Table 1.
Gut microbiota profiles of SARS-CoV-2-infected subjects.
| Microorganism | Phylum | Family | Relative abundance (SARS-CoV-2-infected subjects vs. healthy controls) | Reference |
|---|---|---|---|---|
| Pathogenic microbes | ||||
| Actinomyces | Actinomycetota | Actinomycetaceae | Enriched | (17–19) |
| Akkermansia | Verrucomicrobiota | Akkermansiaceae | Enriched | |
| Collinsella | Actinomycetota | Coriobacteriaceae | Enriched | |
| Enterococcus | Firmicutes | Enterococcaceae | Enriched | |
| Lactobacillus | Firmicutes | Lactobacillaceae | Enriched | |
| Lactococcus | Firmicutes | Streptococcaceae | Enriched | |
| Methanobrevibacter | Euryarchaeota | Methanobacteriaceae | Enriched | |
| Odoribacter | Bacteroidetes | Odoribacteraceae | Enriched | |
| Parabacteroides | Bacteroidetes | Tannerellaceae | Enriched | |
| Phascolarctobacterium | Firmicutes | Acidaminococcaceae | Enriched | |
| Serratia | Pseudomonadota | Yersiniaceae | Enriched | |
| Staphylococcus | Firmicutes | Staphylococcaceae | Enriched | |
| Enterococcus faecium | Firmicutes | Enterococcaceaes | Enriched | (20) |
| Escherichia coli | Pseudomonadota | Enterobacteriaceae | Enriched | |
| Klebsiella pneumoniae | Pseudomonadota | Enterobacteriaceae | Enriched | |
| Salmonella enterica | Pseudomonadota | Enterobacteriaceae | Enriched | |
| Staphylococcus auricularis | Firmicutes | Staphylococcaceae | Enriched | |
| Acinetobacter | Pseudomonadota | Moraxellaceae | Enriched | |
| Rhodococcus | Actinomycetota | Nocardiaceae | Enriched | |
| Dorea | Firmicutes | Lachnospiraceae | Enriched | (18, 19, 21) |
| Streptococcus | Firmicutes | Streptococcaceae | Enriched | |
| Bacteroides | Bacteroidetes | Bacteroidaceae | Enriched | (19, 21, 22) |
| Corynebacterium | Actinomycetota | Corynebacteriaceae | Enriched | |
| Enterocloster | Firmicutes | Lachnospiraceae | Enriched | |
| Flavonifractor | Firmicutes | Oscillospiraceae | Enriched | |
| Collinsella aerofaciens | Actinomycetota | Coriobacteriaceae | Enriched | (23) |
| Collinsella tanakaei | Actinomycetota | Coriobacteriaceae | Enriched | |
| Morganella morganii | Pseudomonadota | Morganellaceae | Enriched | |
| Streptococcus infantis | Firmicutes | Streptococcaceae | Enriched | |
| Ruminococcus gnavus | Firmicutes | Lachnospiraceae | Enriched | |
| Clostridium hathewayi | Firmicutes | Clostridiaceae | Enriched | |
| Enterococcus avium | Firmicutes | Enterococcaceae | Enriched | |
| Prevotellaceae | Bacteroidetes | – | Enriched | (24) |
| Clostridium aldenense | Firmicutes | Lachnospiraceae | Enriched | (25, 26) |
| Escherichia unclassified | Pseudomonadota | Enterobacteriaceae | Enriched | |
| Intestinibacter bartlettii | Firmicutes | Peptostreptococcaceae | Enriched | |
| Clostridium bolteae | Firmicutes | Lachnospiraceae | Enriched | |
| Flavonifractor plautii | Firmicutes | Oscillospiraceae | Enriched | |
| Clostridium ramosum | Firmicutes | Clostridiaceae | Enriched | |
| Candida albicans | Ascomycota | Debaryomycetaceae | Enriched | (27, 28) |
| Beneficial microbes | ||||
| Blautia | Firmicutes | Lachnospiraceae | Depleted | (17, 20–22, 24) |
| Coprococcus | Firmicutes | Lachnospiraceae | Depleted | |
| Dialister | Firmicutes | Veillonellaceae | Depleted | |
| Faecalibacterium | Firmicutes | Oscillospiraceae | Depleted | |
| Lachnospira | Firmicutes | Lachnospiraceae | Depleted | |
| Oscillospira | Firmicutes | Oscillospiraceae | Depleted | |
| Prevotella | Bacteroidetes | Prevotellaceae | Depleted | |
| Roseburia | Firmicutes | Lachnospiraceae | Depleted | |
| Ruminococcus | Firmicutes | Oscillospiraceae | Depleted | |
| Bacteroides vulgatus | Bacteroidetes | Bacteroidaceae | Depleted | (20, 26) |
| Eubacterium eligens | Firmicutes | Eubacteriaceae | Depleted | |
| Faecalibacterium prausnitzii | Firmicutes | Clostridia | Depleted | |
| Veillonella | Firmicutes | Veillonellaceae | Depleted | |
| Megasphaera | Firmicutes | Veillonellaceae | Depleted | (21) |
| Alistipes onderdonkii | Bacteroidetes | Rikenellaceae | Depleted | (23) |
| Bacteroides stercoris | Bacteroidetes | Bacteroidaceae | Depleted | |
| Lachnospiraceae bacterium 1_1_57FAA | Firmicutes | Lachnospiraceae | Depleted | |
| Parabacteroides merdae | Bacteroidetes | Tannerellaceae | Depleted | |
| Bacteroides uniformis | Bacteroidetes | Bacteroidaceae | Depleted | |
| Parabacteroides distasonis | Bacteroidetes | Tannerellaceae | Depleted | |
| Adlercreutzia | Actinomycetota | Eggerthellaceae | Depleted | (22, 24) |
| Bacteroidaceae | Bacteroidetes | – | Depleted | |
| Eubacterium brachy | Firmicutes | Eubacteriales Family XIII. Incertae Sedis | Depleted | |
| Lachnospiraceae | Firmicutes | – | Depleted | |
| Ruminococcaceae | Firmicutes | – | Depleted | |
| Butyricicoccus pullicaecorum | Firmicutes | Clostridiaceae | Depleted | (25, 26) |
| Eubacterium hallii | Firmicutes | Lachnospiraceae | Depleted | |
| Fusicatenibacter saccharivorans | Firmicutes | Lachnospiraceae | Depleted | |
| Intestinimonas butyriciproducens | Firmicutes | – | Depleted | |
| Roseburia inulinivorans | Firmicutes | Lachnospiraceae | Depleted | |
| Ruminococcus bromii | Firmicutes | Oscillospiraceae | Depleted | |
| Firmicutes | – | – | Depleted | (22) |
| Aspergillus | Ascomycota | Aspergillaceae | Depleted | (27) |
| Candida parapsilosis | Ascomycota | Debaryomycetaceae | Depleted | |
| Malassezia yamatoensis | Basidiomycota | Malasseziaceae | Depleted | |
| Moesziomyces aphidis | Basidiomycota | Ustilaginaceae | Depleted | |
| Mucor racemosus | Mucoromycota | Mucoraceae | Depleted | |
| Penicillium citrinum | Ascomycota | Aspergillaceae | Depleted | |
| Penicillium polonicum | Ascomycota | Aspergillaceae | Depleted | |
| Rhodotorula mucilaginosa | Basidiomycota | Sporidiobolaceae | Depleted | |
| Talaromyces wortmannii | Ascomycota | Trichocomaceae | Depleted | |
| Trechispora sp. | Basidiomycota | Hydnodontaceae | Depleted | |
| Wallemia sebi | Basidiomycota | Wallemiaceae | Depleted | |