Comparison of the respiratory tract microbiome in hospitalized COVID‐19 patients with different disease severity

Abstract

Background: Little is known about the characteristics of respiratory tract microbiome in Coronavirus disease 2019 inpatients with different severity. Methods: A cross-sectional study was conducted to characterize respiratory tract microbial communities of 69 COVID-19 inpatients from 64 nasopharyngeal swabs and 5 sputum specimens using 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing. The bacterial pro les were used to nd potential biomarkers by the two-step method, the combination of random forest model and the linear discriminant analysis effect size (LEfSe), and explore the connections with clinical characteristics by Spearman's rank test.Results: Compared with mild COVID-19 patients, severe patients had signi cantly decreased bacterial diversity (Pvalues were less than 0.05 in the alpha and beta diversity) and relative lower abundance of opportunistic pathogens, including Actinomyces, Prevotella, Rothia, Streptococcus, Veillonella. Eight potential biomarkers including Treponema, Lachnoanaerobaculum, Parvimonas, Selenomonas, Alloprevotella, Porphyromonas, GemellaandStreptococcus were found to distinguish the mild COVID-19 patients from the severe COVID-19 patients. The genera of Actinomyces andPrevotella were negatively correlated with age and inpatient days. Intensive Care Unit (ICU) admission, neutrophil count (GRA) and lymphocyte count (LYMPH) were signi cantly correlated with different genera in the two groups. In addition, there were a positive correlation between Klebsiella and white blood cell count (WBC) in two groups. Conclusion:The respiratory tract microbiome had signi cant difference in COVID-19 patients with different severity. The value of the respiratory tract microbiome as predictive biomarkers for COVID-19 severity merits further exploration.

The causal role of gut microbiota in susceptibility and severity of COVID‐19: A bidirectional Mendelian randomization study

“…Alloprevotella was found as one of the community types of oropharyngeal microbiota in patients with COVID‐19 infection, 26 and the enriched Alloprevotella identified in COVID‐19 patients was an inflammation‐associated microbe that had a positive correlation with serum levels of C‐reactive protein 27 . Alloprevotella was also identified in another study as a potential microbial biomarker to distinguish mild COVID‐19 patients from severe COVID‐19 patients 28 . In the MR analyses, we found that fecal Alloprevotella could causally increase COVID‐19 susceptibility by 1.08‐fold but had no causal effects on severe virus‐related symptoms.…”

“…27 Alloprevotella was also identified in another study as a potential microbial biomarker to distinguish mild COVID-19 patients from severe COVID-19 patients. 28 In the MR analyses, we found that fecal disease and colorectal cancer. 29 Higher levels of Erysipelotrichaceae were also associated with higher BMIs which have also been a risk factor to causally increase COVID-19 risks.…”

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

“…However, the specific microbiome changes that have been associated with severity vary among studies. Together, these early findings suggest that the airway microbiome may be an important factor in indicating or influencing COVID‐19 clinical outcomes and should be investigated further 17,20,21 …”

The nasopharyngeal microbiome in COVID-19

“…Another controversial question is whether COVID-19 patients could present an increased abundance of pathobionts in the nasopharynx that may result in a higher incidence of secondary bacterial infections and aggravate pneumonia. Regarding this, although Chen and colleagues, who analyzed nasopharyngeal swabs from 64 hospitalized COVID-19 patients with different disease severities, found that severe patients had lower abundance of opportunistic pathogens compared to mild patients, including the bacterial genera Actinomyces , Prevotella , Rothia , Streptococcus , and Veillonella (Table S1) [ 56 ], the majority of studies analyzing this issue support the idea that SARS-CoV-2 infection alters the symbiosis between commensal bacteria and opportunistic pathogens that are present in the nasopharynx, resulting in an over-proliferation of pathogenic bacteria that predispose to the development of comorbidities (Table S1) [ 50 , 52 , 55 , 66 , 71 ]. In this regard, Bai and colleagues reported an increased abundance of pathogenic bacteria in critically ill COVID-19 patients compared to uninfected subjects (Table S1) [ 52 ].…”