{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,25]],"date-time":"2025-12-25T01:26:00Z","timestamp":1766625960066,"version":"build-2065373602"},"reference-count":29,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,7,19]],"date-time":"2024-07-19T00:00:00Z","timestamp":1721347200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Regione Campania","award":["FESR 2014\/2020","B14I20001980006","2014\/2020","B41C17000080007"],"award-info":[{"award-number":["FESR 2014\/2020","B14I20001980006","2014\/2020","B41C17000080007"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The nasopharyngeal tract contains a complex microbial community essential to maintaining host homeostasis. Recent studies have shown that SARS-CoV-2 infection changes the microbial composition of the nasopharynx. Still, little is known about how it affects the fungal microbiome, which could provide valuable insights into disease pathogenesis. Nasopharyngeal swabs were collected from 55 patients, during three distinct COVID-19 waves that occurred in the Campania Region (southern Italy). An RNA-seq-based analysis was performed to evaluate changes in mycobiota diversity, showing variations depending on the disease\u2019s severity and the sample collection wave. The phyla Basidiomycota and Ascomycota were shown to have higher abundance in patients with severe symptoms. Furthermore, the diversity of the fungal population was greater in the second wave. Conclusion: According to our research, COVID-19 induces significant dysbiosis of the fungal microbiome, which may contribute to disease pathogenesis, and understanding its underlying mechanisms could contribute to developing effective treatments.<\/jats:p>","DOI":"10.3390\/microorganisms12071468","type":"journal-article","created":{"date-parts":[[2024,7,19]],"date-time":"2024-07-19T09:14:53Z","timestamp":1721380493000},"page":"1468","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Influence of Mycobiota in the Nasopharyngeal Tract of COVID-19 Patients"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7406-9882","authenticated-orcid":false,"given":"Veronica","family":"Folliero","sequence":"first","affiliation":[{"name":"Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0758-5059","authenticated-orcid":false,"given":"Carlo","family":"Ferravante","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Medical Genomics Program, AOU \u2018S. Giovanni di Dio e Ruggi d\u2019Aragona\u2019, University of Salerno, 84131 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1654-8500","authenticated-orcid":false,"given":"Federica","family":"Dell\u2019Annunziata","sequence":"additional","affiliation":[{"name":"Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6374-693X","authenticated-orcid":false,"given":"Rosario Nicola","family":"Brancaccio","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1890-6682","authenticated-orcid":false,"given":"Ylenia","family":"D\u2019Agostino","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Medical Genomics Program, AOU \u2018S. Giovanni di Dio e Ruggi d\u2019Aragona\u2019, University of Salerno, 84131 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giorgio","family":"Giurato","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Genome Research Center for Health\u2014CRGS, Campus of Medicine, University of Salerno, 84081 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roberta","family":"Manente","sequence":"additional","affiliation":[{"name":"Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2926-9068","authenticated-orcid":false,"given":"Ilaria","family":"Terenzi","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rita","family":"Greco","sequence":"additional","affiliation":[{"name":"UOC Microbiologia e Virologia, AORN S. Anna e S. Sebastiano, 81100 Caserta, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7757-6855","authenticated-orcid":false,"given":"Giovanni","family":"Boccia","sequence":"additional","affiliation":[{"name":"Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"UOC Igiene Ospedaliera ed Epidemiologia, DAI Igiene Sanitaria e Valutativa, San Giovanni di Dio e Ruggi D\u2019Aragona, University of Salerno, 84131 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8109-0655","authenticated-orcid":false,"given":"Pasquale","family":"Pagliano","sequence":"additional","affiliation":[{"name":"Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Infectious Disease Unit, San Giovanni di Dio e Ruggi D\u2019Aragona, University of Salerno, 84131 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0455-2083","authenticated-orcid":false,"given":"Alessandro","family":"Weisz","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Medical Genomics Program, AOU \u2018S. Giovanni di Dio e Ruggi d\u2019Aragona\u2019, University of Salerno, 84131 Salerno, Italy"},{"name":"Genome Research Center for Health\u2014CRGS, Campus of Medicine, University of Salerno, 84081 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3321-4331","authenticated-orcid":false,"given":"Gianluigi","family":"Franci","sequence":"additional","affiliation":[{"name":"Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D\u2019Aragona, University of Salerno, 84131 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1783-5015","authenticated-orcid":false,"given":"Francesca","family":"Rizzo","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry \u201cScuola Medica Salernitana\u201d, University of Salerno, 84081 Salerno, Italy"},{"name":"Genome Research Center for Health\u2014CRGS, Campus of Medicine, University of Salerno, 84081 Salerno, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1038\/s41422-020-0332-7","article-title":"Interaction between Microbiota and Immunity in Health and Disease","volume":"30","author":"Zheng","year":"2020","journal-title":"Cell Res."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Belvoncikova, P., Splichalova, P., Videnska, P., and Gardlik, R. (2022). The Human Mycobiome: Colonization, Composition and the Role in Health and Disease. J. Fungi, 8.","DOI":"10.3390\/jof8101046"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Tang, S., Jin, L., Lei, P., Shao, C., Wu, S., Yang, Y., He, Y., Ren, R., and Xu, J. (2022). Whole-Genome Assembly and Analysis of a Medicinal Fungus: Inonotus Hispidus. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.967135"},{"key":"ref_4","unstructured":"Prevel, R., Boyer, P., Beaufils, F., Orieux, A., Berger, P., Boyer, A., Delhaes, L., and Gruson, D. (2020). The Influence of Lung and Oropharyngeal Microbiota-Mycobiota on Ventilator-Associated Pneumonia Occurrence in Critically Ill Patients: A Systematic Review. Microbiota Health Dis., 2."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2022","DOI":"10.1080\/21505594.2022.2146568","article-title":"Specific Associations between Fungi and Bacteria in Broncho-Alveolar Aspirates from Mechanically Ventilated Intensive Care Unit Patients","volume":"13","author":"Shajiei","year":"2022","journal-title":"Virulence"},{"key":"ref_6","unstructured":"Cascella, M., Rajnik, M., Aleem, A., Dulebohn, S.C., and Di Napoli, R. (2023). Features, Evaluation, and Treatment of Coronavirus (COVID-19). StatPearls, StatPearls Publishing."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.idc.2022.01.003","article-title":"COVID-19 Pathogenesis and Clinical Manifestations","volume":"36","author":"Marcelin","year":"2022","journal-title":"Infect. Dis. Clin. N. Am."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Harding, J.N., Siefker, D., Vu, L., You, D., DeVincenzo, J., Pierre, J.F., and Cormier, S.A. (2020). Altered Gut Microbiota in Infants Is Associated with Respiratory Syncytial Virus Disease Severity. BMC Microbiol., 20.","DOI":"10.1186\/s12866-020-01816-5"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2005","DOI":"10.1093\/infdis\/jiz021","article-title":"Serum Metabolome Is Associated With the Nasopharyngeal Microbiota and Disease Severity Among Infants With Bronchiolitis","volume":"219","author":"Stewart","year":"2019","journal-title":"J. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1136\/gutjnl-2020-323020","article-title":"Gut Microbiota Composition Reflects Disease Severity and Dysfunctional Immune Responses in Patients with COVID-19","volume":"70","author":"Yeoh","year":"2021","journal-title":"Gut"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Soffritti, I., D\u2019Accolti, M., Fabbri, C., Passaro, A., Manfredini, R., Zuliani, G., Libanore, M., Franchi, M., Contini, C., and Caselli, E. (2021). Oral Microbiome Dysbiosis Is Associated With Symptoms Severity and Local Immune\/Inflammatory Response in COVID-19 Patients: A Cross-Sectional Study. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.687513"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"105506","DOI":"10.1016\/j.micpath.2022.105506","article-title":"NGS Analysis of Nasopharyngeal Microbiota in SARS-CoV-2 Positive Patients during the First Year of the Pandemic in the Campania Region of Italy","volume":"165","author":"Giugliano","year":"2022","journal-title":"Microb. Pathog."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2275","DOI":"10.1002\/jmv.27571","article-title":"Nasopharyngeal Virome Analysis of COVID-19 Patients during Three Different Waves in Campania Region of Italy","volume":"94","author":"Ferravante","year":"2022","journal-title":"J. Med. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"101401","DOI":"10.1016\/j.beha.2022.101401","article-title":"COVID-19 Disease and Immune Dysregulation","volume":"35","author":"Davitt","year":"2022","journal-title":"Best. Pract. Res. Clin. Haematol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"5567","DOI":"10.1002\/jmv.27998","article-title":"Dynamics of Nasopharyngeal Tract Phageome and Association with Disease Severity and Age of Patients during Three Waves of COVID-19","volume":"94","author":"Ferravante","year":"2022","journal-title":"J. Med. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Ferravante, C., Memoli, D., Palumbo, D., Ciaramella, P., Di Loria, A., D\u2019Agostino, Y., Nassa, G., Rizzo, F., Tarallo, R., and Weisz, A. (2021). HOME-BIO (SHOtgun MEtagenomic Analysis of BIOlogical Entities): A Specific and Comprehensive Pipeline for Metagenomic Shotgun Sequencing Data Analysis. BMC Bioinform., 22.","DOI":"10.1186\/s12859-021-04004-y"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s41479-021-00083-w","article-title":"The Role of Co-Infections and Secondary Infections in Patients with COVID-19","volume":"13","author":"Feldman","year":"2021","journal-title":"Pneumonia (Nathan)"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e2165970","DOI":"10.1080\/22221751.2023.2165970","article-title":"The Nasopharyngeal Microbiome in COVID-19","volume":"12","author":"Candel","year":"2023","journal-title":"Emerg. Microbes Infect."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"96","DOI":"10.4068\/cmj.2022.58.3.96","article-title":"COVID-19 and the Human Gut Microbiome: An Under-Recognized Association","volume":"58","author":"Abbasi","year":"2022","journal-title":"Chonnam Med. J."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Merenstein, C., Bushman, F.D., and Collman, R.G. (2022). Alterations in the Respiratory Tract Microbiome in COVID-19: Current Observations and Potential Significance. Microbiome, 10.","DOI":"10.1186\/s40168-022-01342-8"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.ijpddr.2018.12.004","article-title":"New Life for an Old Drug: In Vitro and in Vivo Effects of the Anthelmintic Drug Niclosamide against Toxoplasma Gondii RH Strain","volume":"9","author":"Zhang","year":"2019","journal-title":"Int. J. Parasitol. Drugs Drug Resist."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1053\/j.gastro.2020.06.048","article-title":"Alterations in Fecal Fungal Microbiome of Patients with COVID-19 During Time of Hospitalization until Discharge","volume":"159","author":"Zuo","year":"2020","journal-title":"Gastroenterology"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Maeda, Y., Motooka, D., Kawasaki, T., Oki, H., Noda, Y., Adachi, Y., Niitsu, T., Okamoto, S., Tanaka, K., and Fukushima, K. (2022). Longitudinal Alterations of the Gut Mycobiota and Microbiota on COVID-19 Severity. BMC Infect. Dis., 22.","DOI":"10.1186\/s12879-022-07358-7"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Hoque, M.N., Rahman, M.S., Sarkar, M.M.H., Habib, M.A., Akter, S., Banu, T.A., Goswami, B., Jahan, I., Hossain, M.A., and Khan, M.S. (2023). Transcriptome Analysis Reveals Increased Abundance and Diversity of Opportunistic Fungal Pathogens in Nasopharyngeal Tract of COVID-19 Patients. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0278134"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Wu, X., Xia, Y., He, F., Zhu, C., and Ren, W. (2021). Intestinal Mycobiota in Health and Diseases: From a Disrupted Equilibrium to Clinical Opportunities. Microbiome, 9.","DOI":"10.1186\/s40168-021-01024-x"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Aragona, M., Haegi, A., Valente, M.T., Riccioni, L., Orzali, L., Vitale, S., Luongo, L., and Infantino, A. (2022). New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?. J. Fungi, 8.","DOI":"10.3390\/jof8070737"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Reinold, J., Farahpour, F., Schoerding, A.-K., Fehring, C., Dolff, S., Konik, M., Korth, J., van Baal, L., Buer, J., and Witzke, O. (2022). The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients. Front. Cell Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.848650"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Seyedjavadi, S.S., Bagheri, P., Nasiri, M.J., Razzaghi-Abyaneh, M., and Goudarzi, M. (2022). Fungal Infection in Co-Infected Patients With COVID-19: An Overview of Case Reports\/Case Series and Systematic Review. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.888452"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Choi, H.M., Moon, S.Y., Yang, H.I., and Kim, K.S. (2021). Understanding Viral Infection Mechanisms and Patient Symptoms for the Development of COVID-19 Therapeutics. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22041737"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/12\/7\/1468\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:19:31Z","timestamp":1760109571000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/12\/7\/1468"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,19]]},"references-count":29,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2024,7]]}},"alternative-id":["microorganisms12071468"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms12071468","relation":{},"ISSN":["2076-2607"],"issn-type":[{"type":"electronic","value":"2076-2607"}],"subject":[],"published":{"date-parts":[[2024,7,19]]}}}