That’s a very nice question which I missed. Looking back at the paper, 13 out of 15 Covid-19 patients were given antiviral therapy (i.e., Lopinavir-Ritonavir). None of the pneumonia controls had these antivirals.

Seems like they did not adjust for antiviral therapy, only antibiotics. So the antivirals could be a confound for the gut dysbiosis. Probably adjusting for antiviral medication wasn’t practical as that would exclude 13 and leave only two patient for analysis.