Table 2.
A snapshot of the microbiome dysbiosis observed in COVID-19.
| Site of sequencing | Positive correlation/enrichment | Negative correlation/decrease in abundance | References |
|---|---|---|---|
| Gut | Coprobacillus sp., Clostridium ramosum, Clostridium hathewayi | Faecalibacterium prausnitzii, Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides massiliensis, Bacteroides ovatus, | (Zuo et al., 2020a) |
| Gut | Candida albicans, Candida auris, Aspergillus flavus | (Zuo et al., 2020b) | |
| Gut | Enterococcus sp., members of Enterobacteriaceae | Faecalibacterium prausnitzii, Clostridium butyricum, Clostridium leptum, Eubacterium rectale | (Tang et al., 2020a) |
| Gut | Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis, Morganella morganii, | Parabacteroides merdae, Bacteroides stercoris, Alistipes onderdonkii, and Lachnospiraceae bacterium 1_1_57FAA | (Zuo et al., 2021) |
| Gut | Faecalibacterium prausnitzii, Eubacterium rectale, Bifidobacteria | (Yeoh et al., 2021) | |
| Gut | Streptococcus, Rothia, Actinomyces, Vellionella | Gu et al., 2020 | |
| Gut | Penicillium, Aspergillus, | Lv et al., 2021a | |
| Lung | Corynebacterium accolens | Propionibacteriaceae | (Mostafa et al., 2020) |
| Lung | Herpesvirade | (Maes et al., 2021) | |
| Lung | Acinetobacter, Chryseobacterium, Burkholderia, Brevundimonas, Sphingobium, Enterobacteriaceae | (Fan et al., 2020) | |
| Lung | Cutaneotricosporon, Issatchenkia, Wallemia, Cladosporium, Alternaria, Dipodascus, Mortierella, Aspergillus, Naganishia, Diutina, and Candida | (Fan et al., 2020) | |
| Lung | alphaherpesvirus 1, rhinovirus B, human orthopneumovirus | (Zhong et al., 2021) | |
| Lung | Burkholderiacepacia complex (BCC), Staphylococcus epidermidis, Mycoplasma spp. (including M. hominis and M. orale) | (Zhong et al., 2021) | |
| Nasopharyngeal | Proteobacteria, Fusobacteria; Leptotrichia, Fusobacterium, Hemophilus, Fusobacterium peridonticum | (Nardelli et al., 2021) | |
| Oral | Streptococcus, Porphyromonas, Abiotrophia, Enterobacter, Neisseria mucosa, Veillonella parvula, Lactobacillus fermentum, Enterococcus faecalis, Atopobium parvulum, Acinetobacter baumannii, Prevotella melaninogenica, jejuni, denticola, and oris; Eikenella corrodens; Capnocytophaga sputigena and gingivalis; and Aggregatibacter aphrophilus), Aspergillus sp., Nakaseomyces sp., and Malassezia sp., Candida sp., Saccharomyces sp., Epstein–Barr virus, Staphylococcus phage ROSA, Streptococcus phage EJ-1, phage PH10, Lactobacillus phage phiadh. | Rothia, Fusobacterium, Haemophilus parainfluenzae and parahaemolyticus, Gemella morbillorum and sanguinis, Parvimonas micra, and Neisseria subflava | (Soffritti et al., 2021) |