{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T17:04:11Z","timestamp":1790528651567,"version":"4.1.0"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,12,15]],"date-time":"2021-12-15T00:00:00Z","timestamp":1639526400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,12,15]],"date-time":"2021-12-15T00:00:00Z","timestamp":1639526400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The microbiota of  the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n\u2009=\u200922) nasopharyngeal swab samples (including COVID-19 patients\u2009=\u20098, recovered humans\u2009=\u20097, and healthy people\u2009=\u20097) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.<\/jats:p>","DOI":"10.1038\/s41598-021-03245-4","type":"journal-article","created":{"date-parts":[[2021,12,15]],"date-time":"2021-12-15T06:05:44Z","timestamp":1639548344000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":55,"title":["SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts"],"prefix":"10.1038","volume":"11","author":[{"given":"M. Nazmul","family":"Hoque","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md. Murshed Hasan","family":"Sarkar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Shaminur","family":"Rahman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahina","family":"Akter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanjina Akhtar","family":"Banu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barna","family":"Goswami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iffat","family":"Jahan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Saddam","family":"Hossain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. K. Mohammad","family":"Shamsuzzaman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tasnim","family":"Nafisa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Maruf Ahmed","family":"Molla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahmuda","family":"Yeasmin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asish Kumar","family":"Ghosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eshrar","family":"Osman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S. K. Saiful","family":"Alam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad Samir","family":"Uzzaman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md Ahashan","family":"Habib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abu Sayeed Mohammad","family":"Mahmud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keith A.","family":"Crandall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tofazzal","family":"Islam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md. Salim","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,12,15]]},"reference":[{"key":"3245_CR1","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1038\/s41591-020-0869-5","volume":"26","author":"X He","year":"2020","unstructured":"He, X. et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat. Med. 26, 672\u2013675 (2020).","journal-title":"Nat. Med."},{"key":"3245_CR2","doi-asserted-by":"publisher","first-page":"e9689","DOI":"10.7717\/peerj.9689","volume":"8","author":"MN Hoque","year":"2020","unstructured":"Hoque, M. N., Chaudhury, A., Akanda, M. A. M., Hossain, M. A. & Islam, M. T. Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease. PeerJ 8, e9689 (2020).","journal-title":"PeerJ"},{"key":"3245_CR3","doi-asserted-by":"publisher","first-page":"1651","DOI":"10.1073\/pnas.96.4.1651","volume":"96","author":"AH Reid","year":"1999","unstructured":"Reid, A. H., Fanning, T. G., Hultin, J. V. & Taubenberger, J. K. Origin and evolution of the 1918 \u201cSpanish\u201d influenza virus hemagglutinin gene. Proc. Natl. Acad. Sci. 96, 1651\u20131656 (1999).","journal-title":"Proc. Natl. Acad. Sci."},{"key":"3245_CR4","first-page":"1","volume":"20","author":"O Gallo","year":"2020","unstructured":"Gallo, O., Locatello, L. G., Mazzoni, A., Novelli, L. & Annunziato, F. The central role of the nasal microenvironment in the transmission, modulation, and clinical progression of SARS-CoV-2 infection. Mucosal Immunol. 20, 1\u201312 (2020).","journal-title":"Mucosal Immunol."},{"key":"3245_CR5","doi-asserted-by":"publisher","first-page":"104941","DOI":"10.1016\/j.micpath.2021.104941","volume":"20","author":"MN Hoque","year":"2021","unstructured":"Hoque, M. N. et al. Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis. Microbial Pathog. 20, 104941 (2021).","journal-title":"Microbial Pathog."},{"key":"3245_CR6","doi-asserted-by":"publisher","first-page":"100997","DOI":"10.1016\/j.genrep.2020.100997","volume":"22","author":"MS Rahman","year":"2021","unstructured":"Rahman, M. S. et al. Mutational insights into the envelope protein of SARS-CoV-2. Gene Rep. 22, 100997 (2021).","journal-title":"Gene Rep."},{"key":"3245_CR7","doi-asserted-by":"publisher","first-page":"1625","DOI":"10.1111\/tbed.13834","volume":"68","author":"MS Rahman","year":"2021","unstructured":"Rahman, M. S. et al. Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: A fast and accurate pipeline. Transbound. Emerg. Dis. 68, 1625\u20131638 (2021).","journal-title":"Transbound. Emerg. Dis."},{"key":"3245_CR8","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1136\/gutjnl-2020-323020","volume":"70","author":"YK Yeoh","year":"2021","unstructured":"Yeoh, Y. K. et al. Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19. Gut 70, 698\u2013706 (2021).","journal-title":"Gut"},{"key":"3245_CR9","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1128\/mBio.01969-20","volume":"11","author":"HH Mostafa","year":"2020","unstructured":"Mostafa, H. H. et al. Metagenomic next-generation sequencing of nasopharyngeal specimens collected from confirmed and suspect covid-19 patients. MBio 11, 25 (2020).","journal-title":"MBio"},{"key":"3245_CR10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-13993-7","volume":"11","author":"D Kaul","year":"2020","unstructured":"Kaul, D. et al. Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection. Nat. Commun. 11, 1\u201312 (2020).","journal-title":"Nat. Commun."},{"key":"3245_CR11","unstructured":"Ren, L. et al. Dynamics of the upper respiratory tract microbiota and its association with fatality in COVID-19 patients (2020)."},{"key":"3245_CR12","doi-asserted-by":"publisher","first-page":"e12966","DOI":"10.1111\/cmi.12966","volume":"20","author":"A Dumas","year":"2018","unstructured":"Dumas, A., Bernard, L., Poquet, Y., Lugo-Villarino, G. & Neyrolles, O. The role of the lung microbiota and the gut\u2013lung axis in respiratory infectious diseases. Cell. Microbiol. 20, e12966 (2018).","journal-title":"Cell. Microbiol."},{"key":"3245_CR13","doi-asserted-by":"publisher","first-page":"2097","DOI":"10.1002\/iub.2356","volume":"72","author":"R Mirzaei","year":"2020","unstructured":"Mirzaei, R. et al. Bacterial co-infections with SARS-CoV-2. IUBMB Life 72, 2097\u20132111 (2020).","journal-title":"IUBMB Life"},{"key":"3245_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12879-018-3366-4","volume":"18","author":"J Quah","year":"2018","unstructured":"Quah, J., Jiang, B., Tan, P. C., Siau, C. & Tan, T. Y. Impact of microbial Aetiology on mortality in severe community-acquired pneumonia. BMC Infect. Dis. 18, 1\u20139 (2018).","journal-title":"BMC Infect. Dis."},{"key":"3245_CR15","doi-asserted-by":"publisher","first-page":"101200","DOI":"10.1016\/j.genrep.2021.101200","volume":"23","author":"MN Hoque","year":"2021","unstructured":"Hoque, M. N. et al. Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases. Gene Rep. 23, 101200 (2021).","journal-title":"Gene Rep."},{"key":"3245_CR16","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/S0140-6736(20)30211-7","volume":"395","author":"N Chen","year":"2020","unstructured":"Chen, N. et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. Lancet 395, 507\u2013513 (2020).","journal-title":"Lancet"},{"key":"3245_CR17","first-page":"20","volume":"20","author":"F Zhou","year":"2020","unstructured":"Zhou, F. et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: A retrospective cohort study. Lancet 20, 20 (2020).","journal-title":"Lancet"},{"key":"3245_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12915-019-0703-z","volume":"17","author":"C Kumpitsch","year":"2019","unstructured":"Kumpitsch, C., Koskinen, K., Sch\u00f6pf, V. & Moissl-Eichinger, C. The microbiome of the upper respiratory tract in health and disease. BMC Biol. 17, 1\u201320 (2019).","journal-title":"BMC Biol."},{"key":"3245_CR19","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1038\/s41590-019-0451-9","volume":"20","author":"TP Wypych","year":"2019","unstructured":"Wypych, T. P., Wickramasinghe, L. C. & Marsland, B. J. The influence of the microbiome on respiratory health. Nat. Immunol. 20, 1279\u20131290 (2019).","journal-title":"Nat. Immunol."},{"key":"3245_CR20","doi-asserted-by":"publisher","first-page":"1168","DOI":"10.3389\/fphys.2018.01168","volume":"9","author":"E Mathieu","year":"2018","unstructured":"Mathieu, E. et al. Paradigms of lung microbiota functions in health and disease, particularly, in asthma. Front. Physiol. 9, 1168 (2018).","journal-title":"Front. Physiol."},{"key":"3245_CR21","doi-asserted-by":"publisher","first-page":"198018","DOI":"10.1016\/j.virusres.2020.198018","volume":"20","author":"D Dhar","year":"2020","unstructured":"Dhar, D. & Mohanty, A. Gut microbiota and Covid-19-possible link and implications. Virus Res. 20, 198018 (2020).","journal-title":"Virus Res."},{"key":"3245_CR22","first-page":"1","volume":"20","author":"V Sencio","year":"2021","unstructured":"Sencio, V., Machado, M. G. & Trottein, F. The lung\u2013gut axis during viral respiratory infections: The impact of gut dysbiosis on secondary disease outcomes. Mucosal Immunol. 20, 1\u20139 (2021).","journal-title":"Mucosal Immunol."},{"key":"3245_CR23","doi-asserted-by":"publisher","first-page":"5188","DOI":"10.1016\/j.ygeno.2020.09.039","volume":"112","author":"MN Hoque","year":"2020","unstructured":"Hoque, M. N. et al. Microbiome dynamics and genomic determinants of bovine mastitis. Genomics 112, 5188\u20135203 (2020).","journal-title":"Genomics"},{"key":"3245_CR24","first-page":"276","volume":"70","author":"T Zuo","year":"2021","unstructured":"Zuo, T. et al. Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. Gut 70, 276\u2013284 (2021).","journal-title":"Gut"},{"key":"3245_CR25","doi-asserted-by":"crossref","unstructured":"Hoque, M. N. et al. Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases. bioRxiv (2020).","DOI":"10.1101\/2020.10.19.345702"},{"key":"3245_CR26","doi-asserted-by":"publisher","first-page":"1840","DOI":"10.3389\/fmicb.2020.01840","volume":"11","author":"L Bao","year":"2020","unstructured":"Bao, L. et al. Oral microbiome and SARS-CoV-2: Beware of lung co-infection. Front. Microbiol. 11, 1840 (2020).","journal-title":"Front. Microbiol."},{"key":"3245_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/2049-2618-1-19","volume":"1","author":"LN Segal","year":"2013","unstructured":"Segal, L. N. et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome 1, 1\u201312 (2013).","journal-title":"Microbiome"},{"key":"3245_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-017-0381-4","volume":"6","author":"AA Pragman","year":"2018","unstructured":"Pragman, A. A. et al. The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease. Microbiome 6, 1\u201319 (2018).","journal-title":"Microbiome"},{"key":"3245_CR29","doi-asserted-by":"crossref","first-page":"20","DOI":"10.3389\/fcimb.2020.00020","volume":"10","author":"SD Zeppa","year":"2020","unstructured":"Zeppa, S. D., Agostini, D., Piccoli, G., Stocchi, V. & Sestili, P. Gut microbiota status in COVID-19: An unrecognized player?. Front. Cell. Infect. Microbiol. 10, 20 (2020).","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"3245_CR30","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-019-0747-x","volume":"7","author":"P Scepanovic","year":"2019","unstructured":"Scepanovic, P. et al. A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals. Microbiome 7, 1\u201315 (2019).","journal-title":"Microbiome"},{"key":"3245_CR31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-70812-6","volume":"10","author":"MR Islam","year":"2020","unstructured":"Islam, M. R. et al. Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity. Sci. Rep. 10, 1\u20139 (2020).","journal-title":"Sci. Rep."},{"key":"3245_CR32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-019-49468-4","volume":"9","author":"MN Hoque","year":"2019","unstructured":"Hoque, M. N. et al. Metagenomic deep sequencing reveals association of microbiome signature with functional biases in bovine mastitis. Sci. Rep. 9, 1\u201314 (2019).","journal-title":"Sci. Rep."},{"key":"3245_CR33","doi-asserted-by":"publisher","first-page":"5179","DOI":"10.1021\/acsnano.0c03402","volume":"14","author":"K Kalantar-Zadeh","year":"2020","unstructured":"Kalantar-Zadeh, K., Ward, S. A., Kalantar-Zadeh, K. & El-Omar, E. M. Considering the effects of microbiome and diet on SARS-CoV-2 infection: Nanotechnology roles. ACS Nano 14, 5179\u20135182 (2020).","journal-title":"ACS Nano"},{"key":"3245_CR34","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/ismej.2015.99","volume":"10","author":"WA de Steenhuijsen Piters","year":"2016","unstructured":"de Steenhuijsen Piters, W. A. et al. Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients. ISME J. 10, 97\u2013108 (2016).","journal-title":"ISME J."},{"key":"3245_CR35","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nrmicro.2017.14","volume":"15","author":"WH Man","year":"2017","unstructured":"Man, W. H., de Steenhuijsen Piters, W. A. & Bogaert, D. The microbiota of the respiratory tract: Gatekeeper to respiratory health. Nat. Rev. Microbiol. 15, 259\u2013270 (2017).","journal-title":"Nat. Rev. Microbiol."},{"key":"3245_CR36","doi-asserted-by":"publisher","first-page":"1328","DOI":"10.1038\/s41564-019-0447-0","volume":"4","author":"HM Rowe","year":"2019","unstructured":"Rowe, H. M. et al. Direct interactions with influenza promote bacterial adherence during respiratory infections. Nat. Microbiol. 4, 1328\u20131336 (2019).","journal-title":"Nat. Microbiol."},{"key":"3245_CR37","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/S1473-3099(20)30484-9","volume":"20","author":"E Petersen","year":"2020","unstructured":"Petersen, E. et al. Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics. Lancet Infect. Dis. 20, 20 (2020).","journal-title":"Lancet Infect. Dis."},{"key":"3245_CR38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-021-99104-3","volume":"11","author":"MS Rahman","year":"2021","unstructured":"Rahman, M. S. et al. Microbiome signature and diversity regulates the level of energy production under anaerobic condition. Sci. Rep. 11, 1\u201323 (2021).","journal-title":"Sci. Rep."},{"key":"3245_CR39","doi-asserted-by":"publisher","first-page":"819","DOI":"10.2478\/s11756-020-00614-8","volume":"76","author":"L Janda","year":"2021","unstructured":"Janda, L., Mihal\u010din, M. & \u0160\u0165astn\u00e1, M. Is a healthy microbiome responsible for lower mortality in COVID-19?. Biologia 76, 819\u2013829 (2021).","journal-title":"Biologia"},{"key":"3245_CR40","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1002\/jmv.25890","volume":"92","author":"J Chaung","year":"2020","unstructured":"Chaung, J., Chan, D., Pada, S. & Tambyah, P. A. Coinfection with COVID-19 and coronavirus HKU1\u2014the critical need for repeat testing if clinically indicated. J. Med. Virol. 92, 1785\u20131786 (2020).","journal-title":"J. Med. Virol."},{"key":"3245_CR41","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1038\/nm1024","volume":"10","author":"L Van Der Hoek","year":"2004","unstructured":"Van Der Hoek, L. et al. Identification of a new human coronavirus. Nat. Med. 10, 368\u2013373 (2004).","journal-title":"Nat. Med."},{"key":"3245_CR42","doi-asserted-by":"publisher","first-page":"153","DOI":"10.2217\/fmb.10.166","volume":"6","author":"BC Fielding","year":"2011","unstructured":"Fielding, B. C. Human coronavirus NL63: A clinically important virus?. Future Microbiol. 6, 153\u2013159 (2011).","journal-title":"Future Microbiol."},{"key":"3245_CR43","doi-asserted-by":"publisher","first-page":"1324","DOI":"10.3201\/eid2606.200299","volume":"26","author":"X Wu","year":"2020","unstructured":"Wu, X. et al. Co-infection with SARS-CoV-2 and influenza A virus in patient with pneumonia, China. Emerg. Infect. Dis. 26, 1324 (2020).","journal-title":"Emerg. Infect. Dis."},{"key":"3245_CR44","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.cmi.2020.08.012","volume":"27","author":"A Calcagno","year":"2021","unstructured":"Calcagno, A. et al. Co-infection with other respiratory pathogens in COVID-19 patients. Clin. Microbiol. Infect. 27, 297\u2013298 (2021).","journal-title":"Clin. Microbiol. Infect."},{"key":"3245_CR45","first-page":"20","volume":"12","author":"B Singh","year":"2020","unstructured":"Singh, B., Kaur, P., Reid, R.-J., Shamoon, F. & Bikkina, M. COVID-19 and influenza co-infection: Report of three cases. Cureus 12, 20 (2020).","journal-title":"Cureus"},{"issue":"86","key":"3245_CR46","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1111\/prd.12363","volume":"2000","author":"SP Szafra\u0144ski","year":"2021","unstructured":"Szafra\u0144ski, S. P., Slots, J. & Stiesch, M. The human oral phageome. Periodontol. 2000(86), 79\u201396 (2021).","journal-title":"Periodontol."},{"key":"3245_CR47","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1128\/IAI.71.2.591-596.2003","volume":"71","author":"PB Eckburg","year":"2003","unstructured":"Eckburg, P. B., Lepp, P. W. & Relman, D. A. Archaea and their potential role in human disease. Infect. Immun. 71, 591\u2013596 (2003).","journal-title":"Infect. Immun."},{"key":"3245_CR48","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1038\/s41579-020-0395-y","volume":"18","author":"TM Rawson","year":"2020","unstructured":"Rawson, T. M., Ming, D., Ahmad, R., Moore, L. S. & Holmes, A. H. Antimicrobial use, drug-resistant infections and COVID-19. Nat. Rev. Microbiol. 18, 409\u2013410 (2020).","journal-title":"Nat. Rev. Microbiol."},{"key":"3245_CR49","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.jhin.2020.05.020","volume":"106","author":"D Don\u00e0","year":"2020","unstructured":"Don\u00e0, D., Di Chiara, C. & Sharland, M. Multi-drug-resistant infections in the COVID-19 era: A framework for considering the potential impact. J. Hosp. Infect. 106, 198\u2013199 (2020).","journal-title":"J. Hosp. Infect."},{"key":"3245_CR50","first-page":"1","volume":"20","author":"J Wu","year":"2020","unstructured":"Wu, J., Wang, K., Wang, X., Pang, Y. & Jiang, C. The role of the gut microbiome and its metabolites in metabolic diseases. Protein Cell 20, 1\u201314 (2020).","journal-title":"Protein Cell"},{"key":"3245_CR51","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1038\/s42255-020-0237-2","volume":"2","author":"JS Ayres","year":"2020","unstructured":"Ayres, J. S. A metabolic handbook for the COVID-19 pandemic. Nat. Metab. 2, 572\u2013585 (2020).","journal-title":"Nat. Metab."},{"key":"3245_CR52","doi-asserted-by":"publisher","first-page":"e1008556","DOI":"10.1371\/journal.ppat.1008556","volume":"16","author":"A Breiman","year":"2020","unstructured":"Breiman, A., Ruv\u00ebn-Clouet, N. & Le Pendu, J. Harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as SARS-CoV-2. PLoS Pathog. 16, e1008556 (2020).","journal-title":"PLoS Pathog."},{"issue":"10","key":"3245_CR53","doi-asserted-by":"publisher","first-page":"giaa111","DOI":"10.1093\/gigascience\/giaa111","volume":"9","author":"KL Kalantar","year":"2020","unstructured":"Kalantar, K. L. et al. IDseq\u2014an open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience 9(10), giaa111 (2020).","journal-title":"Gigascience"},{"key":"3245_CR54","doi-asserted-by":"publisher","first-page":"pdb. prot5368","DOI":"10.1101\/pdb.prot5368","volume":"2010","author":"EM Glass","year":"2010","unstructured":"Glass, E. M., Wilkening, J., Wilke, A., Antonopoulos, D. & Meyer, F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harbor Protoc. 2010, pdb. prot5368 (2010).","journal-title":"Cold Spring Harbor Protoc."},{"key":"3245_CR55","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gky962","volume":"47","author":"M Kanehisa","year":"2019","unstructured":"Kanehisa, M., Sato, Y., Furumichi, M., Morishima, K. & Tanabe, M. New approach for understanding genome variations in KEGG. Nucleic Acids Res. 47, D590\u2013D595 (2019).","journal-title":"Nucleic Acids Res."},{"key":"3245_CR56","doi-asserted-by":"publisher","first-page":"860","DOI":"10.3389\/fmicb.2020.00860","volume":"11","author":"MN Hoque","year":"2020","unstructured":"Hoque, M. N. et al. Insights into the resistome of bovine clinical mastitis microbiome, a key factor in disease complication. Front. Microbiol. 11, 860 (2020).","journal-title":"Front. Microbiol."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-03245-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-03245-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-03245-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,3]],"date-time":"2022-12-03T13:12:44Z","timestamp":1670073164000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-021-03245-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,15]]},"references-count":56,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,12]]}},"alternative-id":["3245"],"URL":"https:\/\/doi.org\/10.1038\/s41598-021-03245-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-480069\/v1","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12,15]]},"assertion":[{"value":"30 May 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 December 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":"24042"}}