{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:10:53Z","timestamp":1772136653852,"version":"3.50.1"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,5,4]],"date-time":"2022-05-04T00:00:00Z","timestamp":1651622400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"},{"start":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T00:00:00Z","timestamp":1683158400000},"content-version":"am","delay-in-days":365,"URL":"http:\/\/rsc.li\/journals-terms-of-use"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/ILS\/Flagship\/2019"],"award-info":[{"award-number":["BT\/ILS\/Flagship\/2019"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/RLF\/Re-entry\/25\/2015"],"award-info":[{"award-number":["BT\/RLF\/Re-entry\/25\/2015"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["CRG\/2018\/002052"],"award-info":[{"award-number":["CRG\/2018\/002052"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/ILS\/Flagship\/2019"],"award-info":[{"award-number":["BT\/ILS\/Flagship\/2019"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/RLF\/Re-entry\/25\/2015"],"award-info":[{"award-number":["BT\/RLF\/Re-entry\/25\/2015"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["CRG\/2018\/002052"],"award-info":[{"award-number":["CRG\/2018\/002052"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["rsc.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2022,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown alterations in nasopharyngeal (NP) microbial diversity, enrichment of opportunistic pathogens and their role in co-infections during respiratory infections. Therefore, we hypothesized that microbial diversity changes, with increase in the population of opportunistic pathogens, during SARS-CoV2 infection in the nasopharynx, which may be involved in co-infection in COVID-19 patients. The 16S rRNA variable regions, V1\u2013V9, of NP samples of control and COVID-19 (symptomatic and asymptomatic) patients were sequenced using the Oxford Nanopore\u2122 technology. Comprehensive bioinformatics analysis for determining alpha\/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index were used to analyze the control and COVID-19-specific NP microbiomes. We observed significant dysbiosis in the COVID-19 NP microbiome with an increase in the abundance of opportunistic pathogens at genus and species levels in asymptomatic\/symptomatic patients. The significant abundance of Mycobacteria spp. and Mycoplasma spp. in symptomatic patients suggests their association and role in co-infections in COVID-19 patients. Furthermore, we found strong correlation of enrichment of Mycobacteria and Mycoplasma with the occurrences of chest pain and fever in symptomatic COVID-19 patients. This is the first study from India to show the abundance of Mycobacteria and Mycoplasma opportunistic pathogens in non-hospitalized COVID-19 patients and their relationship with symptoms, indicating the possibility of co-infections.<\/jats:p>\n                  <jats:p\/>","DOI":"10.1039\/d2mo00044j","type":"journal-article","created":{"date-parts":[[2022,5,4]],"date-time":"2022-05-04T08:52:45Z","timestamp":1651654365000},"page":"490-505","update-policy":"https:\/\/doi.org\/10.1039\/rsc_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of\n                    <i>Mycobacterium<\/i>\n                    and\n                    <i>Mycoplasma<\/i>\n                    in COVID-19 patients: a potential source of co-infection"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9132-6078","authenticated-orcid":false,"given":"Punit","family":"Prasad","sequence":"first","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7513-7325","authenticated-orcid":false,"given":"Soumendu","family":"Mahapatra","sequence":"additional","affiliation":[{"name":"Kalinga Institute of Industrial Technology (KIIT), School of Biotechnology b , Bhubaneswar, Odisha, India"},{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2354-7503","authenticated-orcid":false,"given":"Rasmita","family":"Mishra","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5568-680X","authenticated-orcid":false,"given":"Krushna Chandra","family":"Murmu","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shifu","family":"Aggarwal","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manisha","family":"Sethi","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Priyanka","family":"Mohapatra","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3259-0124","authenticated-orcid":false,"given":"Arup","family":"Ghosh","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rina","family":"Yadav","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiren","family":"Dodia","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shamima Azma","family":"Ansari","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saikat","family":"De","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deepak","family":"Singh","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amol","family":"Suryawanshi","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rupesh","family":"Dash","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shantibhushan","family":"Senapati","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tushar K","family":"Beuria","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 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punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sunil K","family":"Raghav","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ajay","family":"Parida","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences a , Bhubaneswar, Odisha, India \u00a0 ajayparida@ils.res.in \u00a0 drajayparida@gmail.com \u00a0 punit@ils.res.in \u00a0 punit.ils@gov.in"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,4]]},"reference":[{"key":"2026010813080212100_cit1","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.3389\/fmicb.2020.01302","article-title":"Main Clinical Features of COVID-19 and Potential Prognostic and Therapeutic Value of the Microbiota in SARS-CoV-2 Infections","volume":"11","author":"He","year":"2020","journal-title":"Front. Microbiol."},{"key":"2026010813080212100_cit2","doi-asserted-by":"crossref","first-page":"100073","DOI":"10.1016\/j.humic.2020.100073","article-title":"Lung microbiome and coronavirus disease 2019 (COVID-19): Possible link and implications","volume":"17","author":"Khatiwada","year":"2020","journal-title":"Hum. Microbiome J."},{"key":"2026010813080212100_cit3","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/s11684-020-0754-0","article-title":"Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to 2019-nCoV infection","volume":"14","author":"Zou","year":"2020","journal-title":"Front. 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