Background: Coronavirus disease 2019 (COVID-19) has rapidly become a global pandemic, and little is known regarding the gut microbiota dynamics of the disease that often features a drastic and swift progression. Here we employed analyses of 16S rRNA gene sequencing and metatranscriptome to investigate the gut microbiome characteristics of a group of COVID-19 patients over the course of a probiotics-assisted therapy. Results: The COVID-19 patients exhibited apparent microbiota alterations characterized by prominent compositional and functional shifts, which included taxonomic changes (e.g., increased relative abundance of Enterococcus and Rhodococcus , and decreased relative abundance of Faecalibacterium and Clostridium XlVa) and transcriptional changes (e.g., increased transcriptional activities of Escherichia coli and Klebsiella pneumoniae , virulence factors, and antibiotic resistance genes, and decreased activities of Faecalibacterium prausnitzii ). Importantly, there were great interpersonal heterogeneity and intertimepoint fluctuations, as the most abundant or transcriptionally active taxa often greatly differed among individual patients and timepoints. Coincided with the resolution of respiratory symptoms, after the therapy some patients showed signs of recovery in the gut microbiome abnormalities. Associations were identified between gut and airway taxa and serum factors. Conclusion: Our findings suggested that there is a lack of gut microbiota stability in COVID-19 patients and that measures are needed to ameliorate the gut microbiome perturbations in the patients to improve the prognosis. In addition, inclusion of probiotics is safe for treating COVID-19 patients and may improve their prognosis. Trial registration ISRCTN, ChiCTR2000029999. Registered 19 February 2020, http://www.chictr.org.cn/showprojen.aspx?proj=49717
The Volatile and Heterogenous Gut Microbiota Shifts of COVID-19 Patients Over The Course of A Probiotics-Assisted Therapy