{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T22:04:34Z","timestamp":1794002674091,"version":"4.8.0"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T00:00:00Z","timestamp":1619395200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T00:00:00Z","timestamp":1619395200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["908\/15"],"award-info":[{"award-number":["908\/15"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"name":"I-CORE program","award":["41\/11"],"award-info":[{"award-number":["41\/11"]}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1144149"],"award-info":[{"award-number":["OPP1144149"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007028","name":"Leona M. and Harry B. Helmsley Charitable Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["758313"],"award-info":[{"award-number":["758313"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining\u2009&gt;\u200975% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.<\/jats:p>","DOI":"10.1038\/s41598-021-88536-6","type":"journal-article","created":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T10:06:16Z","timestamp":1619431576000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition"],"prefix":"10.1038","volume":"11","author":[{"given":"Tzipi","family":"Braun","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiraz","family":"Halevi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rotem","family":"Hadar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilate","family":"Efroni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Efrat","family":"Glick Saar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natahan","family":"Keller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amnon","family":"Amir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon","family":"Amit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yael","family":"Haberman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,4,26]]},"reference":[{"issue":"8","key":"88536_CR1","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1001\/jama.2020.12839","volume":"324","author":"WJ Wiersinga","year":"2020","unstructured":"Wiersinga, W. J., Rhodes, A., Cheng, A. C., Peacock, S. J. & Prescott, H. C. Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19): a review. JAMA 324(8), 782\u2013793 (2020).","journal-title":"JAMA"},{"key":"88536_CR2","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1007\/s11845-020-02218-2","volume":"189","author":"J Wang","year":"2020","unstructured":"Wang, J. & Du, G. COVID-19 may transmit through aerosol. Irish J. Med. Sci. 189, 1143\u20131144 (2020).","journal-title":"Irish J. Med. Sci."},{"key":"88536_CR3","doi-asserted-by":"publisher","DOI":"10.1007\/s42399-020-00498-4","author":"R Karia","year":"2020","unstructured":"Karia, R., Gupta, I., Khandait, H., Yadav, A. & Yadav, A. COVID-19 and its modes of transmission. SN Compr. Clin. Med. https:\/\/doi.org\/10.1007\/s42399-020-00498-4 (2020).","journal-title":"SN Compr. Clin. Med."},{"key":"88536_CR4","doi-asserted-by":"crossref","unstructured":"De Maio, F., Posteraro, B., Ponziani, F. R., Cattani, P., Gasbarrini, A. & Sanguinetti, M. Nasopharyngeal microbiota profiling of SARS-CoV-2 infected patients (2020).","DOI":"10.21203\/rs.3.rs-27326\/v1"},{"issue":"3","key":"88536_CR5","doi-asserted-by":"publisher","first-page":"e64","DOI":"10.1016\/j.jinf.2020.06.047","volume":"81","author":"J Fan","year":"2020","unstructured":"Fan, J. et al. The lung tissue microbiota features of 20 deceased patients with COVID-19. J. Infect. 81(3), e64\u2013e67 (2020).","journal-title":"J. Infect."},{"issue":"11","key":"88536_CR6","doi-asserted-by":"publisher","first-page":"694","DOI":"10.21037\/atm-20-2793","volume":"8","author":"KK Sahu","year":"2020","unstructured":"Sahu, K. K., Mishra, A. K. & Lal, A. Trajectory of the COVID-19 pandemic: chasing a moving target. Ann. Transl. Med. 8(11), 694. https:\/\/doi.org\/10.21037\/atm-20-2793 (2020).","journal-title":"Ann. Transl. Med."},{"issue":"7","key":"88536_CR7","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1093\/qjmed\/hcaa117","volume":"113","author":"KK Sahu","year":"2020","unstructured":"Sahu, K. K., Mishra, A. K. & Lal, A. COIVD-19 disease: tackling a pandemic in 21st century. QJM 113(7), 519\u2013520. https:\/\/doi.org\/10.1093\/qjmed\/hcaa117 (2020).","journal-title":"QJM"},{"key":"88536_CR8","doi-asserted-by":"publisher","first-page":"2372","DOI":"10.3389\/fmicb.2017.02372","volume":"8","author":"I De Boeck","year":"2017","unstructured":"De Boeck, I. et al. Comparing the healthy nose and nasopharynx microbiota reveals continuity as well as niche-specificity. Front. Microbiol. 8, 2372 (2017).","journal-title":"Front. Microbiol."},{"issue":"9","key":"88536_CR9","doi-asserted-by":"publisher","first-page":"1104","DOI":"10.1164\/rccm.201602-0220OC","volume":"194","author":"WAA de Steenhuijsen Piters","year":"2016","unstructured":"de Steenhuijsen Piters, W. A. A. et al. Nasopharyngeal microbiota, host transcriptome, and disease severity in children with respiratory syncytial virus infection. Am. J. Respir. Crit. Care Med. 194(9), 1104\u20131115 (2016).","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"88536_CR10","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.annepidem.2019.07.013","volume":"37","author":"KH Lee","year":"2019","unstructured":"Lee, K. H. et al. The respiratory microbiota: associations with influenza symptomatology and viral shedding. Ann. Epidemiol. 37, 51\u201356 (2019).","journal-title":"Ann. Epidemiol."},{"issue":"1","key":"88536_CR11","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/2049-2618-2-22","volume":"2","author":"EK Allen","year":"2014","unstructured":"Allen, E. K. et al. Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge. Microbiome 2(1), 22 (2014).","journal-title":"Microbiome"},{"key":"88536_CR12","doi-asserted-by":"crossref","unstructured":"Mostafa, H. H., Fissel, J. A., Fanelli, B. et al. Metagenomic next-generation sequencing of nasopharyngeal specimens collected from confirmed and suspect COVID-19 patients. MBio 11(6) (2020).","DOI":"10.1128\/mBio.01969-20"},{"key":"88536_CR13","doi-asserted-by":"crossref","unstructured":"Jiang, L., Amir, A., Morton, J. T., Heller, R., Arias-Castro, E. & Knight, R. Discrete false-discovery rate improves identification of differentially abundant microbes. MSystems 2(6) (2017).","DOI":"10.1128\/mSystems.00092-17"},{"key":"88536_CR14","unstructured":"Mallick, H., McIver, L. J., Rahnavard, A. et al. Multivariable association in population-scale meta-omics studies."},{"issue":"1","key":"88536_CR15","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1080\/22221751.2021.1872351","volume":"10","author":"G Qu\u00e9rom\u00e8s","year":"2021","unstructured":"Qu\u00e9rom\u00e8s, G. et al. Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France. Emerg Microbes Infect. 10(1), 167\u2013177. https:\/\/doi.org\/10.1080\/22221751.2021.1872351 (2021).","journal-title":"Emerg Microbes Infect."},{"key":"88536_CR16","doi-asserted-by":"publisher","DOI":"10.3791\/56845","author":"A Di Segni","year":"2018","unstructured":"Di Segni, A. et al. Guided protocol for fecal microbial characterization by 16S rRNA-amplicon sequencing. J. Vis. Exp. https:\/\/doi.org\/10.3791\/56845 (2018).","journal-title":"J. Vis. Exp."},{"issue":"8","key":"88536_CR17","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37(8), 852\u2013857. https:\/\/doi.org\/10.1038\/s41587-019-0209-9 (2019).","journal-title":"Nat. Biotechnol."},{"key":"88536_CR18","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00191-16","author":"A Amir","year":"2017","unstructured":"Amir, A. et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems https:\/\/doi.org\/10.1128\/mSystems.00191-16 (2017).","journal-title":"mSystems"},{"issue":"2","key":"88536_CR19","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/ismej.2010.133","volume":"5","author":"C Lozupone","year":"2011","unstructured":"Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5(2), 169\u2013172. https:\/\/doi.org\/10.1038\/ismej.2010.133 (2011).","journal-title":"ISME J."},{"key":"88536_CR20","doi-asserted-by":"publisher","DOI":"10.1142\/9789814366496_0024","author":"S Mirarab","year":"2012","unstructured":"Mirarab, S., Nguyen, N. & Warnow, T. S. E. P. P. SAT\u00e9-enabled phylogenetic placement. Pac. Symp. Biocomput. https:\/\/doi.org\/10.1142\/9789814366496_0024 (2012).","journal-title":"Pac. Symp. Biocomput."},{"key":"88536_CR21","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00269-18","author":"ZZ Xu","year":"2019","unstructured":"Xu, Z. Z. et al. Calour: An interactive, microbe-centric analysis tool. mSystems https:\/\/doi.org\/10.1128\/mSystems.00269-18 (2019).","journal-title":"mSystems"},{"key":"88536_CR22","unstructured":"Oksanen, J., Blanchet, F. G., Friendly, M. et al. vegan: Community Ecology Package (2019)."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-88536-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-88536-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-88536-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,3]],"date-time":"2022-12-03T07:16:16Z","timestamp":1670051776000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-88536-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,26]]},"references-count":22,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,12]]}},"alternative-id":["88536"],"URL":"https:\/\/doi.org\/10.1038\/s41598-021-88536-6","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,26]]},"assertion":[{"value":"5 January 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 April 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 April 2021","order":3,"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"}}],"article-number":"8922"}}