Abstract
Patients with COVID-19 have been reported to experience gastrointestinal symptoms as well as respiratory symptoms, but the effects of COVID-19 on the gut microbiota are poorly understood. We explored gut microbiome profiles associated with the respiratory infection of SARS-CoV-2 during the recovery phase in patients with asymptomatic or mild COVID-19. A longitudinal analysis was performed using the same patients to determine whether the gut microbiota changed after recovery from COVID-19. We applied 16S rRNA amplicon sequencing to analyze two paired fecal samples from 12 patients with asymptomatic or mild COVID-19. Fecal samples were selected at two time points: during SARS-CoV-2 infection (infected state) and after negative conversion of the viral RNA (recovered state). We also compared the microbiome data with those from 36 healthy controls. Microbial evenness of the recovered state was significantly increased compared with the infected state. SARS-CoV-2 infection induced the depletion of Bacteroidetes, while an abundance was observed with a tendency to rapidly reverse in the recovered state. The Firmicutes/Bacteroidetes ratio in the infected state was markedly higher than that in the recovered state. Gut dysbiosis was observed after infection even in patients with asymptomatic or mild COVID-19, while the composition of the gut microbiota was recovered after negative conversion of SARS-CoV-2 RNA. Modifying intestinal microbes in response to COVID-19 might be a useful therapeutic alternative.
Highlights
Two paired fecal samples were selected from 12 patients as follows: (1) a fecal sample collected on or before the positive detection of SARS-COV-2 RNA from the respiratory tract, defined as respiratory positive (RP) SARS-CoV-2 and (2) another fecal sample collected on or after the negative conversion for SARS-COV-2 RNA from the respiratory tract, defined as respiratory negative (RN) SARS-CoV-2
We found a high abundance of the families Bacteroidaceae, Marinifilaceae, and Tannerellaceae and the genus Bacteroides belonging to Bacteroidetes and a low abundance of the family Actinomycetaceae and the genus Actinomyces belonging to Actinobacteria in the RN SARS-CoV-2 compared to the RP SARS-CoV-2 when we used the relaxed false discovery rate (FDR) level (q < 0.1) (Supplementary Table S1)
We investigated the gut microbiota in patients with COVID-19 compared with HCs who had never been exposed to SARS-CoV-2
Summary
Coronavirus disease (COVID-19) is a respiratory illness caused by a novel coronavirus (severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)). Since the first case of COVID-19 was reported in Wuhan, China in 2019, more than 60 million people worldwide have contracted the virus as of 1 December 2020. Most patients with COVID-19 have fever, along with respiratory symptoms, and human-to-human transmission usually occurs among close contacts, mainly through respiratory droplets and direct contact. The angiotensin-converting enzyme 2 (ACE2) receptor, used by SARS-CoV-2 to enter the host, is highly expressed in both the respiratory and gastrointestinal (GI) tracts [1,2]; up to Microorganisms 2021, 9, 1237.
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