput Biol. 2009;5: e1000465.","journal-title":"PLoS Comput Biol"},{"key":"5637_CR33","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1038\/nbt.2676","volume":"31","author":"MG Langille","year":"2013","unstructured":"Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814\u201321.","journal-title":"Nat Biotechnol"},{"key":"5637_CR34","first-page":"11","volume":"4","author":"EW Myers","year":"1988","unstructured":"Myers EW, Miller W. Optimal alignments in linear space. Comput Appl Biosci. 1988;4:11\u20137.","journal-title":"Comput Appl Biosci"},{"key":"5637_CR35","doi-asserted-by":"publisher","first-page":"2487","DOI":"10.1093\/bioinformatics\/btt403","volume":"29","author":"TJ Wheeler","year":"2013","unstructured":"Wheeler TJ, Eddy SR. nhmmer: DNA homology search with profile HMMs. Bioinformatics. 2013;29:2487\u20139.","journal-title":"Bioinformatics"},{"key":"5637_CR36","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2584","volume":"4","author":"T Rognes","year":"2016","unstructured":"Rognes T, Flouri T, Nichols B, Quince C, Mah\u00e9 F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4: e2584.","journal-title":"PeerJ"},{"key":"5637_CR37","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","volume":"67","author":"SH Yoon","year":"2017","unstructured":"Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613\u20137.","journal-title":"Int J Syst Evol Microbiol"},{"key":"5637_CR38","doi-asserted-by":"publisher","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","volume":"27","author":"RC Edgar","year":"2011","unstructured":"Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194\u2013200.","journal-title":"Bioinformatics"},{"key":"5637_CR39","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20:257.","journal-title":"Genome Biol"},{"key":"5637_CR40","doi-asserted-by":"publisher","first-page":"204","DOI":"10.3390\/pathogens9030204","volume":"9","author":"M Chalita","year":"2020","unstructured":"Chalita M, Ha SM, Kim YO, Oh HS, Yoon SH, Chun J. Improved metagenomic taxonomic profiling using a curated core gene-based bacterial database reveals unrecognized species in the genus Streptococcus. Pathogens. 2020;9:204.","journal-title":"Pathogens"},{"key":"5637_CR41","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357\u20139.","journal-title":"Nat Methods"},{"key":"5637_CR42","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009;25:2078\u20139.","journal-title":"Bioinformatics"},{"key":"5637_CR43","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841\u20132.","journal-title":"Bioinformatics"},{"key":"5637_CR44","first-page":"32","volume":"26","author":"MJ Anderson","year":"2001","unstructured":"Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32\u201346.","journal-title":"Austral Ecol"},{"key":"5637_CR45","doi-asserted-by":"publisher","first-page":"e65088","DOI":"10.7554\/eLife.65088","volume":"10","author":"F Beghini","year":"2021","unstructured":"Beghini F, McIver LJ, Blanco-M\u00edguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife. 2021;10:e65088.","journal-title":"eLife"},{"key":"5637_CR46","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1016\/j.cell.2015.07.037","volume":"162","author":"E Arias-Palomo","year":"2015","unstructured":"Arias-Palomo E, Berger JM. An atypical AAA+ ATPase assembly controls efficient transposition through DNA remodeling and transposase recruitment. Cell. 2015;162:860\u201371.","journal-title":"Cell"},{"key":"5637_CR47","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1016\/j.chom.2016.07.001","volume":"20","author":"M Kim","year":"2016","unstructured":"Kim M, Qie Y, Park J, Kim CH. Gut microbial metabolites fuel host antibody responses. Cell Host Microbe. 2016;20:202\u201314.","journal-title":"Cell Host Microbe"},{"key":"5637_CR48","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1038\/nature12721","volume":"504","author":"Y Furusawa","year":"2013","unstructured":"Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, Nakanishi Y, Uetake C, Kato K, Kato T, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 2013;504:446\u201350.","journal-title":"Nature"},{"key":"5637_CR49","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1126\/science.1241165","volume":"341","author":"PM Smith","year":"2013","unstructured":"Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly YM, Glickman JN, Garrett WS. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science. 2013;341:569\u201373.","journal-title":"Science"},{"key":"5637_CR50","doi-asserted-by":"publisher","first-page":"1536","DOI":"10.3389\/fimmu.2018.01536","volume":"9","author":"MM Xie","year":"2018","unstructured":"Xie MM, Dent AL. Unexpected help: follicular regulatory T cells in the germinal center. Front Immunol. 2018;9:1536.","journal-title":"Front Immunol"},{"issue":"323","key":"5637_CR51","first-page":"1488","volume":"2009","author":"M Tsuji","year":"1979","unstructured":"Tsuji M, Komatsu N, Kawamoto S, Suzuki K, Kanagawa O, Honjo T, Hori S, Fagarasan S. Preferential generation of follicular B helper T cells from Foxp3+ T cells in gut Peyer\u2019s patches. Science. 1979;2009(323):1488\u201392.","journal-title":"Science"},{"key":"5637_CR52","doi-asserted-by":"publisher","first-page":"3626","DOI":"10.4049\/jimmunol.1302062","volume":"192","author":"A Caro-Maldonado","year":"2014","unstructured":"Caro-Maldonado A, Wang R, Nichols AG, Kuraoka M, Milasta S, Sun LD, Gavin AL, Abel ED, Kelsoe G, Green DR, Rathmell JC. Metabolic reprogramming is required for antibody production that is suppressed in anergic but exaggerated in chronically BAFF-exposed B cells. J Immunol. 2014;192:3626\u201336.","journal-title":"J Immunol"},{"key":"5637_CR53","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1053\/j.gastro.2013.04.056","volume":"145","author":"MH Kim","year":"2013","unstructured":"Kim MH, Kang SG, Park JH, Yanagisawa M, Kim CH. Short-chain fatty acids activate GPR41 and GPR43 on intestinal epithelial cells to promote inflammatory responses in mice. Gastroenterology. 2013;145:396-406.e391-310.","journal-title":"Gastroenterology."},{"key":"5637_CR54","doi-asserted-by":"publisher","first-page":"25481","DOI":"10.1074\/jbc.M301403200","volume":"278","author":"E Le Poul","year":"2003","unstructured":"Le Poul E, Loison C, Struyf S, Springael JY, Lannoy V, Decobecq ME, Brezillon S, Dupriez V, Vassart G, Van Damme J, et al. Functional characterization of human receptors for short chain fatty acids and their role in polymorphonuclear cell activation. J Biol Chem. 2003;278:25481\u20139.","journal-title":"J Biol Chem"},{"key":"5637_CR55","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1038\/mi.2014.44","volume":"8","author":"J Park","year":"2015","unstructured":"Park J, Kim M, Kang SG, Jannasch AH, Cooper B, Patterson J, Kim CH. Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR-S6K pathway. Mucosal Immunol. 2015;8:80\u201393.","journal-title":"Mucosal Immunol"},{"key":"5637_CR56","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1574-6968.2009.01514.x","volume":"294","author":"P Louis","year":"2009","unstructured":"Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett. 2009;294:1\u20138.","journal-title":"FEMS Microbiol Lett"},{"key":"5637_CR57","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.3390\/ijms23031105","volume":"23","author":"P Portincasa","year":"2022","unstructured":"Portincasa P, Bonfrate L, Vacca M, De Angelis M, Farella I, Lanza E, Khalil M, Wang DQ, Sperandio M, Di Ciaula A. Gut microbiota and short chain fatty acids: implications in glucose homeostasis. Int J Mol Sci. 2022;23:1105.","journal-title":"Int J Mol Sci"},{"key":"5637_CR58","doi-asserted-by":"publisher","first-page":"143","DOI":"10.3389\/fimmu.2019.00143","volume":"10","author":"J Alameddine","year":"2019","unstructured":"Alameddine J, Godefroy E, Papargyris L, Sarrabayrouse G, Tabiasco J, Bridonneau C, Yazdanbakhsh K, Sokol H, Altare F, Jotereau F. Faecalibacterium prausnitzii skews human DC to prime IL10-producing T cells through TLR2\/6\/JNK signaling and IL-10, IL-27, CD39, and IDO-1 induction. Front Immunol. 2019;10:143.","journal-title":"Front Immunol"},{"key":"5637_CR59","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1146\/annurev.immunol.25.022106.141623","volume":"30","author":"SZ Josefowicz","year":"2012","unstructured":"Josefowicz SZ, Lu LF, Rudensky AY. Regulatory T cells: mechanisms of differentiation and function. Annu Rev Immunol. 2012;30:531\u201364.","journal-title":"Annu Rev Immunol"},{"key":"5637_CR60","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/j.mib.2013.06.003","volume":"16","author":"S Miquel","year":"2013","unstructured":"Miquel S, Mart\u00edn R, Rossi O, Berm\u00fadez-Humar\u00e1n LG, Chatel JM, Sokol H, Thomas M, Wells JM, Langella P. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol. 2013;16:255\u201361.","journal-title":"Curr Opin Microbiol"},{"key":"5637_CR61","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0227047","volume":"15","author":"E Valli","year":"2020","unstructured":"Valli E, Baudier RL, Harriett AJ, Norton EB. LTA1 and dmLT enterotoxin-based proteins activate antigen-presenting cells independent of PKA and despite distinct cell entry mechanisms. PLoS ONE. 2020;15: e0227047.","journal-title":"PLoS ONE"},{"key":"5637_CR62","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.canlet.2019.12.012","volume":"472","author":"Y Jeong","year":"2020","unstructured":"Jeong Y, Kim GB, Ji Y, Kwak GJ, Nam GH, Hong Y, Kim S, An J, Kim SH, Yang Y, et al. Dendritic cell activation by an E coli-derived monophosphoryl lipid A enhances the efficacy of PD-1 blockade. Cancer Lett. 2020;472:19\u201328.","journal-title":"Cancer Lett."},{"key":"5637_CR63","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1128\/IAI.00486-06","volume":"75","author":"S Fernandez","year":"2007","unstructured":"Fernandez S, Palmer DR, Simmons M, Sun P, Bisbing J, McClain S, Mani S, Burgess T, Gunther V, Sun W. Potential role for Toll-like receptor 4 in mediating Escherichia coli maltose-binding protein activation of dendritic cells. Infect Immun. 2007;75:1359\u201363.","journal-title":"Infect Immun"},{"key":"5637_CR64","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.612336","volume":"11","author":"L Michaelis","year":"2020","unstructured":"Michaelis L, Tre\u00df M, L\u00f6w HC, Klees J, Klameth C, Lange A, Grie\u00dfhammer A, Sch\u00e4fer A, Menz S, Steimle A, et al. Gut Commensal-induced I\u03baB\u03b6 expression in dendritic cells influences the Th17 response. Front Immunol. 2020;11: 612336.","journal-title":"Front Immunol"},{"key":"5637_CR65","doi-asserted-by":"publisher","first-page":"2899","DOI":"10.1128\/JVI.76.6.2899-2911.2002","volume":"76","author":"S Mercier","year":"2002","unstructured":"Mercier S, Gah\u00e9ry-Segard H, Monteil M, Lengagne R, Guillet JG, Eloit M, Denesvre C. Distinct roles of adenovirus vector-transduced dendritic cells, myoblasts, and endothelial cells in mediating an immune response against a transgene product. J Virol. 2002;76:2899\u2013911.","journal-title":"J Virol"},{"key":"5637_CR66","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1016\/j.fshw.2022.04.002","volume":"11","author":"J Cheng","year":"2022","unstructured":"Cheng J, Hu J, Geng F, Nie S. Bacteroides utilization for dietary polysaccharides and their beneficial effects on gut health. Food Sci Human Wellness. 2022;11:1101\u201310.","journal-title":"Food Sci Human Wellness"},{"key":"5637_CR67","doi-asserted-by":"publisher","first-page":"680","DOI":"10.1016\/j.chom.2019.10.013","volume":"26","author":"H Fehlner-Peach","year":"2019","unstructured":"Fehlner-Peach H, Magnabosco C, Raghavan V, Scher JU, Tett A, Cox LM, Gottsegen C, Watters A, Wiltshire-Gordon JD, Segata N, et al. Distinct polysaccharide utilization profiles of human intestinal prevotella copri isolates. Cell Host Microbe. 2019;26:680-690.e685.","journal-title":"Cell Host Microbe"},{"key":"5637_CR68","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/nature12726","volume":"504","author":"N Arpaia","year":"2013","unstructured":"Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, deRoos P, Liu H, Cross JR, Pfeffer K, Coffer PJ, Rudensky AY. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504:451\u20135.","journal-title":"Nature"},{"key":"5637_CR69","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1016\/j.immuni.2014.10.004","volume":"41","author":"S Crotty","year":"2014","unstructured":"Crotty S. T follicular helper cell differentiation, function, and roles in disease. Immunity. 2014;41:529\u201342.","journal-title":"Immunity"},{"key":"5637_CR70","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a037770","volume":"13","author":"JL Raynor","year":"2021","unstructured":"Raynor JL, Chapman NM, Chi H. Metabolic control of memory T-cell generation and stemness. Cold Spring Harb Perspect Biol. 2021;13: a037770.","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"5637_CR71","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1006\/mben.2001.0203","volume":"4","author":"G Galili","year":"2002","unstructured":"Galili G, H\u00f6fgen R. Metabolic engineering of amino acids and storage proteins in plants. Metab Eng. 2002;4:3\u201311.","journal-title":"Metab Eng"},{"issue":"244","key":"5637_CR72","first-page":"174","volume":"1989","author":"PN Benfey","year":"1979","unstructured":"Benfey PN, Chua NH. Regulated genes in transgenic plants. Science. 1979;1989(244):174\u201381.","journal-title":"Science"},{"key":"5637_CR73","doi-asserted-by":"publisher","first-page":"4042","DOI":"10.1074\/jbc.M512223200","volume":"281","author":"J Wu","year":"2006","unstructured":"Wu J, Woodard RW. New insights into the evolutionary links relating to the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase subfamilies. J Biol Chem. 2006;281:4042\u20138.","journal-title":"J Biol Chem"},{"key":"5637_CR74","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1186\/s12985-021-01649-2","volume":"18","author":"S Kavil","year":"2021","unstructured":"Kavil S, Otti G, Bouvaine S, Armitage A, Maruthi MN. PAL1 gene of the phenylpropanoid pathway increases resistance to the Cassava brown streak virus in cassava. Virol J. 2021;18:184.","journal-title":"Virol J"},{"key":"5637_CR75","doi-asserted-by":"publisher","first-page":"3166","DOI":"10.1073\/pnas.92.8.3166","volume":"92","author":"J G\u00f6rlach","year":"1995","unstructured":"G\u00f6rlach J, Raesecke HR, Rentsch D, Regenass M, Roy P, Zala M, Keel C, Boller T, Amrhein N, Schmid J. Temporally distinct accumulation of transcripts encoding enzymes of the prechorismate pathway in elicitor-treated, cultured tomato cells. Proc Natl Acad Sci USA. 1995;92:3166\u201370.","journal-title":"Proc Natl Acad Sci USA"},{"key":"5637_CR76","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/S1521-6616(03)00204-3","volume":"109","author":"S Pradhan","year":"2003","unstructured":"Pradhan S, Esteve PO. Mammalian DNA (cytosine-5) methyltransferases and their expression. Clin Immunol. 2003;109:6\u201316.","journal-title":"Clin Immunol"},{"key":"5637_CR77","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/s41541-023-00627-9","volume":"8","author":"P Zimmermann","year":"2023","unstructured":"Zimmermann P. The immunological interplay between vaccination and the intestinal microbiota. Npj Vaccines. 2023;8:24.","journal-title":"Npj Vaccines"},{"key":"5637_CR78","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1016\/j.chom.2020.06.014","volume":"28","author":"SE de Jong","year":"2020","unstructured":"de Jong SE, Olin A, Pulendran B. The impact of the microbiome on immunity to vaccination in humans. Cell Host Microbe. 2020;28:169\u201379.","journal-title":"Cell Host Microbe"},{"key":"5637_CR79","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.immuni.2014.08.009","volume":"41","author":"JZ Oh","year":"2014","unstructured":"Oh JZ, Ravindran R, Chassaing B, Carvalho FA, Maddur MS, Bower M, Hakimpour P, Gill KP, Nakaya HI, Yarovinsky F, et al. TLR5-mediated sensing of gut microbiota is necessary for antibody responses to seasonal influenza vaccination. Immunity. 2014;41:478\u201392.","journal-title":"Immunity"},{"key":"5637_CR80","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1093\/infdis\/jiw518","volume":"215","author":"VC Harris","year":"2017","unstructured":"Harris VC, Armah G, Fuentes S, Korpela KE, Parashar U, Victor JC, Tate J, de Weerth C, Giaquinto C, Wiersinga WJ, et al. Significant correlation between the infant gut microbiome and rotavirus vaccine response in rural Ghana. J Infect Dis. 2017;215:34\u201341.","journal-title":"J Infect Dis"}],"container-title":["Journal of Translational Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12967-024-05637-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12967-024-05637-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12967-024-05637-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T18:04:10Z","timestamp":1725645850000},"score":1,"resource":{"primary":{"URL":"https:\/\/translational-medicine.biomedcentral.com\/articles\/10.1186\/s12967-024-05637-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,6]]},"references-count":80,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["5637"],"URL":"https:\/\/doi.org\/10.1186\/s12967-024-05637-2","relation":{},"ISSN":["1479-5876"],"issn-type":[{"value":"1479-5876","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,6]]},"assertion":[{"value":"3 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 August 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 September 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"827"}}