Frontiers in Microbiology 01 frontiersin.org Gut microbiota profle of COVID-19 patients: Prognosis and risk stratifcation (MicroCOVID-19 study) José Guilherme Nobre 1,2,3 , Mariana Delgadinho 4 , Carina Silva 4,5 , Joana Mendes 4 , Vanessa Mateus 4 , Edna Ribeiro 4 , Diogo Alpuim Costa 6,7 , Miguel Lopes 8 , Ana Isabel Pedroso 9 , Frederico Trigueiros 10 , Maria Inês Rodrigues 10 , Cristina Lino de Sousa 11 and Miguel Brito 4 * 1 Faculty of Medicine, Lisbon University, Lisbon, Portugal, 2 Faculdade de Medicina, Instituto de Saúde Ambiental, Universidade de Lisboa, Lisboa, Portugal, 3 PTSurg – Portuguese Surgical Research Collaborative, Lisbon, Portugal, 4 H&TRC- Health and Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal, 5 Centro de Estatística e Aplicações, Universidade de Lisboa, Lisbon, Portugal, 6 Breast Cancer Unit, CUF Oncologia, Lisbon, Portugal, 7 Faculdade de Ciências Médicas, NOVA Medical School, Lisbon, Portugal, 8 Departamento de Pneumologia, Hospital Garcia de Orta, Almada, Portugal, 9 Serviço de Medicina Intensiva, Hospital de Cascais Dr. José de Almeida, Cascais, Portugal, 10 Departamento de Medicina Interna I, Centro Hospitalar Lisboa Norte – Hospital de Santa Maria, Lisbon, Portugal, 11 Departamento de Medicina Interna, Hospital da Luz, Lisbon, Portugal Background: Gut microbiota is intrinsically associated with the immune system and can promote or suppress infectious diseases, especially viral infections. This study aims to characterize and compare the microbiota profle of infected patients with SARS-CoV-2 (milder or severe symptoms), non-infected people, and recovered patients. This is a national, transversal, observational, multicenter, and case–control study that analyzed the microbiota of COVID-19 patients with mild or severe symptoms at home, at the hospital, or in the intensive care unit, patients already recovered, and healthy volunteers cohabiting with COVID-19 patients. DNA was isolated from stool samples and sequenced in a NGS platform. A demographic questionnaire was also applied. Statistical analysis was performed in SPSS. Results: Firmicutes/Bacteroidetes ratios were found to be signifcantly lower in infected patients (1.61 and 2.57) compared to healthy volunteers (3.23) and recovered patients (3.89). Furthermore, the microbiota composition difered signifcantly between healthy volunteers, mild and severe COVID-19 patients, and recovered patients. Furthermore, Escherichia coli, Actinomyces naeslundii, and Dorea longicatena were shown to be more frequent in severe cases. The most common COVID-19 symptoms were linked to certain microbiome groups. Conclusion: We can conclude that microbiota composition is signifcantly afected by SARS-CoV-2 infection and may be used to predict COVID-19 TYPE Original Research PUBLISHED 22 November 2022 DOI 10.3389/fmicb.2022.1035422 OPEN ACCESS EDITED BY Maurizio Sanguinetti, Catholic University of the Sacred Heart, Italy REVIEWED BY Eugenia Bezirtzoglou, Democritus University of Thrace, Greece Gislane Lelis Vilela de Oliveira, São Paulo State University, Brazil Karolina Kaźmierczak-Siedlecka, Medical University of Gdansk, Poland Sofa Viana, University of Coimbra, Portugal *CORRESPONDENCE Miguel Brito miguel.brito@estesl.ipl.pt SPECIALTY SECTION This article was submitted to Infectious Agents and Disease, a section of the journal Frontiers in Microbiology RECEIVED 02 September 2022 ACCEPTED 27 September 2022 PUBLISHED 22 November 2022 CITATION Nobre JG, Delgadinho M, Silva C, Mendes J, Mateus V, Ribeiro E, Alpuim Costa D, Lopes M, Pedroso AI, Trigueiros F, Rodrigues MI, de Sousa CL and Brito M (2022) Gut microbiota profle of COVID-19 patients: Prognosis and risk stratifcation (MicroCOVID-19 study). Front. Microbiol. 13:1035422. doi: 10.3389/fmicb.2022.1035422 COPYRIGHT © 2022 Nobre, Delgadinho, Silva, Mendes, Mateus, Ribeiro, Alpuim Costa, Lopes, Pedroso, Trigueiros, Rodrigues, de Sousa and Brito. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.