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Schult, D.* ; Reitmeier, S.* ; Koyumdzhieva, P.* ; Lahmer, T.* ; Middelhof, M.* ; Erber, J.* ; Schneider, J.* ; Kager, J.* ; Frolova, M.* ; Horstmann, J.* ; Fricke, L.* ; Steiger, K.* ; Jesinghaus, M.* ; Janssen, K.P.* ; Protzer, U. ; Neuhaus, K.* ; Schmid, R.M.* ; Haller, D.* ; Quante, M.*

Gut bacterial dysbiosis and instability is associated with the onset of complications and mortality in COVID-19.

Gut Microbes 14:2031840 (2022)

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There is a growing debate about the involvement of the gut microbiome in COVID-19, although it is not conclusively understood whether the microbiome has an impact on COVID-19, or vice versa, especially as analysis of amplicon data in hospitalized patients requires sophisticated cohort recruitment and integration of clinical parameters. Here, we analyzed fecal and saliva samples from SARS-CoV-2 infected and post COVID-19 patients and controls considering multiple influencing factors during hospitalization. 16S rRNA gene sequencing was performed on fecal and saliva samples from 108 COVID-19 and 22 post COVID-19 patients, 20 pneumonia controls and 26 asymptomatic controls. Patients were recruited over the first and second corona wave in Germany and detailed clinical parameters were considered. Serial samples per individual allowed intra-individual analysis. We found the gut and oral microbiota to be altered depending on number and type of COVID-19-associated complications and disease severity. The occurrence of individual complications was correlated with low-risk (e.g., Faecalibacterium prausznitzii) and high-risk bacteria (e.g., Parabacteroides ssp.). We demonstrated that a stable gut bacterial composition was associated with a favorable disease progression. Based on gut microbial profiles, we identified a model to estimate mortality in COVID-19. Gut microbiota are associated with the occurrence of complications in COVID-19 and may thereby influencing disease severity. A stable gut microbial composition may contribute to a favorable disease progression and using bacterial signatures to estimate mortality could contribute to diagnostic approaches. Importantly, we highlight challenges in the analysis of microbial data in the context of hospitalization.

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