SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome
Open accessAbstract
Background Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, and the upper respiratory tract (URT) microbiome.Objective We sought to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults and to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19.Methods We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild to moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the ⍺-diversity, β-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex.Results The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (β linear regression coefficient = 7.53; 95% CI, 0.17-14.89; P = .045). In differential abundance testing, 9 amplicon sequence variants were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified amplicon sequence variant being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified amplicon sequence variants were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19.Conclusions Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19.
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High intake of oil, vitamin D, and vitamin K reduces COVID-19 risk, while increased alcohol intake and smoking are associated with increased COVID-19 risk.
“Changes in lifestyle, i.e. high intake of oil, vitamin D, and vitamin K reduces the COVID-19 risk, while increased intake of alcohol and smoking are associated with increased COVID-19 risk [29].”
From Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe (2022) · cites this paper as [29]
The Introduction and Results and discussion (page not provided) examine associations between SARS-CoV-2 infection, viral load, and the upper respiratory tract microbiome. Searches for oil, vitamin D, vitamin K, alcohol, smoking, and lifestyle risk found no passage addressing the claimed effects on COVID-19 risk. (LLM, conf=0.78)
Experimental — accuracy not yet measuredEconomic inequality, per capita hospital beds, and blood types are factors responsible for increased cases and mortality worldwide, with blood Group B and AB protective against COVID-19.
“Generally, numerous other factors responsible for the increase in the number of cases and mortality throughout the world are economic inequality, per capita hospital beds, and blood types, with Group B and AB being protective against COVID-19.”
From Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe (2022) · cites this paper as [29]
The Results and discussion section examines upper-respiratory-tract microbiome differences by SARS-CoV-2 infection status and viral load (page unavailable). Searches for economic inequality, hospital beds, and protective effects of blood groups B and AB found no passage in our copy addressing those claims. (LLM, conf=0.76)
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Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works
vegan: Community Ecology Package
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099 · see citing works
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,013 · see citing works
A new method for non-parametric multivariate analysis of variance
Anderson, M. J. (2001) · Austral Ecology · doi:10.1111/j.1442-9993.2001.01070.pp.x · Cited by 13,828 · see citing works
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., & Schloss, P. D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01043-13 · Cited by 7,004 · see citing works
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682 · see citing works
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018) · Microbiome · doi:10.1186/s40168-018-0605-2 · Cited by 3,493 · see citing works
HCA Lung Biological Network, Sungnak, W., Huang, N., Bécavin, C., Berg, M., Queen, R., Litvinukova, M., Talavera-López, C., Maatz, H., Reichart, D., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0868-6 · Cited by 2,501 · see citing works
Viral dynamics in mild and severe cases of COVID-19
Liu, Y., Yan, L.-M., Wan, L., Xiang, T.-X., Le, A., Liu, J.-M., Peiris, M., Poon, L. L. M., & Zhang, W. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30232-2 · Cited by 1,727 · see citing works
Co-infections in people with COVID-19: a systematic review and meta-analysis.
Lansbury, L., Lim, B., Baskaran, V., & Lim, W. S. (2020) · Journal of Infection · doi:10.1016/j.jinf.2020.05.046 · Cited by 1,619 · see citing works
The microbiota of the respiratory tract: gatekeeper to respiratory health
Man, W. H., de Steenhuijsen Piters, W. A. A., & Bogaert, D. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.14 · Cited by 1,384 · see citing works
Sungnak, W., Huang, N., Bécavin, C., & Berg, M. (2020) · PubMed · Cited by 1,196 · see citing works
Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza
Gu, S., Chen, Y., Wu, Z., Chen, Y., Gao, H., Lv, L., Guo, F., Zhang, X., Luo, R., Huang, C., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa709 · Cited by 790 · see citing works
Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens
Kim, D., Quinn, J., Pinsky, B., Shah, N. H., & Brown, I. (2020) · JAMA · doi:10.1001/jama.2020.6266 · Cited by 769 · see citing works
SARS-CoV-2 viral load predicts COVID-19 mortality
Pujadas, E., Chaudhry, F. F., McBride, R. B., Richter, F., Zhao, S., Wajnberg, A., Nadkarni, G. N., Glicksberg, B. S., Houldsworth, J., & Cordon‐Cardo, C. (2020) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(20)30354-4 · Cited by 534 · see citing works
Shen, Z., Xiao, Y., Kang, L., Ma, W., Shi, L., Zhang, L., Zhou, Z., Yang, J., Zhong, J., Yang, D., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa203 · Cited by 513 · see citing works
Piters, W. A. A. D. S., Heinonen, S., Hasrat, R., Bunsow, E., Smith, B., Suárez-Arrabal, M. C., Chaussabel, D., Cohen, D. M., Sanders, E. A. M., Ramilo, O., et al. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201602-0220oc · Cited by 423 · see citing works
Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients
Maio, F. D., Posteraro, B., Ponziani, F. R., Cattani, P., Gasbarrini, A., & Sanguinetti, M. (2020) · Biological Procedures Online · doi:10.1186/s12575-020-00131-7 · Cited by 115 · see citing works
The lung tissue microbiota features of 20 deceased patients with COVID-19
Fan, J., Li, X., Gao, Y., Zhou, J., Wang, S., Huang, B., Wu, J., Cao, Q., Chen, Y., Wang, Z., et al. (2020) · Journal of Infection · doi:10.1016/j.jinf.2020.06.047 · Cited by 106 · see citing works
Rosas-Salazar, C., Shilts, M. H., Tovchigrechko, A., Schobel, S., Chappell, J. D., Larkin, E. K., Shankar, J., Yooseph, S., Nelson, K. E., Halpin, R. A., et al. (2016) · Journal of Infectious Diseases · doi:10.1093/infdis/jiw456 · Cited by 102 · see citing works
Self-citationRosas‐Salazar, C., Shilts, M. H., Tovchigrechko, A., Schobel, S., Chappell, J. D., Larkin, E. K., Gebretsadik, T. S., Halpin, R., Nelson, K. E., Moore, M. L., et al. (2018) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.10.049 · Cited by 98 · see citing works
Self-citationDietary Arginine Regulates Severity of Experimental Colitis and Affects the Colonic Microbiome
Singh, K., Gobert, A. P., Coburn, L. A., Barry, D. P., Allaman, M. M., Asim, M., Luis, P. B., Schneider, C. G., Milne, G. L., Boone, H. H., et al. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00066 · Cited by 98 · see citing works
Self-citationZhang, H., Ai, J., Yang, W., Zhou, X., He, F., Xie, S., Zeng, W., Li, Y., Yu, Y., Gou, X., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa663 · Cited by 94 · see citing works
Ederveen, T. H. A., Ferwerda, G., Ahout, I. M. L., Vissers, M., de Groot, R., Boekhorst, J., Timmerman, H. M., Huynen, M. A., van Hijum, S. A. F. T., & de Jonge, M. I. (2018) · Microbiome · doi:10.1186/s40168-017-0395-y · Cited by 93 · see citing works
Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection
Sonawane, A. R., Tian, L., Chu, C., Qiu, X., Wang, L., Holden‐Wiltse, J., Grier, A., Gill, S. R., Caserta, M. T., Falsey, A. R., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-50217-w · Cited by 54 · see citing works
Hiremath, G. S., Shilts, M. H., Boone, H. H., Correa, H., Acra, S. A., Tovchigrechko, A., Rajagopala, S. V., & Das, S. R. (2019) · Clinical and Translational Gastroenterology · doi:10.14309/ctg.0000000000000039 · Cited by 49 · see citing works
Self-citationKimura, K. S., Freeman, M. H., Wessinger, B. C., Gupta, V., Sheng, Q., Huang, L., Wahlde, K. V., Das, S. R., Chowdhury, N. I., & Turner, J. H. (2020) · International Forum of Allergy & Rhinology · doi:10.1002/alr.22703 · Cited by 35 · see citing works
Self-citationShilts, M. H., Rosas‐Salazar, C., Turi, K. N., Rajan, D., Rajagopala, S. V., Patterson, M. F., Gebretsadik, T. S., Anderson, L. J., Peebles, R. S., Hartert, T. V., et al. (2020) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2020.06.023 · Cited by 20 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 5
- Kimura K.S. Freeman M.H. Wessinger B.C. Gupta V. Sheng Q. Huang L.C. Interim analysis of an open-label randomized controlled trial evaluating nasal irrigations in non-hospitalized patients with COVID-19 Int Forum Allergy Rhinol 10 2020 1325 1328 32914928 PMC7722064
- Singh K. Gobert A.P. Coburn L.A. Barry D.P. Allaman M. Asim M. Dietary arginine regulates severity of experimental colitis and affects the colonic microbiome Front Cell Infect Microbiol 9 2019 66 30972302 PMC6443829
- Hiremath G. Shilts M.H. Boone H.H. Correa H. Acra S. Tovchigrechko A. The salivary microbiome is altered in children with eosinophilic esophagitis and correlates with disease activity Clin Transl Gastroenterol 10 2019 e00039 PMC6613866 31107724
- Kozich J.J. Westcott S.L. Baxter N.T. Highlander S.K. Schloss P.D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform Appl Environ Microbiol 79 2013 5112 5120 23793624 PMC3753973
- Love M.I. Huber W. Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biol 15 2014 550 25516281 PMC4302049
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Ancona, G., Alagna, L., Alteri, C., Palomba, E., Tonizzo, A., Pastena, A., Muscatello, A., Gori, A., & Bandera, A. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1080043 · Cited by 117 · see citing works
Hernández‐Terán, A., Mejía-Nepomuceno, F., Herrera, M. T., Barreto, O., García, E., Castillejos-López, M. D. J., Boukadida, C., Matías‐Florentino, M., Rincón-Rubio, A., Ávila‐Ríos, S., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-00851-0 · Cited by 80 · see citing works
Merenstein, C., Bushman, F. D., & Collman, R. G. (2022) · Microbiome · doi:10.1186/s40168-022-01342-8 · Cited by 67 · see citing works
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Gang, J., Wang, H., Xue, X., & Zhang, S. J. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.963488 · Cited by 61 · see citing works
Hurst, J. H., McCumber, A. W., Aquino, J. N., Rodriguez, J., Heston, S. M., Lugo, D. J., Rotta, A. T., Turner, N., Pfeiffer, T. S., Gurley, T. C., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciac184 · Cited by 59 · see citing works
Oral dysbiosis and its linkage with SARS-CoV-2 infection
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Zhou, T., Wu, J., Zeng, Y., Li, J., Yan, J., Meng, W., Han, H., Feng, F., He, J., Zhao, S., et al. (2022) · MedComm · doi:10.1002/mco2.112 · Cited by 40 · see citing works
Bataineh, M. T. A., Henschel, A., Mousa, M., Daou, M., Waasia, F. Z., Kannout, H., Khalili, M., Kayasseh, M. A., AlKhajeh, A. S., Uddin, M., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.761067 · Cited by 36 · see citing works
Li, H., Wu, X., Zeng, H., Chang, B., Cui, Y. J., Zhang, J., Wang, R., & Ding, T. (2023) · Microbiome · doi:10.1186/s40168-023-01597-9 · Cited by 36 · see citing works
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Chen, Y., & Lei, X. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.919380 · Cited by 24 · see citing works
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Pozzi, C., Levi, R., Braga, D., Carli, F., Darwich, A., Spadoni, I., Oresta, B., Dioguardi, C. C., Peano, C., Ubaldi, L., et al. (2022) · Gastro Hep Advances · doi:10.1016/j.gastha.2021.12.006 · Cited by 23 · see citing works
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Qin, T., Wang, Y., Deng, J., Xu, B., Zhu, X., Wang, J., Zhou, H., Zhao, N., Jin, F., Ren, H., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.01956-21 · Cited by 22 · see citing works
Kumar, D., Pandit, R. J., Sharma, S., Raval, J. N., Patel, Z. Z., Joshi, M. N., & Joshi, C. G. (2022) · Microbial Pathogenesis · doi:10.1016/j.micpath.2022.105829 · Cited by 22 · see citing works
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Fiorito, S., Soligo, M., Gao, Y., Öğülür, İ., Akdiş, C. A., & Bonini, S. (2022) · Allergy · doi:10.1111/all.15239 · Cited by 20 · see citing works
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Odiase, P., Rachakonda, K., Kress, M., Villalta, F., & Rachakonda, G. (2021) · Microorganisms · doi:10.3390/microorganisms9091965 · Cited by 10 · see citing works
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Li, W., & Ma, Z. S. (2022) · Microbial Ecology · doi:10.1007/s00248-022-02148-9 · Cited by 9 · see citing works
Bayram, H., Konyalılar, N., Akpinar‐Elci, M., Rajabi, H., Aksoy, G. T., Mortazavi, D., Kayalar, Ö., Dikensoy, Ö., Taborda‐Barata, L., & Viegi, G. (2024) · Pulmonology · doi:10.1016/j.pulmoe.2024.04.005 · Cited by 8 · see citing works
Viral–Bacterial Interactions That Impact Viral Thermostability and Transmission
Gonzalez, L. R., Tat, R. P., Greaves, J., & Robinson, C. M. (2023) · Viruses · doi:10.3390/v15122415 · Cited by 7 · see citing works
Crosstalk between COVID-19 and the gut-brain axis: a gut feeling
Kalam, N., & Balasubramaniam, V. R. M. T. (2024) · Postgraduate Medical Journal · doi:10.1093/postmj/qgae030 · Cited by 8 · see citing works
Esther, C. R., Kimura, K. S., Mikami, Y., Edwards, C. E., Das, S. R., Freeman, M. H., Strickland, B. A., Brown, H. M., Wessinger, B. C., Gupta, V. C., et al. (2022) · International Forum of Allergy & Rhinology · doi:10.1002/alr.22975 · Cited by 7 · see citing works
Self-citationAnalysis of the upper respiratory tract microbiota in mild and severe COVID-19 patientsPreprint
Babenko, V. V., Bakhtyev, R., Baklaushev, V. P., Балыкова, Л. А., Bashkirov, P. V., Bespyatykh, J., Blagonravova, A. S., Boldyreva, D. I., Fedorov, D., Gafurov, I., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.20.461025 · Cited by 7 · see citing works
Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection
Romani, L., CHIERICO, F. D., Pane, S., Ristori, M. V., Pirona, I., Guarrasi, V., Cotugno, N., Bernardi, S., Lancella, L., Perno, C. F., et al. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03009-23 · Cited by 6 · see citing works
Глебовна, Т. И., Meerovich, G. A., Zulufova, I. D., Akhlyustina, E. V., Ovchinnikov, R. S., Solovyev, A. I., Romanishkin, I. D., Kozlikina, E. I., Nekhoroshev, A. V., Glechik, D. A., et al. (2022) · Photodiagnosis and Photodynamic Therapy · doi:10.1016/j.pdpdt.2022.102753 · Cited by 6 · see citing works
Role of nasal microbiota in regulating host anti-influenza immunity in dogs
Geng, J., Dong, Y., Huang, H., Wen, X., Xu, T., Zhao, Y., & Liu, Y. (2025) · Microbiome · doi:10.1186/s40168-025-02031-y · Cited by 5 · see citing works
Galeeva, J. S., Starikova, E. V., Fedorov, D. E., Manolov, A. I., Pavlenko, A. V., Konanov, D. N., Krivonos, D. V., Babenko, V. V., Klimina, K. M., Veselovsky, V. A., et al. (2023) · Frontiers in Microbiomes · doi:10.3389/frmbi.2023.1067019 · Cited by 5 · see citing works
Sekaran, K., Varghese, R. P., Doss, C. G. P., Alsamman, A. M., Zayed, H., & Allali, A. E. (2023) · PLoS ONE · doi:10.1371/journal.pone.0289891 · Cited by 5 · see citing works
The nasopharyngeal and salivary microbiomes in COVID‐19 patients with and without asthma
Kim, J. G., Zhang, A., Rauseo, A. M., Goss, C. W., Mudd, P. A., O’Halloran, J. A., & Wang, L. (2022) · Allergy · doi:10.1111/all.15438 · Cited by 5 · see citing works
Bernard, R., Shilts, M. H., Strickland, B. A., Boone, H. H., Payne, D. C., Brown, R. F., Edwards, K. M., Das, S. R., & Nicholson, M. R. (2023) · Journal of Cystic Fibrosis · doi:10.1016/j.jcf.2023.11.002 · Cited by 5 · see citing works
Self-citationBacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection
Bourumeau, W., Tremblay, K., Jourdan, G., Girard, C., & Laprise, C. (2023) · Microorganisms · doi:10.3390/microorganisms11112703 · Cited by 4 · see citing works
Meta-transcriptomics Reveals Dysbiosis of the Respiratory Microbiome in Older Adults with Long COVID
Liao, M., Cai, J., Zhu, F., Lan, Y., Xu, T., Guo, J., Xue, Q., Wen, Y., Zou, F., Zhang, Y. J., et al. (2025) · Research · doi:10.34133/research.0720 · Cited by 3 · see citing works
The upper respiratory tract microbiome and its role in human health: barrier function
Starikova, E. V., Galeeva, J. S., & Ilina, E. N. (2022) · PULMONOLOGIYA · doi:10.18093/0869-0189-2022-32-6-876-884 · Cited by 3 · see citing works
The gut microbiota as an early predictor of COVID-19 severity
Fabbrini, M., D’Amico, F., van der Gun, B. T. F., Barone, M., Conti, G., Roggiani, S., Wold, K. I., Vincenti-Gonzalez, M. F., de Boer, G., Veloo, A. C. M., et al. (2024) · mSphere · doi:10.1128/msphere.00181-24 · Cited by 3 · see citing works
Nasopharyngeal microbiome composition by SARS-CoV-2 presence and severity
Claus, J., Top, J., Paganelli, F. L., ten Doesschate, T., Paternotte, N., Youngapelian, M. J., Schuurman, R., Willems, R. J. L., Leavis, H. L., & van de Wijgert, J. H. H. M. (2025) · Scientific Reports · doi:10.1038/s41598-025-01764-y · Cited by 3 · see citing works
Microflora of sputum and autopsy material of patients with COVID-19
Maksimova, E. A., Kozlov, A. V., Lyamin, A. V., Zhestkov, A. V., Gusyakova, O. A., & Zolotov, M. O. (2022) · Russian Clinical Laboratory Diagnostics · doi:10.51620/0869-2084-2022-67-6-380-384 · Cited by 4 · see citing works
Petrea, C. L., Ciortea, D.-A., Gurău, G., Matei, M. N., Pleșea-Condratovici, A., Zaharia, A. E., (Ivașcu), C. B., Verga, G. I., & Berbece, S. I. (2026) · Biomedicines · doi:10.3390/biomedicines14020258 · Cited by 2 · see citing works
General dynamics of the URT microbiome and microbial signs of recovery in COVID-19 patients
Ignatyeva, O. A., Валерьевич, Г. В., Taraskina, A. N., Tsvetkova, I. A., Pavlova, P. A., Sulian, O. S., Андреевич, А. В., Likholetova, D., Сергеевна, Ч. П., Nikitina, E. V., et al. (2024) · Beneficial Microbes · doi:10.1163/18762891-bja00004 · Cited by 2 · see citing works
Microbiota of upper respiratory tract in COVID-19
Isaeva, G. S., & Chumarev, N. S. (2024) · Clinical Microbiology and Antimicrobial Chemotherapy · doi:10.36488/cmac.2024.1.21-30 · Cited by 2 · see citing works
Antiseptics: An expeditious third force in the prevention and management of coronavirus diseases
Okeke, K. N. C., Ahamefule, C. S., Nnabuife, O. O., Orabueze, I. N., Iroegbu, C. U., Egbe, K. A., & Ike, A. C. (2024) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2024.100293 · Cited by 2 · see citing works
Hu, Y., & Ding, T. (2021) · PubMed Central · Cited by 2 · see citing works
Hickman, E., Hinton, A. L., Zorn, B., Rebuli, M. E., Robinette, C., Wolfgang, M. C., Mucha, P. J., & Jaspers, I. (2021) · Research Square · doi:10.21203/rs.3.rs-725763/v1 · Cited by 2 · see citing works
The Upper Airway Microbiome and Lung Injury in COVID-19
McGinniss, J. E., & Collman, R. G. (2021) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.202109-2226ed · Cited by 2 · see citing works
SARS-CoV-2 triggered excessive inflammation and abnormal energy metabolism in gut microbiotaPreprint
Zhou, T., Zeng, Y., Wu, J., Li, J., Yan, J., Meng, W., Han, H., Feng, F., He, J., Zhao, S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.08.467715 · Cited by 2 · see citing works
Hagihara, M., Yamashita, M., Ariyoshi, T., Minemura, A., Yoshida, C., Higashi, S., Oka, K., Takahashi, M., Ota, A., Maenaka, A., et al. (2025) · iScience · doi:10.1016/j.isci.2025.113502 · Cited by 1 · see citing works
Nasopharyngeal and oral microbiota profiling in SARS-CoV-2 infected pregnant women
Giovannini, N., Limena, A., Ercolino, C., Renteria, S. U., Strati, F., Giuffrè, M. R., Maragno, P., Carbone, I. F., Facciotti, F., Ceriotti, F., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-19344-5 · Cited by 1 · see citing works
Tomar, S. S., & Khairnar, K. (2025) · PHAGE · doi:10.1177/26416549251395011 · Cited by 1 · see citing works
Interaction of SARS-CoV-2 with gut microbiota
Soldatova, O. V., Goryanskaya, I. Y., Namazova, L. E., & Abramova, K. I. (2023) · Экспериментальная и клиническая гастроэнтерология · doi:10.31146/1682-8658-ecg-220-12-59-67 · Cited by 1 · see citing works
Hickman, E., Hinton, A. L., Zorn, B., Rebuli, M. E., Robinette, C., Wolfgang, M. C., Mucha, P. J., & Jaspers, I. (2021) · Research Square · doi:10.21203/rs.3.rs-725763/v2 · Cited by 1 · see citing works
Pharmacokinetic-based failure of a detergent virucidal for SARS-COV-2 nasal infectionsPreprint
Esther, C. R., Kimura, K. S., Mikami, Y., Edwards, C. E., Das, S. R., Freeman, M. H., Strickland, B. A., Brown, H. M., Wessinger, B. C., Gupta, V. C., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-500168/v1
Self-citationMICROBIAL MARKERS IN CHILDREN WITH INFLAMMATORY DISEASES OF THE UPPER RESPIRATORY TRACT
(2023) · Russian Clinical Laboratory Diagnostics · doi:10.51620/0869-2084-2023-68-2-111-116
Microbiome and the COVID-19 pandemic
Patel, P. R., & Bhattacharjee, M. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-90144-4.00008-2
Akorli, J., Opoku, M., Appiah-Twum, F., Akpo, M. S., Ismail, R. B. Y., Boamah, G. Y. K., Obeng-Aboagye, E., Adu-Asamoah, D., & Donkor, I. O. (2024) · BMC Infectious Diseases · doi:10.1186/s12879-024-09948-z
Symptômes prolongés après un COVID-19 : pistes physiopathologiques
Gaudry, C., Dhersin, R., & Dubée, V. (2024) · Revue des Maladies Respiratoires · doi:10.1016/j.rmr.2024.07.009
Immune and Microbial Signatures in Immunocompetent and Immunocompromised Patients with PneumoniaPreprint
Zhan, Y., Zhou, J., Li, S., Hu, B., Du, Q., Wang, H., Li, Z., Sun, W., Yang, J., Qiu, Y., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-5225770/v1
Cheng, C., Su, Y.-S., Chen, C., Chang, M., Huang, S.-W., Huang, P.-N., Shih, S., Hsu, Y., & Chiu, C. (2024) · Human Vaccines & Immunotherapeutics · doi:10.1080/21645515.2024.2432105
Cruz, A. M. S., Cardoso, J. F., Pinheiro, K. D. C., Ferreira, J. A., Barbagelata, L. S., da Silva, S. P., das Chagas, W. D., Lobo, P. D. S., Teixeira, D. M., Junior, W. A., et al. (2025) · Microorganisms · doi:10.3390/microorganisms13051088
Tadount, F., Boivin, G., Longtin, Y., Savard, P., Cheng, M. P., Decaluwe, H., Serres, G. D., Fortin, É., & Quach, C. (2025) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofaf544
Akorli, J., Opoku, M., Appiah-Twum, F., Akpo, M. S., Ismail, R. Y., Boamah, G. Y. K., Obeng-Aboagye, E., Adu-Asamoah, D., & Donkor, I. O. (2024) · Figshare · doi:10.6084/m9.figshare.27078842
Akorli, J., Opoku, M., Appiah-Twum, F., Akpo, M. S., Ismail, R. Y., Boamah, G. Y. K., Obeng-Aboagye, E., Adu-Asamoah, D., & Donkor, I. O. (2024) · Figshare · doi:10.6084/m9.figshare.27078845
Li, H., Wu, X., Zeng, H., Chang, B., Cui, Y., Zhang, J., Wang, R., & Ding, T. (2024) · Figshare · doi:10.6084/m9.figshare.26606047
Ishizaka, A., Koga, M., Mizutani, T., Uraki, R., Yamayoshi, S., Iwatsuki‐Horimoto, K., Yamamoto, S., Imai, M., Tsutsumi, T., Suzuki, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23682270
Akorli, J., Opoku, M., Appiah-Twum, F., Akpo, M. S., Ismail, R. Y., Boamah, G. Y. K., Obeng-Aboagye, E., Adu-Asamoah, D., & Donkor, I. O. (2024) · Figshare · doi:10.6084/m9.figshare.27078836
Akorli, J., Opoku, M., Appiah-Twum, F., Akpo, M. S., Ismail, R. Y., Boamah, G. Y. K., Obeng-Aboagye, E., Adu-Asamoah, D., & Donkor, I. O. (2024) · Figshare · doi:10.6084/m9.figshare.27078839
Li, H., Wu, X., Zeng, H., Chang, B., Cui, Y., Zhang, J., Wang, R., & Ding, T. (2024) · Figshare · doi:10.6084/m9.figshare.26606050
Oropharyngeal Microbiota Associated with Sore Throat in Acute Upper Respiratory Tract Infections
Huang, C., Zou, H., Cai, Y., Zhang, H., & Zou, X. (2026) · Current Microbiology · doi:10.1007/s00284-026-04861-x
SARS‑CoV‑2 Associated Shifts in the Upper Respiratory Tract Mycobiome in Non-hospitalized Cases
Tomar, S. S., & Khairnar, K. (2026) · Mycopathologia · doi:10.1007/s11046-026-01096-z
Ye, X., Yue, M., Lee, S., Li, A., Wang-Erickson, A. F., Forno, E., Eddens, T. J., Shaikh, N., & Chen, W. (2026) · BMC Genomics · doi:10.1186/s12864-026-13054-6
Immunosuppression is associated with loss of airway microbiome resilience in severe COVID-19
Chung, M., Barnett, C. R., Hunger, L., Sulaiman, I., Wu, B. G., Li, Y., Tsay, J.-C. J., Brosnahan, S. B., Chung, C. J., Angel, L., et al. (2026) · Microbiome · doi:10.1186/s40168-026-02462-1
Turi, K. N., Wu, X., Li, Y., Rosas‐Salazar, C., Gebretsadik, T. S., Shilts, M. H., Das, S. R., Gern, J., Xu, Y., & Hartert, T. V. (2026) · Metabolomics · doi:10.1007/s11306-026-02540-3
Self-citation
- Authors
- Rosas-Salazar, C., Kimura, K. S., Shilts, M. H., Strickland, B. A., Freeman, M. H., Wessinger, B. C., Gupta, V., Brown, H. M., Rajagopala, S. V., Turner, J. H., & Das, S. R.
- Affiliations
- Vanderbilt University Medical Center (US)
- Vanderbilt University (US)
- Corresponding author
- Turner, Justin H.
- Das, Suman R.
- ORCID
- Venue
- Journal of Allergy and Clinical Immunology
- Publisher
- Elsevier BV
- Published
- 2021-04
- Volume
- 147
- Issue
- 4
- Pages
- 1226-1233.e2
- ISSN
- 0091-6749 (ISSN-L)
- PMC
- PMC7871823
- OpenAlex
- W3128287277
- Cited by
- 92
- References
- 31
- Citations by year
- 2026: 6 · 2025: 9 · 2024: 17 · 2023: 18 · 2022: 26 · 2021: 16
- FWCI
- 6.19
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Allergy and Clinical Immunology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (G20RR030956, UL1RR024975, P30EY08126, P30CA68485)
- NIAID DMID (R21AI154016, R21AI149262, R21AI142321)
- National Heart, Lung, and Blood Institute (K23HL148638, R01HL146401)
- National Institute of Allergy and Infectious Diseases
- CDC
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Keywords
- SARS-CoV-2, COVID-19 pandemic, upper respiratory tract microbiome, viral load, bacterial taxa, Prevotella, Corynebacterium, Staphylococcus haemolyticus, viral-bacterial interactions, bacterial diversity
- MeSH terms
- Host Microbial Interactions, COVID-19, SARS-CoV-2, Adult, Female, Humans, Male, Middle Aged, Respiratory System, RNA, Ribosomal, 16S, Species Specificity, Case-Control Studies, Viral Load, Biodiversity, Pandemics, Microbiota
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