{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T22:38:23Z","timestamp":1780094303240,"version":"3.54.0"},"update-to":[{"DOI":"10.12688\/gatesopenres.13561.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,3,20]],"date-time":"2024-03-20T00:00:00Z","timestamp":1710892800000}}],"reference-count":39,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2024,3,20]],"date-time":"2024-03-20T00:00:00Z","timestamp":1710892800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH\/NIAID","award":["1RO1AI133080"],"award-info":[{"award-number":["1RO1AI133080"]}]},{"name":"NIH","award":["U01CA220413"],"award-info":[{"award-number":["U01CA220413"]}]},{"name":"NIH","award":["R01GM127430"],"award-info":[{"award-number":["R01GM127430"]}]}],"content-domain":{"domain":["gatesopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Gates Open Res"],"abstract":"<ns3:p>\n                    Background Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or are a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed. Methods We conducted a retrospective analysis of NP samples collected in a longitudinal birth cohort study of Zambian mother-infant pairs. Samples were collected every two weeks from 1-week through 14-weeks of age. Ten of the infants in the cohort who developed LRTI were matched 1:3 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed and compared the NP microbiome of the healthy infants to infants who developed LRTI. Results The infant NP microbiome maturation was characterized by transitioning from\n                    <ns3:italic>Staphylococcus<\/ns3:italic>\n                    dominant to respiratory-genera dominant profiles during the first three months of life, similar to what is described in the literature. Interestingly, infants who developed LRTI had distinct NP microbiome characteristics before infection, in most cases as early as the first week of life. Their NP microbiome was characterized by the presence of\n                    <ns3:italic>Novosphingobium, Delftia<\/ns3:italic>\n                    , high relative abundance of\n                    <ns3:italic>Anaerobacillus, Bacillus<\/ns3:italic>\n                    , and low relative abundance of\n                    <ns3:italic>Dolosigranulum,<\/ns3:italic>\n                    compared to the healthy controls. Mothers of infants with LRTI also had low relative abundance of\n                    <ns3:italic>Dolosigranulum<\/ns3:italic>\n                    in their baseline samples compared to mothers of infants that did not develop an LRTI. Conclusions Our results suggest that specific characteristics of the NP microbiome precede LRTI in young infants and may be present in their mothers as well. Early dysbiosis may play a role in the causal pathway leading to LRTI or could be a marker of underlying immunological, environmental, or genetic characteristics that predispose to LRTI.\n                  <\/ns3:p>","DOI":"10.12688\/gatesopenres.13561.2","type":"journal-article","created":{"date-parts":[[2024,3,20]],"date-time":"2024-03-20T08:50:14Z","timestamp":1710924614000},"page":"48","update-policy":"https:\/\/doi.org\/10.12688\/gatesopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study"],"prefix":"10.12688","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4398-1588","authenticated-orcid":false,"given":"Rotem","family":"Lapidot","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler","family":"Faits","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4672-5915","authenticated-orcid":false,"given":"Arshad","family":"Ismail","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mushal","family":"Allam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zamantungwak","family":"Khumalo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8003-8874","authenticated-orcid":false,"given":"William","family":"MacLeod","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0151-8883","authenticated-orcid":false,"given":"Geoffrey","family":"Kwenda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachariah","family":"Mupila","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Nakazwe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Segr\u00e8","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William Evan","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donald M","family":"Thea","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3034-749X","authenticated-orcid":false,"given":"Lawrence","family":"Mwananyanda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3353-0617","authenticated-orcid":false,"given":"Christopher J","family":"Gill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2024,3,20]]},"reference":[{"key":"ref-1","article-title":"FastQC","author":"S Andrews","year":"2010"},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"1-48","DOI":"10.18637\/jss.v067.i01","article-title":"Fitting linear mixed-effects models using lme4.","volume":"67","author":"D Bates","year":"2015","journal-title":"J Stat Softw."},{"key":"ref-4","doi-asserted-by":"crossref","first-page":"289-300","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"298-308","DOI":"10.1164\/rccm.201401-0073OC","article-title":"The impact of breastfeeding on nasopharyngeal microbial communities in infants.","volume":"190","author":"G Biesbroek","year":"2014","journal-title":"Am J Respir Crit Care Med."},{"key":"ref-6","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aad7121","article-title":"Antibiotics, birth mode, and diet shape microbiome maturation during early life.","volume":"8","author":"N Bokulich","year":"2016","journal-title":"Sci Transl Med."},{"key":"ref-7","doi-asserted-by":"publisher","first-page":"2114-2120","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data.","volume":"30","author":"A Bolger","year":"2014","journal-title":"Bioinformatics."},{"key":"ref-9","doi-asserted-by":"publisher","first-page":"1582-1590","DOI":"10.1164\/rccm.201703-0554OC","article-title":"Maturation of the infant respiratory microbiota, environmental drivers, and health consequences. 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De Steenhuijsen Piters, Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, 23 Jul 2024, version 2, indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-48\/v2#referee-response-36205","order":0,"name":"referee-response-36205","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/gatesopenres.16786.r36206, Frank A Scannapieco, University at Buffalo, NY, 13 Apr 2024, version 2, indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-48\/v2#referee-response-36206","order":1,"name":"referee-response-36206","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/gatesopenres.16786.r36204, Carter Merenstein, University of Pennsylvania, Pennsylvania, 12 Apr 2024, version 2, indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-48\/v2#referee-response-36204","order":2,"name":"referee-response-36204","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by The Southern Africa Mother Infant Pertussis Study, PI Gill funded by the Gates Foundation, OPP1105094 and the SAMIPS \u2013 Nasopharyngeal Carriage (SAMIPS-NPC). PI Gill. Funder NIH\/NIAID (1R01AI133080). WEJ and TF were supported by funds from the NIH, U01CA220413 and R01GM127430. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}