Patients with SARS-CoV-2 infection

Bowel flora changes:

  • reduction in good germs
  • increase in bad germs

15 Patients, shotgun genetic anaylsis
Hong Kong, Feb 5 - Mar 17, 2020

Patients with Covid had:

  • not enough good germs
    • "depletion of beneficial commensals"
  • too many bad germs
    • , "enrichment of opportunistic pathogens"

Good guys decrease
<technical> names

  • Faecalibacterium prausnitzii
    •  anti-inflammatory
  • Bacterioides dorei
  • Bacterioides thetaiotaomicron
  • Bacterioides massiliensis
  • Bacterioides ovatus
    • anti-ACE2 receptor
    • Covid attaches to ACE2 receptors (novel)

Bad guys increase
<technical> names

  1. Coprobacillus
  2. Clostridium ramosum
  3. Clostridium hatewayi

1. Coprobacillus

  • Intestinal germ
  • grows without oxygen
  • may die if exposed to oxygen

2. Clostridium ramosum

  • environment germ
  • grows with oxygen
  • ferments ketone sugar derivatives (fructose)
  • common in fermentive rumen animals

3. Clostridium hathewayi

  • identified 2001
  • grows without oxygen, anaerobic
  • ferments carbohydrates
  • Spore-forming


  • mild -
    • no radiographic evidence of pneumonia
  • moderate -
    • pneumonia was present
  • severe -
    • respiratory rate ≥30/min, or oxygen saturation ≤93% when breathing ambient air
  • critical -
    • respiratory failure requiring mechanical ventilation, shock, or organ failure requiring intensive care

Common features of Covid germs:

  • ferment
  • love sugar

Stop eating sugar


  • low sugar foods
  • sweet tasting food
    • don't kid yourself anylonger
  • gluten-free grains
  • grains
  • fruit


--- The Real Medical Study

--- Hong Kong - Feb 5 through to March 17, 2020
--- Peer reviewed,  published

Gastroenterology. 2020 May 19; S0016-5085(20)34701-6. doi: 10.1053/j. gastro.2020.05.048.
Online ahead of print.

Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization

Tao Zuo 1, Fen Zhang 1, Grace C Y Lui 2, Yun Kit Yeoh 3, Amy Y L Li 4, Hui Zhan 1, Yating Wan 1, Arthur Chung 1, Chun Peng Cheung 1, Nan Chen 1, Christopher K C Lai 5, Zigui Chen 5, Eugene Y K Tso 6, Kitty S C Fung 7, Veronica Chan 6, Lowell Ling 8, Gavin Joynt 8, David S C Hui 2, Francis K L Chan 9, Paul K S Chan 10, Siew C Ng 11

PMID: 32442562
PMCID: PMC7237927
DOI: 10.1053/j.gastro.2020.05.048

Backgroud & aims: Although SARS-CoV-2 infects gastrointestinal tissues, little is known about the roles of gut commensal microbes in susceptibility to and severity of infection. We investigated changes in fecal microbiomes of patients with SARS-CoV-2 infection during hospitalization and associations with severity and fecal shedding of virus.

Methods: We performed shotgun metagenomic sequencing analyses of fecal samples from 15 patients with COVID-19 in Hong Kong, from February 5 through March 17, 2020. Fecal samples were collected 2 or 3 times per week from time of hospitalization until discharge; disease was categorized as mild (no radiographic evidence of pneumonia), moderate (pneumonia was present), severe (respiratory rate ≥30/min, or oxygen saturation ≤93% when breathing ambient air), or critical (respiratory failure requiring mechanical ventilation, shock, or organ failure requiring intensive care). We compared microbiome data with those from 6 subjects with community-acquired pneumonia and 15 healthy individuals (controls). We assessed gut microbiome profiles in association with disease severity and changes in fecal shedding of SARS-CoV-2.

Results: Patients with COVID-19 had significant alterations in fecal microbiomes compared with controls, characterized by enrichment of opportunistic pathogens and depletion of beneficial commensals, at time of hospitalization and at all timepoints during hospitalization. Depleted symbionts and gut dysbiosis persisted even after clearance of SARS-CoV-2 (determined from throat swabs) and resolution of respiratory symptoms. The baseline abundance of Coprobacillus, Clostridium ramosum, and Clostridium hathewayi correlated with COVID-19 severity; there was an inverse correlation between abundance of Faecalibacterium prausnitzii (an anti-inflammatory bacterium) and disease severity. Over the course of hospitalization, Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides massiliensis, and Bacteroides ovatus, which downregulate expression of ACE2 in murine gut, correlated inversely with SARS-CoV-2 load in fecal samples from patients.

Conclusions: In a pilot study of 15 patients with COVID-19, we found persistent alterations in the fecal microbiome during the time of hospitalization, compared with controls. Fecal microbiota alterations were associated with fecal levels of SARS-CoV-2 and COVID-19 severity. Strategies to alter the intestinal microbiota might reduce disease severity.

Keywords: bacteria; coronavirus; fecal nucleic acid; gut microbiome.

Copyright © 2020 AGA Institute. Published by Elsevier Inc. All rights reserved.