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BMC infectious diseases
Aug 18, 2023;23 (1): 537.

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

Tatiana Galperine, Yangji Choi, Jean-Luc Pagani, Antonios Kritikos, Matthaios Papadimitriou-Olivgeris, Marie Méan, Valentin Scherz, Onya Opota, Gilbert Greub, Benoit Guery, Claire Bertelli, RegCOVID Study Group
Author Information
  1. Tatiana Galperine: Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland.
  2. Yangji Choi: Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
  3. Jean-Luc Pagani: Service of Intensive Care, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
  4. Antonios Kritikos: Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland.
  5. Matthaios Papadimitriou-Olivgeris: Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland.
  6. Marie Méan: Division of Internal Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
  7. Valentin Scherz: Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
  8. Onya Opota: Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
  9. Gilbert Greub: Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
  10. Benoit Guery: Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland. benoit.guery@chuv.ch.
  11. Claire Bertelli: Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
PMID: 37596518 DOI: 10.1186/s12879-023-08511-6

Abstract

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms. Several evidences suggest that the intestine is a critical site of immune cell development, gut microbiota could therefore play a key role in lung immune response. We designed a monocentric longitudinal observational study to describe the gut microbiota profile in COVID-19 patients and compare it to a pre-existing cohort of ventilated non-COVID-19 patients.
METHODS: From March to December 2020, we included patients admitted for COVID-19 in medicine (43 not ventilated) or intensive care unit (ICU) (14 ventilated) with a positive SARS-CoV-2 RT-PCR assay in a respiratory tract sample. 16S metagenomics was performed on rectal swabs from these 57 COVID-19 patients, 35 with one and 22 with multiple stool collections. Nineteen non-COVID-19 ICU controls were also enrolled, among which 14 developed ventilator-associated pneumonia (pneumonia group) and five remained without infection (control group). SARS-CoV-2 viral loads in fecal samples were measured by qPCR.
RESULTS: Although similar at inclusion, Shannon alpha diversity appeared significantly lower in COVID-19 and pneumonia groups than in the control group at day 7. Furthermore, the microbiota composition became distinct between COVID-19 and non-COVID-19 groups. The fecal microbiota of COVID-19 patients was characterized by increased Bacteroides and the pneumonia group by Prevotella. In a distance-based redundancy analysis, only COVID-19 presented significant effects on the microbiota composition. Moreover, patients in ICU harbored increased Campylobacter and decreased butyrate-producing bacteria, such as Lachnospiraceae, Roseburia and Faecalibacterium as compared to patients in medicine. Both the stay in ICU and patient were significant factors affecting the microbiota composition. SARS-CoV-2 viral loads were higher in ICU than in non-ICU patients.
CONCLUSIONS: Overall, we identified distinct characteristics of the gut microbiota in COVID-19 patients compared to control groups. COVID-19 patients were primarily characterized by increased Bacteroides and decreased Prevotella. Moreover, disease severity showed a negative correlation with butyrate-producing bacteria. These features could offer valuable insights into potential targets for modulating the host response through the microbiota and contribute to a better understanding of the disease's pathophysiology.
TRIAL REGISTRATION: CER-VD 2020-00755 (05.05.2020) & 2017-01820 (08.06.2018).

Keywords

COVID-19 Gut microbiota Gut-lung axis Microbiota profiling SARS-CoV-2

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MeSH Term

Humans
COVID-19
SARS-CoV-2
Microbiota
Gastrointestinal Microbiome
Bacteroides
Butyrates

Chemicals

Butyrates
Observational Study Journal Article

Word Cloud

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