16S rRNA gene sequencing of rectal swab in patients affected by COVID-19

PLoS One. 2021 Feb 17;16(2):e0247041. doi: 10.1371/journal.pone.0247041. eCollection 2021.


COronaVIrus Disease-2019 (COVID-19) is a pandemic respiratory infection caused by a new betacoronavirus, the Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2). Few data are reported on the gut microbiota in COVID-19 patients. 16S rRNA gene sequencing was performed to reveal an altered composition of the gut microbiota in patients with COVID-19 pneumonia admitted in intensive care unit (ICU) (i-COVID19), or in infectious disease wards (w-COVID19) as compared to controls (CTRL). i-COVID19 patients showed a decrease of Chao1 index as compared to CTRL and w-COVID19 patients indicating that patients in ICU displayed a lower microbial richness while no change was observed as for Shannon Index. At the phylum level, an increase of Proteobacteria was detected in w-COVID19 patients as compared to CTRL. A decrease of Fusobacteria and Spirochetes has been found, with the latter decreased in i-COVID19 patients as compared to CTRL. Significant changes in gut microbial communities in patients with COVID-19 pneumonia with different disease severity compared to CTRL have been identified. Our preliminary data may provide valuable information and promising biomarkers for the diagnosis of the disease and, when validated in larger cohort, it could facilitate the stratification of patients based on the microbial signature.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Bacteria / genetics
  • COVID-19 / genetics
  • COVID-19 / microbiology*
  • COVID-19 / virology
  • Cohort Studies
  • Female
  • Gastrointestinal Microbiome / genetics*
  • Hospitalization
  • Humans
  • Intensive Care Units
  • Italy / epidemiology
  • Male
  • Middle Aged
  • Pandemics
  • RNA, Ribosomal, 16S / genetics*
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / isolation & purification


  • RNA, Ribosomal, 16S

Grant support

This study was supported by funds to the Istituto Nazionale per le Malattie Infettive (INMI) Lazzaro Spallanzani IRCCS, Rome, Italy, from the Ministero della Salute (Ricerca Corrente, linea 1; COVID- 2020-12371817), the European Commission – Horizon 2020 (EU project 101003544 – CoNVat; EU project 101003551 – EXSCALATE4CoV; EU project 101005111 DECISION; EU project 101005075-Unità Operativa Complessa Microbiologia e Banca Biologica Direttore: Dr. Antonino Di Caro- Tel. 0655170685 Fax 065594555 KRONO) and the European Virus Archive – GLOBAL (grants no. 653316 and no. 871029). Valerio Pazienza is supported by Italian Association for Cancer Research (AIRC) under IG 2019 - ID. 23006 project – P.I. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.