Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection
Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene se...
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| Language: | English |
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Frontiers Media S.A.
2022-03-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2022.824578/full |
| _version_ | 1819158746229637120 |
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| author | Yong-Lin Shi Mao-Zhang He Mao-Zhen Han Hong-Ya Gui Peng Wang Jun-Ling Yu Ying-Lu Ge Yong Sun Sheng-Hai Huang Sheng-Hai Huang |
| author_facet | Yong-Lin Shi Mao-Zhang He Mao-Zhen Han Hong-Ya Gui Peng Wang Jun-Ling Yu Ying-Lu Ge Yong Sun Sheng-Hai Huang Sheng-Hai Huang |
| author_sort | Yong-Lin Shi |
| collection | DOAJ |
| description | Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province. |
| first_indexed | 2024-12-22T16:29:33Z |
| format | Article |
| id | doaj.art-4cf0a215106045b98faf9c1750327694 |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-12-22T16:29:33Z |
| publishDate | 2022-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-4cf0a215106045b98faf9c17503276942022-12-21T18:20:05ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882022-03-011210.3389/fcimb.2022.824578824578Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 InfectionYong-Lin Shi0Mao-Zhang He1Mao-Zhen Han2Hong-Ya Gui3Peng Wang4Jun-Ling Yu5Ying-Lu Ge6Yong Sun7Sheng-Hai Huang8Sheng-Hai Huang9Anhui Provincial Centers for Disease Control and Prevention, Hefei, ChinaDepartment of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, ChinaSchool of Life Sciences, Anhui Medical University, Hefei, ChinaDepartment of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, ChinaAnhui Provincial Centers for Disease Control and Prevention, Hefei, ChinaAnhui Provincial Centers for Disease Control and Prevention, Hefei, ChinaAnhui Provincial Centers for Disease Control and Prevention, Hefei, ChinaAnhui Provincial Centers for Disease Control and Prevention, Hefei, ChinaDepartment of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, ChinaSchool of Life Sciences, Anhui Medical University, Hefei, ChinaCoronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province.https://www.frontiersin.org/articles/10.3389/fcimb.2022.824578/fulloral swab specimensnanopore sequencingfull-length 16S rRNAmicrobial analysisSARS-CoV-2 patientsoral microbiota |
| spellingShingle | Yong-Lin Shi Mao-Zhang He Mao-Zhen Han Hong-Ya Gui Peng Wang Jun-Ling Yu Ying-Lu Ge Yong Sun Sheng-Hai Huang Sheng-Hai Huang Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection Frontiers in Cellular and Infection Microbiology oral swab specimens nanopore sequencing full-length 16S rRNA microbial analysis SARS-CoV-2 patients oral microbiota |
| title | Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection |
| title_full | Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection |
| title_fullStr | Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection |
| title_full_unstemmed | Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection |
| title_short | Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection |
| title_sort | characterization of altered oropharyngeal microbiota in hospitalized patients with mild sars cov 2 infection |
| topic | oral swab specimens nanopore sequencing full-length 16S rRNA microbial analysis SARS-CoV-2 patients oral microbiota |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2022.824578/full |
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