biostudies-literatureNguyen LHNCATS NIH HHSNIDDK NIH HHSNCIMark and Lisa SchwartzNHLBI NIH HHSCrohn&apos;s and Colitis FoundationMassachusetts Consortium on Pathogen ReadinessNIDDKAmerican Gastroenterological Association49https://www.ebi.ac.uk/biostudies/studies/S-EPMC10337137biostudies-literatureUnknown15(1)<h4>Background</h4>The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.<h4>Methods</h4>We profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.<h4>Results</h4>Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital deplGenome medicineMetagenomic assessment of gut microbial communities and risk of severe COVID-19.PMC103371372021-5102K01 DK120742K23 DK125838UL1 TR002541Research Fellowship AwardK23DK125838Research Scholars AwardT32 HL116275K01DK120742Career Development AwardReinicke TWoo JEMagicheva-Gupta MDrew DAKim MLai PSJesudasen SJThompson KNNguyen LHMcIver LOkin DBhosle ALo CHCaraballo AChan ATHuttenhower CSui HYBattista VMKuntz TMDas Adhikari UGoldberg MBKwon DSHuang CYVieira JBerra LfalseMetagenomic assessment of gut microbial communities and risk of severe COVID-19.<h4>Background</h4>The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.<h4>Methods</h4>We profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.<h4>Results</h4>Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depl2023-01-01T00:00:00Z2023 Jul2025-07-12T03:06:18.158Z2025-04-05T00:08:08.216ZS-EPMC103371373743879710.1186/s13073-023-01202-6