Alteration of the respiratory microbiome in COVID-19 patients with different severities

Li, Zhengtu; Li, Yinhu; Li, Linghua; Mo, Xiaoneng; Li, Shaoqiang; Xie, Mingzhou; Zhan, Yangqing; Yang, Lin; Li, Zhun; Xie, Min; Chen, Zhaoming; Zhu, Airu; Ren, Ying; Yu, Le; Zhao, Jincun; Li, Shuai Cheng; Cai, Weiping; Ye, Feng

doi:10.1016/j.jgg.2021.11.002

Cited by 8 publications

(12 citation statements)

References 12 publications

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“…The SARS-CoV-2-induced URT microbiome dysbiosis itself, rather than consistent changes in specific bacterial taxa, could be associated with an increased risk of severe disease. However, while the overall antibiotic usage in our study was low, in other manuscripts examining the association of respiratory microbiome with COVID-19 severity, patient antibiotic use was either not reported ( Mostafa et al., 2020 ; Rueca et al., 2021 ; Ventero et al., 2021 ), reported as high in all groups ( Merenstein et al., 2021 ), or reported as highest in patients with the most severe COVID-19 ( Hernández-Terán et al., 2021 ; Li et al., 2021 ). Potentially, dysbiosis in some patients could be linked to administration of antibiotics rather than the SARS-CoV-2 infection.…”

Section: Discussioncontrasting

confidence: 85%

“…For example, in our study, we identified a Corynebacterium ASV that decreased with COVID-19 severity, while Rueca et al. found that Bifidobacterium and Clostridium were depleted in those in the ICU ( Rueca et al., 2021 ), and in another study, the most severe COVID-19 patients had reduced Neisseria , Rothia , and Prevotella ( Li et al., 2021 ). In contrast, Salmonella , Scardovia , Serratia , and Pseudomonadaceae were more abundant in the nasopharynx of ICU patients compared with those with mild or moderate symptoms, while Ventero et al.…”

Section: Discussionmentioning

confidence: 47%

“…Other studies have similarly reported respiratory microbiome dysbiosis in patients with COVID-19 compared with controls ( Engen et al., 2021 ; Merenstein et al., 2021 ) and in those with the most severe disease ( Hernández-Terán et al., 2021 ). SARS-CoV-2-induced instability in the microbiome might make it challenging to identify specific taxa associated with disease severity as the changes could be stochastic and less likely to be shared among different patients, a finding also reported by Li et al., who found that patients with the most severe COVID-19 each had a distinct respiratory microbiome ( Li et al., 2021 ). The SARS-CoV-2-induced URT microbiome dysbiosis itself, rather than consistent changes in specific bacterial taxa, could be associated with an increased risk of severe disease.…”

Section: Discussionmentioning

confidence: 91%

“…Previous studies have examined the association of SARS-CoV-2 infection with the respiratory microbiome ( De Maio et al., 2020 ; Mostafa et al., 2020 ; Shen et al., 2020 ; Zhang et al., 2020 ; Haiminen et al., 2021 ; Maes et al., 2021 ; Nardelli et al., 2021 ; Rosas-Salazar et al., 2021 ; Rueca et al., 2021 ; Ventero et al., 2021 ; Xu et al., 2021 ), focusing mostly on comparing SARS-CoV-2-infected and uninfected control patients, rather than on associations of the URT microbiome with disease severity among those with SARS-CoV-2. However, there have been studies that have examined the URT microbiome over a spectrum of different COVID-19 severities ( Mostafa et al., 2020 ; Hernández-Terán et al., 2021 ; Li et al., 2021 ; Merenstein et al., 2021 ; Rueca et al., 2021 ; Ventero et al., 2021 ). Similar to others, we found that overall URT community composition significantly differed among COVID-19 severity groups ( Mostafa et al., 2020 ; Rueca et al., 2021 ; Ventero et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…However, understanding of the association of the URT microbiome with clinical outcomes related to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)—the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic—is limited, despite the URT being a major portal of entry for this virus ( Gallo et al., 2020 ). While previous research has focused mostly on comparing the respiratory microbiome during COVID-19 to uninfected controls ( De Maio et al., 2020 ; Shen et al., 2020 ; Zhang et al., 2020 ; Haiminen et al., 2021 ; Maes et al., 2021 ; Nardelli et al., 2021 ; Rosas-Salazar et al., 2021 ; Xu et al., 2021 ), studies examining the association between the URT microbiome and COVID-19 severity have been limited thus far ( Mostafa et al., 2020 ; Hernández-Terán et al., 2021 ; Li et al., 2021 ; Merenstein et al., 2021 ; Rueca et al., 2021 ; Ventero et al., 2021 ). To start filling this gap in knowledge, we compared the URT microbiome among uninfected adults and adults with mild, moderate, severe [but without the necessity for intensive care unit (ICU) admission], and very severe (admitted to the ICU) COVID-19.…”

Section: Introductionmentioning

confidence: 99%

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Severe COVID-19 Is Associated With an Altered Upper Respiratory Tract Microbiome

Shilts

Rosas‐Salazar

Strickland

et al. 2022

Front. Cell. Infect. Microbiol.

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BackgroundThe upper respiratory tract (URT) is the portal of entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and SARS-CoV-2 likely interacts with the URT microbiome. However, understanding of the associations between the URT microbiome and the severity of coronavirus disease 2019 (COVID-19) is still limited.ObjectiveOur primary objective was to identify URT microbiome signature/s that consistently changed over a spectrum of COVID-19 severity.MethodsUsing data from 103 adult participants from two cities in the United States, we compared the bacterial load and the URT microbiome between five groups: 20 asymptomatic SARS-CoV-2-negative participants, 27 participants with mild COVID-19, 28 participants with moderate COVID-19, 15 hospitalized patients with severe COVID-19, and 13 hospitalized patients in the ICU with very severe COVID-19.ResultsURT bacterial load, bacterial richness, and within-group microbiome composition dissimilarity consistently increased as COVID-19 severity increased, while the relative abundance of an amplicon sequence variant (ASV), Corynebacterium_unclassified.ASV0002, consistently decreased as COVID-19 severity increased.ConclusionsWe observed that the URT microbiome composition significantly changed as COVID-19 severity increased. The URT microbiome could potentially predict which patients may be more likely to progress to severe disease or be modified to decrease severity. However, further research in additional longitudinal cohorts is needed to better understand how the microbiome affects COVID-19 severity.

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Section: Discussioncontrasting

confidence: 85%

Section: Discussionmentioning

confidence: 47%

Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Severe COVID-19 Is Associated With an Altered Upper Respiratory Tract Microbiome

Shilts

Rosas‐Salazar

Strickland

et al. 2022

Front. Cell. Infect. Microbiol.

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Retracted: Gut microbiota and COVID‐19: A systematic review

SeyedAlinaghi

Afzalian

Pashaei

et al. 2023

Health Science Reports

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Background and Aims Alteration in humans' gut microbiota was reported in patients infected with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2). The gut and upper respiratory tract (URT) microbiota harbor a dynamic and complex population of microorganisms and have strong interaction with host immune system homeostasis. However, our knowledge about microbiota and its association with SARS‐CoV‐2 is still limited. We aimed to systematically review the effects of gut microbiota on the SARS‐CoV‐2 infection and its severity and the impact that SARS‐CoV‐2 could have on the gut microbiota. Methods We searched the keywords in the online databases of Web of Science, Scopus, PubMed, and Cochrane on December 31, 2021. After duplicate removal, we performed the screening process in two stages; title/abstract and then full‐text screening. The data of the eligible studies were extracted into a pre‐designed word table. This study adhered to the PRISMA checklist and Newcastle−Ottawa Scale Bias Assessment tool. Results Sixty‐three publications were included in this review. Our study shows that among COVID‐19 patients, particularly moderate to severe cases, the gut and lung microbiota was different compared to healthy individuals. In addition, the severity, and viral load of COVID‐19 disease would probably also be influenced by the gut, and lung microbiota's composition. Conclusion Our study concludes that there was a significant difference in the composition of the URT, and gut microbiota in COVID‐19 patients compared to the general healthy individuals, with an increase in opportunistic pathogens. Further, research is needed to investigate the probable bidirectional association of COVID‐19 and human microbiome.

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The salivary and nasopharyngeal microbiomes are associated with SARS‐CoV‐2 infection and disease severity

Kim

Rauseo

et al. 2023

Journal of Medical Virology

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Emerging evidence suggests the oral and upper respiratory microbiota may play important roles in modulating host immune responses to viral infection. As the host microbiome may be involved in the pathophysiology of coronavirus disease 2019 , we investigated associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Oral Bifidobacterium, Lactobacillus, and Solobacterium were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19.Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F and monocyte chemoattractant protein-1. Our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.

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Alteration of the respiratory microbiome in COVID-19 patients with different severities

Cited by 8 publications

References 12 publications

Severe COVID-19 Is Associated With an Altered Upper Respiratory Tract Microbiome

Severe COVID-19 Is Associated With an Altered Upper Respiratory Tract Microbiome

Retracted: Gut microbiota and COVID‐19: A systematic review

The salivary and nasopharyngeal microbiomes are associated with SARS‐CoV‐2 infection and disease severity

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