Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients

• Published in: Microbiology spectrum Vol. 10; no. 6; p. e0219622
• Main Authors: Lai, Christopher K C, Cheung, Man Kit, Lui, Grace C Y, Ling, Lowell, Chan, Jason Y K, Ng, Rita W Y, Chan, Hiu Ching, Yeung, Apple C M, Ho, Wendy C S, Boon, Siaw Shi, Chan, Paul K S, Chen, Zigui
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 21.12.2022
• Subjects: 16S rRNA; Bacteria - genetics; Clinical Microbiology; COVID-19; hospitalized; Humans; Microbiota - genetics; naso-oropharyngeal microbiome; Oropharynx - microbiology; Research Article; RNA, Ribosomal, 16S - genetics; SARS-CoV-2; SARS-CoV-2 - genetics; COVID-19; hospitalized; 16S rRNA; SARS-CoV-2; naso-oropharyngeal microbiome
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.02196-22

Numerous studies have reported dysbiosis in the naso- and/or oro-pharyngeal microbiota of COVID-19 patients compared with healthy individuals; however, only a few small-scale studies have also included a disease control group. In this study, we characterized and compared the bacterial communities of pooled nasopharyngeal and throat swabs from hospitalized COVID-19 patients (  = 76), hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses (  = 69), and local community controls (  = 76) using 16S rRNA gene V3-V4 amplicon sequencing. None of the subjects received antimicrobial therapy within 2 weeks prior to sample collection. Both COVID-19 and non-COVID-19 hospitalized patients differed in the composition, alpha and beta diversity, and metabolic potential of the naso-oropharyngeal microbiota compared with local controls. However, the microbial communities in the two hospitalized patient groups did not differ significantly from each other. Differential abundance analysis revealed the enrichment of nine bacterial genera in the COVID-19 patients compared with local controls; however, six of them were also enriched in the non-COVID-19 patients. Bacterial genera uniquely enriched in the COVID-19 patients included and . In contrast, and were dramatically decreased in COVID-19 patients only. Association analysis revealed that in COVID-19 patients was positively correlated with the level of the inflammation biomarker C-reactive protein. Our findings reveal a limited impact of SARS-CoV-2 on the naso-oropharyngeal microbiota in hospitalized patients and suggest that and are more specific biomarkers for COVID-19 detection. Our results showed that while both COVID-19 and non-COVID-19 hospitalized patients differed in the composition, alpha and beta diversity, and metabolic potential of the naso-oropharyngeal microbiota compared with local controls, the microbial communities in the two hospitalized patient groups did not differ significantly from each other, indicating a limited impact of SARS-CoV-2 on the naso-oropharyngeal microbiota in hospitalized patients. Besides, we identified and as bacterial genera uniquely enriched in COVID-19 patients, which may serve as more specific biomarkers for COVID-19 detection.