Intestinal Microbiota of Patients Hospitalized With Sars-CoV-2 (MICRODIGCOV)

The study investigators hypothesize that SARS-Cov2 infection alters the composition of the digestive microbiota and its functionality, resulting in changes in intestinal permeability and consequently in microbial digestive translocation. These changes may correlate with the magnitude of the SARS-CoV-2 viral load in the gastrointestinal tract and may have an impact on the clinical manifestations and evolvability of COVID-19.

Study Overview

• Status: Active, not recruiting
• Conditions: COVID-19
• Intervention / Treatment: Other: Fecal sample

• Study Type: Observational
• Enrollment (Actual): 15

Contacts and Locations

Study Locations

• France
  • Nîmes, France
    • CHU de Nîmes

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years and older (Adult, Older Adult)
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

All adult patients hospitalized in the Nimes University Hoptial with SARS-CoV-2 infection confirmed by RT-PCR

Description

Inclusion Criteria:

• patient hospitalized at in Nimes University hospital
• Infection with SARS-CoV-2 confirmed by RT-PCR
• The patient must have signed the consent form
• The patient must be a member or beneficiary of a health insurance plan

Exclusion Criteria:

• The subject is participating in an interventional study susceptible to modify the intestinal microbiota, or is in a period of exclusion determined by a previous study
• It is impossible to give the subject informed information
• The patient is under safeguard of justice or state guardianship
• Patient with a chronic digestive pathology or having been operated in the previous year or having enteral nutrition or having had bariatric surgery
• Patient is pregnant, parturient or breastfeeding

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Patients with high viral load of SARS-CoV-2 in feces	Other: Fecal sample; Fecal sample taken to investigate intestinal microbiota
Patients with low viral load of SARS-CoV-2 in feces	Other: Fecal sample; Fecal sample taken to investigate intestinal microbiota

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Number of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg)	RT-qPCR of SARS-CoV-2 to calculate copies/mg	Day 0

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Age of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	Age in years	Day 0
Sex of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	Male/female	Day 0
Clinical features of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	Date of start of symptoms, current therapeutics, antibiotic therapy, blood pressure, heart rate, respiration rate, oxygen saturation, symptoms, Covid stage (ordinal 8 stage scale)	Day 0
Total blood count of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested	lymphocyte count, eosinophil count	Day 0
C-reactive protein level biological data of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested	concentration	Day 0
Fibrinogen level of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested	concentration	Day 0
Lactate Dehydrogenase of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested	concentration	Day 0
D-dimer level of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested	concentration	Day 0
Ferritin levels, of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested	Concentration	Day 0
Albumin levels of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	concentration	Day 0
Calcium levels of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested	concentration	Day 0
Glomerular filtration rate of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested	volume per time	Day 0
Liver function tests of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested		Day 0
Cytobacteriological urine exam of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested		Day 0
Blood cultures of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested		Day 0
Other infectious samples (other than SARS-CoV-2) of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested		Day 0
Taxonomic features of intestinal microbiota of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	Number of Operational Taxonomic Unit	Day 0
Diversity of intestinal microbiota of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	Shannon Index	Day 0
Diversity of intestinal microbiota of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	Bray Curtis Index	Day 0
LPS-binding Protein concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	pg/ml ELISA	Day 0
soluble CD14 concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	ng/ml ELISA	Day 0
RNA16s concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	PCR and sequencing	Day 0
RNA18 concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	PCR and sequencing	Day 0
I-FAB concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	ng/ml:ELISA	Day 0
Claudin 3 concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	ng/ml:ELISA	Day 0
Percentage of Operational Taxonomic Units in intestinal microbiota of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg)	%	Day 0

Collaborators and Investigators

• Sponsor: Centre Hospitalier Universitaire de Nīmes
• Investigators: Principal Investigator: Albert Sotto, CHU Nîmes

Study record dates

Study Major Dates

• Study Start (Actual): January 11, 2022
• Primary Completion (Actual): January 9, 2024
• Study Completion (Estimated): June 1, 2026

Study Registration Dates

• First Submitted: December 18, 2021
• First Submitted That Met QC Criteria: January 3, 2022
• First Posted (Actual): January 5, 2022

Study Record Updates

• Last Update Posted (Estimated): November 17, 2025
• Last Update Submitted That Met QC Criteria: November 14, 2025
• Last Verified: November 1, 2025

More Information

Terms related to this study

• Keywords: microbiota; translocation; gastrointestinal microbiome
• Additional Relevant MeSH Terms: Respiratory Tract Infections; Infections; RNA Virus Infections; Virus Diseases; Respiratory Tract Diseases; Lung Diseases; Pneumonia, Viral; Pneumonia; Coronavirus Infections; Coronaviridae Infections; Nidovirales Infections; COVID-19
• Other Study ID Numbers: NIMAO/2021-1/AS-01

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No