Temporal changes in fecal microbiota of COVID-19 patients: a longitudinal cohort

COVID-19, primarily characterized by respiratory manifestations, also causes gastrointestinal symptoms. Furthermore, the respiratory tract is known to interact with the gut via “gut-lung axis”. However, despite the potential interest of the gut microbiota in COVID-19, it is still poorly defined. Thus, we aimed to study the impact of COVID-19 and the severity on the gut microbiota of a longitudinal cohort. We collected 100 fecal samples from 57 COVID-19 patients in ICU or non-ICU every 7 days, as well as from 19 non-COVID patients in ICU (inclusion and day 7), among which 14 developed ventilator-associated pneumonia (Pneumonia group, antibiotics) and five without infection (Control group, non-antibiotics). The 16S rRNA genes (V3V4) sequenced on a MiSeq were processed by our in-house bioinformatic pipeline (https://github.com/metagenlab/zAmp). Statistical analyses were performed in R. In distance-based redundancy analyses (db-RDA), “COVID-19”, “ICU”, “antibiotics”, “timepoint” and “patient” were set as fixed effects. SARS-CoV-2 viral loads in fecal samples were measured by qPCR. Unlike at inclusion, at day 7, Shannon alpha-diversity appeared significantly lower in COVID-19/Pneumonia groups than in Control group, and the microbiota composition became distinct between COVID-19 and non-COVID-19 groups. COVID-19 patients were characterized by Bacteroides and Pneumonia group by Prevotella. In a db-RDA, only “COVID-19” and “patient” presented significant effects. Further, among COVID-19 patients, ICU patients harbored increased Campylobacter and decreased short-chain fatty acids producing bacteria, such as Lachnospiraceae, Roseburia and Faecalibacterium. In a db-RDA, only “ICU” and “patient” were significant. Fecal viral loads were higher in ICU than in non-ICU.