{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T03:04:06Z","timestamp":1792724646389,"version":"4.5.0"},"reference-count":98,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,9,11]],"date-time":"2021-09-11T00:00:00Z","timestamp":1631318400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"},{"start":{"date-parts":[[2021,9,11]],"date-time":"2021-09-11T00:00:00Z","timestamp":1631318400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2021,9,11]],"date-time":"2021-09-11T00:00:00Z","timestamp":1631318400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Streptococcus pneumoniae (pneumococcus) is a leading cause of severe infections among children and adults. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniae are poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniae colonization during infancy and to describe development of the upper respiratory microbiome during infancy in a sub-Saharan African setting. We collected nasopharyngeal swabs monthly (0\u20136 months of age) or bimonthly (6\u201312 months of age) from 179 mother\u2013infant dyads in Botswana. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and identified S. pneumoniae colonization using a species-specific PCR assay. We detect S. pneumoniae colonization in 144 (80%) infants at a median age of 71 days and identify a strong negative association between the relative abundance of the bacterial genera Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium species isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacterium relative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniae and suggest that the nasopharyngeal microbiome may be a previously unrecognized mechanism by which environmental factors influence the risk of pneumococcal infections during childhood. Moreover, this work lays the foundation for future studies seeking to use targeted manipulation of the nasopharyngeal microbiome to prevent infections caused by S. pneumoniae.<\/jats:p>","DOI":"10.1038\/s41396-021-01108-4","type":"journal-article","created":{"date-parts":[[2021,9,12]],"date-time":"2021-09-12T13:03:46Z","timestamp":1631451826000},"page":"655-665","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":38,"title":["Non-diphtheriae <i>Corynebacterium<\/i> species are associated with decreased risk of pneumococcal colonization during infancy"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8819-2315","authenticated-orcid":false,"given":"Matthew S","family":"Kelly","sequence":"first","affiliation":[{"name":"Botswana-University of Pennsylvania Partnership , Gaborone, Botswana"},{"name":"Division of Pediatric Infectious Diseases, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Plunkett","sequence":"additional","affiliation":[{"name":"Division of Pediatric Infectious Diseases, Feinberg School of Medicine, Northwestern University , Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yahe","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Mathematics, North Carolina State University , Raleigh, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jhoanna N","family":"Aquino","sequence":"additional","affiliation":[{"name":"Division of Pediatric Infectious Diseases, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sweta M","family":"Patel","sequence":"additional","affiliation":[{"name":"Division of Pulmonary Allergy, and Critical Care Medicine, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jillian H","family":"Hurst","sequence":"additional","affiliation":[{"name":"Division of Pediatric Infectious Diseases, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca R","family":"Young","sequence":"additional","affiliation":[{"name":"Division of Pediatric Infectious Diseases, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Smieja","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, McMaster University , Hamilton, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew P","family":"Steenhoff","sequence":"additional","affiliation":[{"name":"Botswana-University of Pennsylvania Partnership , Gaborone, Botswana"},{"name":"Global Health Center, Children\u2019s Hospital of Philadelphia , Philadelphia, PA, USA"},{"name":"Division of Pediatric Infectious Diseases, Children\u2019s Hospital of Philadelphia , Philadelphia, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tonya","family":"Arscott-Mills","sequence":"additional","affiliation":[{"name":"Botswana-University of Pennsylvania Partnership , Gaborone, Botswana"},{"name":"Global Health Center, Children\u2019s Hospital of Philadelphia , Philadelphia, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristen A","family":"Feemster","sequence":"additional","affiliation":[{"name":"Division of Pediatric Infectious Diseases, Children\u2019s Hospital of Philadelphia , Philadelphia, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sefelani","family":"Boiditswe","sequence":"additional","affiliation":[{"name":"Botswana-University of Pennsylvania Partnership , Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tirayaone","family":"Leburu","sequence":"additional","affiliation":[{"name":"Botswana-University of Pennsylvania Partnership , Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiny","family":"Mazhani","sequence":"additional","affiliation":[{"name":"University of Botswana School of Medicine , Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed Z","family":"Patel","sequence":"additional","affiliation":[{"name":"University of Botswana School of Medicine , Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5976-5206","authenticated-orcid":false,"given":"John F","family":"Rawls","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayanth","family":"Jawahar","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samir S","family":"Shah","sequence":"additional","affiliation":[{"name":"Divisions of Hospital Medicine and Infectious Diseases, Cincinnati Children\u2019s Hospital Medical Center , Cincinnati, OH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher R","family":"Polage","sequence":"additional","affiliation":[{"name":"Department of Pathology, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7725-3052","authenticated-orcid":false,"given":"Coleen K","family":"Cunningham","sequence":"additional","affiliation":[{"name":"Division of Pediatric Infectious Diseases, Duke University , Durham, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick C","family":"Seed","sequence":"additional","affiliation":[{"name":"Division of Pediatric Infectious Diseases, Feinberg School of Medicine, Northwestern University , Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,9,11]]},"reference":[{"key":"2024011018050884500_CR1","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1186\/s12879-016-1648-2","article-title":"Epidemiology of invasive pneumococcal infections: manifestations, incidence and case fatality rate correlated to age, gender and risk factors","volume":"16","author":"Backhaus","year":"2016","journal-title":"BMC Infect Dis"},{"key":"2024011018050884500_CR2","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1016\/S1473-3099(04)00938-7","article-title":"Streptococcus pneumoniae colonisation: the key to pneumococcal disease","volume":"4","author":"Bogaert","year":"2004","journal-title":"Lancet Infect Dis"},{"key":"2024011018050884500_CR3","doi-asserted-by":"publisher","first-page":"e744","DOI":"10.1016\/S2214-109X(18)30247-X","article-title":"Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000-15","volume":"6","author":"Wahl","year":"2018","journal-title":"Lancet Glob Health"},{"key":"2024011018050884500_CR4","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1016\/S2214-109X(18)30408-X","article-title":"Global, regional, and national estimates of pneumonia morbidity and mortality in children younger than 5 years between 2000 and 2015: a systematic analysis","volume":"7","author":"McAllister","year":"2019","journal-title":"Lancet Glob Health"},{"key":"2024011018050884500_CR5","doi-asserted-by":"publisher","first-page":"e30787","DOI":"10.1371\/journal.pone.0030787","article-title":"The prevalence and risk factors for pneumococcal colonization of the nasopharynx among children in Kilifi District, Kenya","volume":"7","author":"Abdullahi","year":"2012","journal-title":"PloS ONE"},{"key":"2024011018050884500_CR6","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1097\/INF.0000000000002174","article-title":"Pneumococcal colonization and the nasopharyngeal microbiota of children in Botswana","volume":"37","author":"Kelly","year":"2018","journal-title":"Pediatr Infect Dis J"},{"key":"2024011018050884500_CR7","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1542\/peds.2008-3099","article-title":"Continued impact of pneumococcal conjugate vaccine on carriage in young children","volume":"124","author":"Huang","year":"2009","journal-title":"Pediatrics"},{"key":"2024011018050884500_CR8","doi-asserted-by":"publisher","first-page":"4349","DOI":"10.1016\/j.vaccine.2014.03.017","article-title":"Pneumococcal carriage in children and adults two years after introduction of the thirteen valent pneumococcal conjugate vaccine in England","volume":"32","author":"van Hoek","year":"2014","journal-title":"Vaccine"},{"key":"2024011018050884500_CR9","doi-asserted-by":"publisher","first-page":"e90974","DOI":"10.1371\/journal.pone.0090974","article-title":"Low prevalence of pneumococcal carriage and high serotype and genotype diversity among adults over 60 years of age living in Portugal","volume":"9","author":"Almeida","year":"2014","journal-title":"PloS ONE"},{"key":"2024011018050884500_CR10","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1542\/peds.113.3.443","article-title":"Decrease of invasive pneumococcal infections in children among 8 children\u2019s hospitals in the United States after the introduction of the 7-valent pneumococcal conjugate vaccine","volume":"113","author":"Kaplan","year":"2004","journal-title":"Pediatrics"},{"key":"2024011018050884500_CR11","doi-asserted-by":"publisher","first-page":"2146","DOI":"10.1016\/S0140-6736(18)33005-8","article-title":"Effect of ten-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya: a longitudinal surveillance study","volume":"393","author":"Hammitt","year":"2019","journal-title":"Lancet"},{"key":"2024011018050884500_CR12","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1016\/S0140-6736(05)71876-6","article-title":"Efficacy of nine-valent pneumococcal conjugate vaccine against pneumonia and invasive pneumococcal disease in The Gambia: randomised, double-blind, placebo-controlled trial","volume":"365","author":"Cutts","year":"2005","journal-title":"Lancet"},{"key":"2024011018050884500_CR13"},{"key":"2024011018050884500_CR14","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1056\/NEJM200102083440602","article-title":"Efficacy of a pneumococcal conjugate vaccine against acute otitis media","volume":"344","author":"Eskola","year":"2001","journal-title":"N. Engl J Med"},{"key":"2024011018050884500_CR15","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1097\/INF.0b013e31803df9ca","article-title":"Emergence of 19A as virulent and multidrug resistant Pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine","volume":"26","author":"Pelton","year":"2007","journal-title":"Pediatr Infect Dis J"},{"key":"2024011018050884500_CR16","doi-asserted-by":"publisher","first-page":"1772","DOI":"10.1001\/jama.298.15.1772","article-title":"Emergence of a multiresistant serotype 19A pneumococcal strain not included in the 7-valent conjugate vaccine as an otopathogen in children","volume":"298","author":"Pichichero","year":"2007","journal-title":"JAMA"},{"key":"2024011018050884500_CR17","doi-asserted-by":"publisher","first-page":"2794","DOI":"10.1016\/j.vaccine.2017.04.019","article-title":"Pneumococcal carriage among children after four years of routine 10-valent pneumococcal conjugate vaccine use in Brazil: the emergence of multidrug resistant serotype 6C","volume":"35","author":"Neves","year":"2017","journal-title":"Vaccine"},{"key":"2024011018050884500_CR18","doi-asserted-by":"publisher","first-page":"e1007911","DOI":"10.1371\/journal.ppat.1007911","article-title":"Selective pressure: rise of the nonencapsulated pneumococcus","volume":"15","author":"Bradshaw","year":"2019","journal-title":"PLoS Pathog"},{"key":"2024011018050884500_CR19","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/S1473-3099(18)30052-5","article-title":"Rapid increase in non-vaccine serotypes causing invasive pneumococcal disease in England and Wales, 2000\u201317: a prospective national observational cohort study","volume":"18","author":"Ladhani","year":"2018","journal-title":"Lancet Infect Dis"},{"key":"2024011018050884500_CR20","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1016\/S1473-3099(18)30349-9","article-title":"Incidence of paediatric pneumococcal meningitis and emergence of new serotypes: a time-series analysis of a 16-year French national survey","volume":"18","author":"Ouldali","year":"2018","journal-title":"Lancet Infect Dis"},{"key":"2024011018050884500_CR21","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.cbpa.2008.01.015","article-title":"Host-bacterial coevolution and the search for new drug targets","volume":"12","author":"Zaneveld","year":"2008","journal-title":"Curr Opin Chem Biol"},{"key":"2024011018050884500_CR22","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/j.chom.2020.07.004","article-title":"Early life microbiota and respiratory tract infections","volume":"28","author":"de Steenhuijsen Piters","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2024011018050884500_CR23","doi-asserted-by":"publisher","first-page":"1871","DOI":"10.1016\/S0140-6736(04)16357-5","article-title":"Colonisation by Streptococcus pneumoniae and Staphylococcus aureus in healthy children","volume":"363","author":"Bogaert","year":"2004","journal-title":"Lancet"},{"key":"2024011018050884500_CR24","doi-asserted-by":"publisher","first-page":"1584","DOI":"10.3201\/eid1410.080119","article-title":"Microbial interactions during upper respiratory tract infections","volume":"14","author":"Pettigrew","year":"2008","journal-title":"Emerg Infect Dis"},{"key":"2024011018050884500_CR25","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1186\/1471-2334-13-483","article-title":"Interrelationship of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus colonization within and between pneumococcal-vaccine na\u00efve mother\u2013child dyads","volume":"13","author":"Shiri","year":"2013","journal-title":"BMC Infect Dis"},{"key":"2024011018050884500_CR26","doi-asserted-by":"publisher","first-page":"2458","DOI":"10.1016\/j.vaccine.2006.09.020","article-title":"Modelling the co-occurrence of Streptococcus pneumoniae with other bacterial and viral pathogens in the upper respiratory tract","volume":"25","author":"Jacoby","year":"2007","journal-title":"Vaccine"},{"key":"2024011018050884500_CR27","doi-asserted-by":"publisher","first-page":"5520","DOI":"10.1016\/j.vaccine.2014.06.091","article-title":"Temporal association of infant immunisation with pneumococcal conjugate vaccine on the ecology of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus nasopharyngeal colonisation in a rural South African community","volume":"32","author":"Nzenze","year":"2014","journal-title":"Vaccine"},{"key":"2024011018050884500_CR28","first-page":"623","article-title":"Changes in nasopharyngeal flora during otitis media of childhood","volume":"9","author":"Faden","year":"1990","journal-title":"Pediatr Infect Dis J"},{"key":"2024011018050884500_CR29","doi-asserted-by":"publisher","first-page":"e02235","DOI":"10.1128\/AEM.02235-18","article-title":"Intranasal Immunization with the commensal Streptococcus mitis confers protective immunity against pneumococcal lung infection","volume":"85","author":"Shekhar","year":"2019","journal-title":"Appl Environ Microbiol"},{"key":"2024011018050884500_CR30","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1111\/j.1574-695X.2001.tb00519.x","article-title":"Protective effect of intranasally inoculated Lactobacillus fermentum against Streptococcus pneumoniae challenge on the mouse respiratory tract","volume":"31","author":"Cangemi de Gutierrez","year":"2001","journal-title":"FEMS Immunol Med Microbiol"},{"key":"2024011018050884500_CR31","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1186\/1756-0500-6-135","article-title":"Inhibition of Streptococcus pneumoniae adherence to human epithelial cells in vitro by the probiotic Lactobacillus rhamnosus GG","volume":"6","author":"Wong","year":"2013","journal-title":"BMC Res Notes"},{"key":"2024011018050884500_CR32","doi-asserted-by":"publisher","first-page":"e00245","DOI":"10.1128\/mBio.00245-10","article-title":"Microbial communities of the upper respiratory tract and otitis media in children","volume":"2","author":"Laufer","year":"2011","journal-title":"mBio"},{"key":"2024011018050884500_CR33","doi-asserted-by":"publisher","first-page":"e01725","DOI":"10.1128\/mBio.01725-15","article-title":"Corynebacterium accolens releases antipneumococcal free fatty acids from human nostril and skin surface triacylglycerols","volume":"7","author":"Bomar","year":"2016","journal-title":"mBio"},{"key":"2024011018050884500_CR34","doi-asserted-by":"publisher","first-page":"e28523","DOI":"10.1371\/journal.pone.0028523","article-title":"Regulation of virulence gene expression resulting from Streptococcus pneumoniae and nontypeable Haemophilus influenzae interactions in chronic disease","volume":"6","author":"Cope","year":"2011","journal-title":"PloS ONE"},{"key":"2024011018050884500_CR35","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1371\/journal.ppat.0010001","article-title":"The role of innate immune responses in the outcome of interspecies competition for colonization of mucosal surfaces","volume":"1","author":"Lysenko","year":"2005","journal-title":"PloS Pathog"},{"key":"2024011018050884500_CR36","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1093\/infdis\/jiq087","article-title":"Divergent mechanisms for passive pneumococcal resistance to \u03b2-lactam antibiotics in the presence of Haemophilus influenzae","volume":"203","author":"Weimer","year":"2011","journal-title":"J Infect Dis"},{"key":"2024011018050884500_CR37","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1111\/2049-632X.12073","article-title":"Haemophilus influenzae and Streptococcus pneumoniae: living together in a biofilm","volume":"69","author":"Tikhomirova","year":"2013","journal-title":"Pathog Dis"},{"key":"2024011018050884500_CR38","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00852-20","article-title":"Dolosigranulum pigrum cooperation and competition in human nasal microbiota","volume":"5","author":"Brugger","year":"2020","journal-title":"mSphere"},{"key":"2024011018050884500_CR39","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1016\/j.chom.2015.03.008","article-title":"The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development","volume":"17","author":"Teo","year":"2015","journal-title":"Cell Host Microbe"},{"key":"2024011018050884500_CR40","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1016\/j.jaci.2014.12.1909","article-title":"Dynamics of the nasal microbiota in infancy: a prospective cohort study","volume":"135","author":"Mika","year":"2015","journal-title":"J Allergy Clin Immunol"},{"key":"2024011018050884500_CR41","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1164\/rccm.201407-1240OC","article-title":"Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children","volume":"190","author":"Biesbroek","year":"2014","journal-title":"Am J Respir Crit Care Med"},{"key":"2024011018050884500_CR42","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1016\/j.ebiom.2016.05.031","article-title":"Development of upper respiratory tract microbiota in infancy is affected by mode of delivery","volume":"9","author":"Bosch","year":"2016","journal-title":"EBioMedicine"},{"key":"2024011018050884500_CR43","doi-asserted-by":"publisher","first-page":"11971","DOI":"10.1073\/pnas.1002601107","article-title":"Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns","volume":"107","author":"Dominguez-Bello","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024011018050884500_CR44","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1164\/rccm.201401-0073OC","article-title":"The impact of breastfeeding on nasopharyngeal microbial communities in infants","volume":"190","author":"Biesbroek","year":"2014","journal-title":"Am J Respir Crit Care Med"},{"key":"2024011018050884500_CR45","doi-asserted-by":"publisher","first-page":"e17035","DOI":"10.1371\/journal.pone.0017035","article-title":"Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis","volume":"6","author":"Bogaert","year":"2011","journal-title":"PloS ONE"},{"key":"2024011018050884500_CR46","first-page":"1078","article-title":"Indoor air pollution in developing countries: a major environmental and public health challenge","volume":"78","author":"Bruce","year":"2000","journal-title":"Bull World Health Organ"},{"key":"2024011018050884500_CR47","doi-asserted-by":"publisher","first-page":"e0176116","DOI":"10.1371\/journal.pone.0176116","article-title":"Household crowding as a potential mediator of socioeconomic determinants of tuberculosis incidence in Brazil","volume":"12","author":"Pelissari","year":"2017","journal-title":"PloS ONE"},{"key":"2024011018050884500_CR48","doi-asserted-by":"publisher","first-page":"1048","DOI":"10.3390\/ijerph14091048","article-title":"Health effects of ambient air pollution in developing countries","volume":"14","author":"Mannucci","year":"2017","journal-title":"Int J Environ Res Public Health"},{"key":"2024011018050884500_CR49","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature"},{"key":"2024011018050884500_CR50","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.chom.2018.06.005","article-title":"Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome","volume":"24","author":"Ferretti","year":"2018","journal-title":"Cell Host Microbe"},{"key":"2024011018050884500_CR51","doi-asserted-by":"publisher","first-page":"4680","DOI":"10.1073\/pnas.1002611107","article-title":"Vaginal microbiome of reproductive-age women","volume":"108","author":"Ravel","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024011018050884500_CR52"},{"key":"2024011018050884500_CR53","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1016\/j.clnu.2009.09.008","article-title":"Lactobacillus GG in the prevention of gastrointestinal and respiratory tract infections in children who attend day care centers: a randomized, double-blind, placebo-controlled trial","volume":"29","author":"Hojsak","year":"2010","journal-title":"Clin Nutr"},{"key":"2024011018050884500_CR54","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1093\/ajcn\/77.2.517","article-title":"Ingested probiotics reduce nasal colonization with pathogenic bacteria (Staphylococcus aureus, Streptococcus pneumoniae, and beta-hemolytic streptococci)","volume":"77","author":"Gluck","year":"2003","journal-title":"Am J Clin Nutr"},{"key":"2024011018050884500_CR55","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1111\/j.1365-2222.2006.02629.x","article-title":"Probiotic-induced suppression of allergic sensitization and airway inflammation is associated with an increase of T regulatory-dependent mechanisms in a murine model of asthma","volume":"37","author":"Feleszko","year":"2007","journal-title":"Clin Exp Allergy"},{"key":"2024011018050884500_CR56","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1016\/j.diagmicrobio.2012.07.001","article-title":"Microbiological investigation and clinical significance of Corynebacterium spp. in respiratory specimens","volume":"74","author":"Nhan","year":"2012","journal-title":"Diagn Microbiol Infect Dis"},{"key":"2024011018050884500_CR57","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1007\/s10096-012-1805-5","article-title":"Non-diphtheriae Corynebacterium species: an emerging respiratory pathogen","volume":"32","author":"D\u00edez-Aguilar","year":"2013","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"2024011018050884500_CR58","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1007\/s15010-017-1017-0","article-title":"Corynebacterium species nasopharyngeal carriage in asymptomatic individuals aged \u2265 65 years in Germany","volume":"45","author":"Teutsch","year":"2017","journal-title":"Infection"},{"key":"2024011018050884500_CR59","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinforma"},{"key":"2024011018050884500_CR60","doi-asserted-by":"publisher","first-page":"e551","DOI":"10.1111\/1469-0691.12286","article-title":"Serum antibody responses to pneumococcal colonization in the first 2 years of life: results from an SE Asian longitudinal cohort study","volume":"19","author":"Turner","year":"2013","journal-title":"Clin Microbiol Infect"},{"key":"2024011018050884500_CR61","doi-asserted-by":"publisher","first-page":"11344","DOI":"10.1038\/srep11344","article-title":"Climate induces seasonality in pneumococcal transmission","volume":"5","author":"Numminen","year":"2015","journal-title":"Sci Rep"},{"key":"2024011018050884500_CR62","doi-asserted-by":"publisher","first-page":"e0126593","DOI":"10.1371\/journal.pone.0126593","article-title":"Association of respiratory viruses with outcomes of severe childhood pneumonia in Botswana","volume":"10","author":"Kelly","year":"2015","journal-title":"PloS ONE"},{"key":"2024011018050884500_CR63","doi-asserted-by":"publisher","first-page":"e95","DOI":"10.1016\/S2214-109X(14)70360-2","article-title":"Incidence and severity of childhood pneumonia in the first year of life in a South African birth cohort: the Drakenstein Child Health Study","volume":"3","author":"le Roux","year":"2015","journal-title":"Lancet Glob Health"},{"key":"2024011018050884500_CR64","doi-asserted-by":"publisher","first-page":"1346","DOI":"10.1093\/cid\/civ059","article-title":"Increased risk and mortality of invasive pneumococcal disease in HIV-exposed-uninfected infants &lt;1 year of age in South Africa, 2009-2013","volume":"60","author":"von Mollendorf","year":"2015","journal-title":"Clin Infect Dis"},{"key":"2024011018050884500_CR65","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1016\/S0022-3476(05)83170-1","article-title":"Invasive pneumococcal disease among infected and uninfected children of mothers with human immunodeficiency virus infection","volume":"124","author":"Farley","year":"1994","journal-title":"J Pediatr"},{"key":"2024011018050884500_CR66","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1111\/tmi.12057","article-title":"Dynamics of nasopharyngeal bacterial colonisation in HIV-exposed young infants in Tanzania","volume":"18","author":"Kinabo","year":"2013","journal-title":"Trop Med Int Health"},{"key":"2024011018050884500_CR67","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12887-018-1119-6","article-title":"Risk factors for carriage of Streptococcus pneumoniae in children","volume":"18","author":"Koliou","year":"2018","journal-title":"BMC Pediatr"},{"key":"2024011018050884500_CR68"},{"key":"2024011018050884500_CR69","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1097\/00013542-199601000-00004","article-title":"Microbiology and epidemiology of diphtheria","volume":"7","author":"Efstratiou","year":"1996","journal-title":"Rev Med Microbiol"},{"key":"2024011018050884500_CR70","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1093\/clinids\/13.2.342","article-title":"Bacteremia due to Corynebacterium jeikeium in a patient with AIDS","volume":"13","author":"Spach","year":"1991","journal-title":"Rev Infect Dis"},{"key":"2024011018050884500_CR71","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1038\/sj.bmt.1702808","article-title":"Corynebacterium jeikeium bacteremia in bone marrow transplant patients with Hickman catheters","volume":"27","author":"Wang","year":"2001","journal-title":"Bone Marrow Transplant"},{"key":"2024011018050884500_CR72","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1093\/clinids\/13.5.887","article-title":"Endocarditis due to Corynebacterium pseudodiphtheriticum: five case reports, review, and antibiotic susceptibilities of nine strains","volume":"13","author":"Morris","year":"1991","journal-title":"Rev Infect Dis"},{"key":"2024011018050884500_CR73","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.idcr.2017.11.004","article-title":"Corynebacterium jeikeium endocarditis: a case report and comprehensive review of an underestimated infection","volume":"11","author":"Bookani","year":"2018","journal-title":"IDCases"},{"key":"2024011018050884500_CR74","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1002\/nmi2.48","article-title":"Respiratory infection by Corynebacterium striatum: epidemiological and clinical determinants","volume":"2","author":"Renom","year":"2014","journal-title":"N. Microbes N. Infect"},{"key":"2024011018050884500_CR75","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.3201\/eid1608.100193","article-title":"Outbreak of Corynebacterium pseudodiphtheriticum infection in cystic fibrosis patients, France","volume":"16","author":"Bittar","year":"2010","journal-title":"Emerg Inf Dis"},{"key":"2024011018050884500_CR76","doi-asserted-by":"publisher","first-page":"e02406","DOI":"10.1128\/AEM.02406-18","article-title":"Competition among nasal bacteria suggests a role for siderophore-mediated interactions in shaping the human nasal microbiota","volume":"85","author":"Stubbendieck","year":"2019","journal-title":"Appl Environ Microbiol"},{"key":"2024011018050884500_CR77","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1007\/s12602-013-9147-x","article-title":"Use of Corynebacterium pseudodiphtheriticum for elimination of Staphylococcus aureus from the nasal cavity in volunteers exposed to abnormal microclimate and altered gaseous environment","volume":"5","author":"Kiryukhina","year":"2013","journal-title":"Probiotics Antimicrob Proteins"},{"key":"2024011018050884500_CR78","first-page":"172","article-title":"Corynebacterium and Dolosigranulum: future probiotic candidates for upper respiratory tract infections","volume":"40","author":"Lappan","year":"2019","journal-title":"Microbiol Aust"},{"key":"2024011018050884500_CR79","doi-asserted-by":"publisher","first-page":"e1913650","DOI":"10.1001\/jamanetworkopen.2019.13650","article-title":"A comparison of pneumococcal nasopharyngeal carriage in very young Fijian infants born by vaginal or cesarean delivery","volume":"2","author":"Neal","year":"2019","journal-title":"JAMA Netw Open"},{"key":"2024011018050884500_CR80"},{"key":"2024011018050884500_CR81"},{"key":"2024011018050884500_CR82"},{"key":"2024011018050884500_CR83"},{"key":"2024011018050884500_CR84","doi-asserted-by":"publisher","first-page":"3446","DOI":"10.1128\/JCM.39.10.3446-3451.2001","article-title":"Sensitive and specific method for rapid identification of Streptococcus pneumoniae using real-time fluorescence PCR","volume":"39","author":"McAvin","year":"2001","journal-title":"J Clin Microbiol"},{"key":"2024011018050884500_CR85","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.jviromet.2015.12.006","article-title":"Performance of Roche CAP\/CTM HIV-1 qualitative test version 2.0 using dried blood spots for early infant diagnosis","volume":"229","author":"Gueye","year":"2016","journal-title":"J Virol Methods"},{"key":"2024011018050884500_CR86","doi-asserted-by":"publisher","first-page":"243","DOI":"10.4056\/sigs.1433550","article-title":"Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project","volume":"3","author":"Gilbert","year":"2010","journal-title":"Stand Genom Sci"},{"key":"2024011018050884500_CR87","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2024011018050884500_CR88","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat Methods"},{"key":"2024011018050884500_CR89","doi-asserted-by":"publisher","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":"2024011018050884500_CR90","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-020-00841-w","article-title":"Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets","volume":"8","author":"Escapa","year":"2020","journal-title":"Microbiome"},{"key":"2024011018050884500_CR91","doi-asserted-by":"publisher","first-page":"226","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":"2024011018050884500_CR92","doi-asserted-by":"publisher","first-page":"e61217","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":"2024011018050884500_CR93","first-page":"719","article-title":"The vegan package","volume":"10","author":"Oksanen","year":"2007","journal-title":"Community Ecol Package"},{"key":"2024011018050884500_CR94","first-page":"32","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","author":"Anderson","year":"2001","journal-title":"Austral Ecol"},{"key":"2024011018050884500_CR95","doi-asserted-by":"publisher","first-page":"201","DOI":"10.3201\/eid2002.131220","article-title":"Seven-valent pneumococcal conjugate vaccine and nasopharyngeal microbiota in healthy children","volume":"20","author":"Biesbroek","year":"2014","journal-title":"Emerg Infect Dis"},{"key":"2024011018050884500_CR96","doi-asserted-by":"publisher","first-page":"349ra100","DOI":"10.1126\/scitranslmed.aaf5103","article-title":"Maternal HIV infection influences the microbiome of HIV-uninfected infants","volume":"8","author":"Bender","year":"2016","journal-title":"Sci Transl Med"},{"key":"2024011018050884500_CR97","doi-asserted-by":"publisher","first-page":"1924","DOI":"10.1093\/infdis\/jiw456","article-title":"Differences in the nasopharyngeal microbiome during acute respiratory tract infection with human rhinovirus and respiratory syncytial virus in infancy","volume":"214","author":"Rosas-Salazar","year":"2016","journal-title":"J Infect Dis"},{"key":"2024011018050884500_CR98"}],"container-title":["The ISME Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41396-021-01108-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41396-021-01108-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/ismej\/article-pdf\/16\/3\/655\/55310904\/41396_2021_article_1108.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/www.nature.com\/articles\/s41396-021-01108-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/academic.oup.com\/ismej\/article-pdf\/16\/3\/655\/55310904\/41396_2021_article_1108.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T18:13:20Z","timestamp":1707934400000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismej\/article\/16\/3\/655-665\/7474182"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,11]]},"references-count":98,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,3,1]]}},"URL":"https:\/\/doi.org\/10.1038\/s41396-021-01108-4","relation":{},"ISSN":["1751-7362","1751-7370"],"issn-type":[{"value":"1751-7362","type":"print"},{"value":"1751-7370","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,3]]},"published":{"date-parts":[[2021,9,11]]},"assertion":[{"value":"28 April 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 August 2021","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 September 2021","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 September 2021","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"This study was approved by the Botswana Ministry of Health, the Princess Marina Hospital ethics committee, and institutional review boards at the University of Pennsylvania, Duke University, and McMaster University. Written informed consent was obtained from all participants or their legal guardians.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}}]}}