Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID‐19 and its Association with Microbiota in the Gut

Abstract

The role of respiratory tract microbes and the relationship between respiratory tract and gut microbiomes in coronavirus disease 2019 (COVID‐19) remain uncertain. Here, the metagenomes of sputum and fecal samples from 66 patients with COVID‐19 at three stages of disease progression are sequenced. Respiratory tract, gut microbiome, and peripheral blood mononuclear cell (PBMC) samples are analyzed to compare the gut and respiratory tract microbiota of intensive care unit (ICU) and non‐ICU (nICU) patients and determine relationships between respiratory tract microbiome and immune response. In the respiratory tract, significantly fewer Streptococcus , Actinomyces , Atopobium , and Bacteroides are found in ICU than in nICU patients, while Enterococcus and Candida increase. In the gut, significantly fewer Bacteroides are found in ICU patients, while Enterococcus increases. Significant positive correlations exist between relative microbiota abundances in the respiratory tract and gut. Defensin‐related pathways in PBMCs are enhanced, and respiratory tract Streptococcus is reduced in patients with COVID‐19. A respiratory tract–gut microbiota model identifies respiratory tract Streptococcus and Atopobium as the most prominent biomarkers distinguishing between ICU and nICU patients. The findings provide insight into the respiratory tract and gut microbial dynamics during COVID‐19 progression, considering disease severity, potentially contributing to diagnosis, and treatment strategies.

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

“…In contrast, Mogibacterium , Lactococcus , and Bifidobacterium were significantly depleted in the surveyed COVID-19 patients compared with non-COVID patients and/or the local controls. Much lower level of Mogibacterium has been reported in COVID-19 patients requiring ICU ( 42 ); several species within the genera Lactococcus and Bifidobacterium play important roles in modulating innate cytokine and immune response, which potentially provides a protective benefit against COVID-19 if the naso-oropharyngeal microbiota approximating healthy condition is restored ( 43 ).…”

Microbiome and intestinal pathophysiology in post-acute sequelae of COVID-19

“… 33 , 34 Similarly, the critical role of the intestinal microbiome in both acute SARS-CoV-2 infections and long COVID has been widely reported, although the mechanisms behind it are still unclear. 12 , 13 , 14 , 17 , 35 , 36 , 37 One of the possibilities is through the intestinal epithelium for their importance in balancing the microbial community, as previously reported that gut microbiome dysbiosis induced by SARS-CoV-2 in mice was correlated with alterations to Paneth cells and goblet cells and markers of barrier permeability. 37 The group from Hong Kong reported that gut dysbiosis could persist for six months and one year in patients with long COVID with significantly lower bacteria diversity and richness and distinctly separated beta diversity.…”

“… 8 , 10 , 11 , 12 The critical role of the intestinal microbiome in these GI symptoms and long COVID were also reported in clinical patients or animal models. 12 , 13 , 14 …”

A systematic review of gut microbiota profile in COVID‐19 patients and among those who have recovered from COVID‐19

“…After removing duplicate studies, screening the title and abstract, and performing a full-text assessment according to the eligibility criteria, 27 studies were finally included in this systematic review (Figure 1). Of the 27 studies, 18 studies compared only COVID-19 patients and HCs, [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24] six compared only recovered COVID-19 patients and HCs, [25][26][27][28][29][30] and three compared both COVID-19 and recovered COVID-19 patients to HCs [31][32][33] (Table 1, Tables S3 and S4). Twenty-two studies were conducted in Asia (17 in China [including 4 in Hong Kong SAR], two in Japan, and one each in United Arab Emirates, India, and Bangladesh), while five others were 1, Table S5).…”