{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T11:33:55Z","timestamp":1769513635101,"version":"3.49.0"},"reference-count":54,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,10,28]],"date-time":"2022-10-28T00:00:00Z","timestamp":1666915200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>After the eradication of polio infection, the plan is to phase-out the live-attenuated oral polio vaccine (OPV). Considering the protective non-specific effects (NSE) of OPV on unrelated pathogens, the withdrawal may impact child health negatively. Within a cluster-randomized trial, we carried out 16S rRNA deep sequencing analysis of fecal and nasopharyngeal microbial content of Bissau\u2013Guinean infants aged 4\u20138 months, before and after 2 months of OPV revaccination (revaccinated infants = 47) vs. no OPV revaccination (control infants = 47). The aim was to address changes in the gut and upper respiratory bacterial microbiotas due to revaccination. Alpha-diversity for both microbiotas increased similarly over time in OPV-revaccinated infants and controls, whereas greater changes over time in the bacterial composition of gut (<jats:italic>p<jats:sub><jats:italic>adjusted<\/jats:italic><\/jats:sub><\/jats:italic> &amp;lt; 0.001) and upper respiratory microbiotas (<jats:italic>p<jats:sub><jats:italic>adjusted<\/jats:italic><\/jats:sub><\/jats:italic> = 0.018) were observed in the former. Taxonomic analysis of gut bacterial microbiota revealed a decrease over time in the median proportion of <jats:italic>Bifidobacterium longum<\/jats:italic> for all infants (25\u201314.3%, <jats:italic>p<\/jats:italic> = 0.0006 in OPV-revaccinated infants and 25.3\u201311.6%, <jats:italic>p<\/jats:italic> = 0.01 in controls), compatible with the reported weaning. Also, it showed a restricted increase in the median proportion of <jats:italic>Prevotella<\/jats:italic>_9 genus in controls (1.4\u20137.1%, <jats:italic>p<\/jats:italic> = 0.02), whereas in OPV revaccinated infants an increase over time in Prevotellaceae family (7.2\u201317.4%, <jats:italic>p<\/jats:italic> = 0.005) together with a reduction in median proportion of potentially pathogenic\/opportunistic genera such as <jats:italic>Escherichia<\/jats:italic>\/<jats:italic>Shigella<\/jats:italic> (5.8\u20133.4%, <jats:italic>p<\/jats:italic> = 0.01) were observed. Taxonomic analysis of upper respiratory bacterial microbiota revealed an increase over time in median proportions of potentially pathogenic\/opportunistic genera in controls, such as <jats:italic>Streptococcus<\/jats:italic> (2.9\u201311.8%, <jats:italic>p<\/jats:italic> = 0.001 and <jats:italic>Hemophilus<\/jats:italic> (11.3\u201320.5%, <jats:italic>p<\/jats:italic> = 0.03), not observed in OPV revaccinated infants. In conclusion, OPV revaccination was associated with a healthier microbiome composition 2 months after revaccination, based on a more abundant and diversified bacterial community of Prevotellaceae and fewer pathogenic\/opportunistic organisms. Further information on species-level differentiation and functional analysis of microbiome content are warranted to elucidate the impact of OPV-associated changes in bacterial microbiota on child health.<\/jats:p>","DOI":"10.3389\/fmicb.2022.1016220","type":"journal-article","created":{"date-parts":[[2022,10,28]],"date-time":"2022-10-28T05:21:46Z","timestamp":1666934506000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Oral polio revaccination is associated with changes in gut and upper respiratory microbiomes of infants"],"prefix":"10.3389","volume":"13","author":[{"given":"M\u00e1rcia Melo","family":"Medeiros","sequence":"first","affiliation":[]},{"given":"Anna C\u00e4cilia","family":"Ingham","sequence":"additional","affiliation":[]},{"given":"Line M\u00f8ller","family":"Nanque","sequence":"additional","affiliation":[]},{"given":"Claudino","family":"Correia","sequence":"additional","affiliation":[]},{"given":"Marc","family":"Stegger","sequence":"additional","affiliation":[]},{"given":"Paal Skyt","family":"Andersen","sequence":"additional","affiliation":[]},{"given":"Ane Baerent","family":"Fisker","sequence":"additional","affiliation":[]},{"given":"Christine Stabell","family":"Benn","sequence":"additional","affiliation":[]},{"given":"Miguel","family":"Lanaspa","sequence":"additional","affiliation":[]},{"given":"Henrique","family":"Silveira","sequence":"additional","affiliation":[]},{"given":"Patr\u00edcia","family":"Abrantes","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2022,10,28]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1016\/S1473-3099(20)30714-3","article-title":"BCG: New life for a centenarian vaccine.","volume":"21","author":"Aaby","year":"2021","journal-title":"Lancet Infect. Dis."},{"key":"B2","doi-asserted-by":"crossref","DOI":"10.1136\/bmj.c6495","article-title":"Non-specific effects of standard measles vaccine at 4.5 and 9 months of age on childhood mortality: Randomised controlled trial.","volume":"341","author":"Aaby","year":"2010","journal-title":"BMJ"},{"key":"B3","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.vaccine.2014.10.075","article-title":"On birth single dose live attenuated OPV and BCG vaccination induces gut cathelicidin LL37 responses at 6 week of age: A natural experiment.","volume":"33","author":"Alam","year":"2015","journal-title":"Vaccine"},{"key":"B4","doi-asserted-by":"publisher","first-page":"e596","DOI":"10.1093\/cid\/ciaa1351","article-title":"National immunization campaigns with oral polio vaccine may reduce all-cause mortality: An analysis of 13 years of demographic surveillance data from an Urban African Area.","volume":"72","author":"Andersen","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2018.00013","article-title":"National immunization campaigns with oral polio vaccine reduce all-cause mortality: A natural experiment within seven randomized trials.","volume":"6","author":"Andersen","year":"2018","journal-title":"Front. Public Health"},{"key":"B6","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.cell.2014.03.011","article-title":"Role of the microbiota in immunity and inflammation.","volume":"157","author":"Belkaid","year":"2014","journal-title":"Cell"},{"key":"B7","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1093\/cid\/cix525","article-title":"Early BCG-Denmark and Neonatal Mortality among Infants Weighing <2500 g: A randomized controlled trial.","volume":"65","author":"Biering-S\u00f8rensen","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"B8","author":"Callahan","year":"2018","journal-title":"Silva taxonomic training data formatted for DADA2 (Silva version 132)."},{"key":"B9","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data.","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"B10","author":"Cao","year":"2020","journal-title":"microbiomeMarker: Microbiome biomarker analysis. R package version 0.0.1.9000."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41385-021-00428-0","article-title":"Mucosal immunity to poliovirus.","volume":"15","author":"Connor","year":"2021","journal-title":"Mucosal Immunol."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.02441","article-title":"Potential role of gut microbiota in induction and regulation of innate immune memory.","volume":"10","author":"Danelishvili","year":"2019","journal-title":"Front. Immunol."},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"key":"B14","doi-asserted-by":"publisher","first-page":"14691","DOI":"10.1073\/pnas.1005963107","article-title":"Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and Rural Africa.","volume":"107","author":"De Filippo","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2021.103293","article-title":"Short chain fatty acids and its producing organisms: An overlooked therapy for IBD?","volume":"66","author":"Deleu","year":"2021","journal-title":"EBioMedicine"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0248924","article-title":"Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol.","volume":"16","author":"Dizzell","year":"2021","journal-title":"PLoS One"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofac470","article-title":"Oral Polio Vaccine (OPV) to mitigate the risk of illness and mortality during the COVID-19 pandemic: A cluster-randomised trial in Guinea-Bissau.","volume":"9","author":"Fisker","year":"2022","journal-title":"Open Forum Infect. Dis."},{"key":"B18","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1017\/S0029665114001463","article-title":"Links between diet, gut microbiota composition and gut metabolism.","volume":"74","author":"Flint","year":"2014","journal-title":"Proc. Nutr. Soc."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005404","article-title":"Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.","volume":"13","author":"Foster","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1016\/S1473-3099(16)30023-8","article-title":"The effect of azithromycin on the immunogenicity of oral poliovirus vaccine: A double-blind randomised placebo-controlled trial in seronegative Indian infants.","volume":"16","author":"Grassly","year":"2016","journal-title":"Lancet Infect. Dis."},{"key":"B21","article-title":"Association of BCG, DTP, and measles containing vaccines with childhood mortality: Systematic review.","volume":"355","author":"Higgins","year":"2016","journal-title":"BMJ"},{"key":"B22","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1097\/MPG.0000000000000597","article-title":"Why is initial bacterial colonization of the intestine important to infants\u2019 and children\u2019s health?","volume":"60","author":"Houghteling","year":"2015","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"B23","doi-asserted-by":"crossref","first-page":"e362","DOI":"10.1542\/peds.2013-3937","article-title":"Stool microbiota and vaccine responses of infants.","volume":"134","author":"Huda","year":"2014","journal-title":"Pediatrics"},{"key":"B24","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/B978-0-12-810541-2.00003-8","article-title":"Chapter 3\u2013Gut microbiota throughout the lifespan","author":"Ishiguro","year":"2018","journal-title":"Gut microbiota"},{"key":"B25","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1159\/000355628","article-title":"Long-lasting effects of BCG vaccination on both heterologous th1\/th17 responses and innate trained immunity.","volume":"6","author":"Kleinnijenhuis","year":"2014","journal-title":"J. Innate Immun."},{"key":"B26","doi-asserted-by":"publisher","first-page":"17537","DOI":"10.1073\/pnas.1202870109","article-title":"Bacille Calmette-Gu\u00e9rin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes.","volume":"109","author":"Kleinnijenhuis","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.","volume":"41","author":"Klindworth","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B28","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1080\/14787210.2017.1349609","article-title":"Respiratory microbiota and lower respiratory tract disease.","volume":"15","author":"Lanaspa","year":"2017","journal-title":"Expert Rev. Anti Infect. Ther."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.00361","article-title":"Mother\u2019s milk: A purposeful contribution to the development of the infant microbiota and immunity.","volume":"9","author":"Le Doare","year":"2018","journal-title":"Front. Immunol."},{"key":"B30","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1093\/cid\/civ617","article-title":"The Effect of oral polio vaccine at birth on infant mortality: A randomized trial.","volume":"61","author":"Lund","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"B31","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads.","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data.","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"B33","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/0092-8674(89)90690-9","article-title":"Cellular receptor for poliovirus: Molecular cloning, nucleotide sequence, and expression of a new member of the immunoglobulin superfamily.","volume":"56","author":"Mendelsohn","year":"1989","journal-title":"Cell"},{"key":"B34","doi-asserted-by":"crossref","DOI":"10.1098\/rsob.190128","article-title":"Temporal development of the infant gut microbiome.","volume":"9","author":"Moore","year":"2019","journal-title":"Open Biol."},{"key":"B35","first-page":"208","author":"Ewbank","year":"1993","journal-title":"Effects of health programs on child mortality in Sub-Saharan Africa"},{"key":"B36","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaf1098","article-title":"Trained immunity: A program of innate immune memory in health and disease.","volume":"352","author":"Netea","year":"2016","journal-title":"Science"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00925","article-title":"Bifidobacteria and their role as members of the human gut microbiota.","volume":"7","author":"O\u2019Callaghan","year":"2016","journal-title":"Front. Microbiol."},{"key":"B38","author":"Oksanen","year":"2019","journal-title":"vegan: Community ecology package. R package version 2.5-5."},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-27074-1","article-title":"Impact of maternal antibodies and microbiota development on the immunogenicity of oral rotavirus vaccine in African, Indian, and European infants.","volume":"12","author":"Parker","year":"2021","journal-title":"Nat. Commun."},{"key":"B40","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1016\/j.vaccine.2017.11.031","article-title":"Influence of the intestinal microbiota on the immunogenicity of oral rotavirus vaccine given to infants in south India.","volume":"36","author":"Parker","year":"2018","journal-title":"Vaccine"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-83641-y","article-title":"Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations.","volume":"11","author":"Pawlowski","year":"2021","journal-title":"Sci. Rep."},{"key":"B42","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1016\/S1473-3099(20)30653-8","article-title":"BCG-induced non-specific effects on heterologous infectious disease in Ugandan neonates: An investigator-blind randomised controlled trial.","volume":"21","author":"Prentice","year":"2021","journal-title":"Lancet Infect. Dis."},{"key":"B43","year":"2021","journal-title":"R: A language and environment for statistical computing."},{"key":"B44","doi-asserted-by":"publisher","first-page":"8615","DOI":"10.1016\/j.vaccine.2011.09.015","article-title":"Viral interference induced by live attenuated virus vaccine (OPV) can prevent otitis media.","volume":"29","author":"Sepp\u00e4l\u00e4","year":"2011","journal-title":"Vaccine"},{"key":"B45","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1136\/adc.2009.157537","article-title":"The non-specific effects of vaccines.","volume":"95","author":"Shann","year":"2010","journal-title":"Arch. Dis. Child."},{"key":"B46","year":"2019","journal-title":"Levels &amp; trends in child mortality: Report 2019, estimates developed by the United Nations Inter-agency Group for Child Mortality Estimation."},{"key":"B47","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1093\/cid\/cix354","article-title":"Nonspecific effects of oral polio vaccine on diarrheal burden and etiology among Bangladeshi infants.","volume":"65","author":"Upfill-brown","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"B48","doi-asserted-by":"crossref","DOI":"10.15406\/ijvv.2015.01.00004","article-title":"40th anniversary of introduction of expanded immunization program (EPI): A literature review of introduction of new vaccines for routine childhood immunization in Sub-Saharan Africa.","volume":"1","author":"Uwizihiwe","year":"2015","journal-title":"Int. J. Vaccines Vaccin."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1186\/s12889-019-7813-y","article-title":"Research protocol of two concurrent cluster-randomized trials: Real-life effect of a CAMPaign with measles vaccination (RECAMP-MV) and real-life effect of a CAMPaign with oral polio vaccination (RECAMP-OPV) on mortality and morbidity among children in rur.","volume":"19","author":"Varma","year":"2019","journal-title":"BMC Public Health"},{"key":"B50","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","author":"Wickham","year":"2016","journal-title":"ggplot2: Elegant graphics for data analysis."},{"key":"B51","year":"","journal-title":"Polio eradication strategy 2022\u20132026: Executive summary: Licence CC BY-NC-SA 3.0 IGO."},{"key":"B52","year":"","journal-title":"Immunization, vaccines and biologicals."},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.907341","article-title":"Vaccination with oral polio vaccine reduces COVID-19 incidence.","volume":"13","author":"Yagovkina","year":"2022","journal-title":"Front. Immunol."},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1038\/s41541-020-0194-5","article-title":"Influence of gut microbiota on mucosal IgA antibody response to the polio vaccine.","volume":"5","author":"Zhao","year":"2020","journal-title":"NPJ Vaccines"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.1016220\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,28]],"date-time":"2022-10-28T05:22:15Z","timestamp":1666934535000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.1016220\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,28]]},"references-count":54,"alternative-id":["10.3389\/fmicb.2022.1016220"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.1016220","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,10,28]]},"article-number":"1016220"}}