Table 4.
Gut microbiota alterations.
| Authors | Intestinal microbial alternations |
|---|---|
| Gu et al. (2020b) |
COVID-19 and H1N1 vs. HC
a
: Microbial diversity↓, Streptococcus spp.↑, Escherichia-Shigella spp.↑ H1N1 vs. COVID-19 and HC: phylum (Actinobacteria↓, Firmicutes↓), class (Actinobacteria↓, Erysipelotrichia↓, Clostridia↓), family (Lachnospiraceae↓, Ruminococcaceae↓), Blautia spp.↓, Agathobacter spp.↓, Anaerostipes spp.↓, Fusicatenibacter spp.↓, Eubacterium hallii group↓, unclassified Lachnospiraceae↓, Dorea spp.↓, Faecalibacterium spp.↓, Ruminococcus-2 spp.↓ COVID-19 vs. HC: Ruminococcaceae UCG-013↓, Roseburia spp.↓, Lachnospiraceae family↓(Fusicatenibacter spp.↓, Anaerostipes spp.↓, Agathobacter spp.↓, unclassified Lachnospiraceae↓, Eubacteriumhallii group↓), Streptococcus spp.↑↑ COVID-19 vs. H1N1: Streptococcus spp. ↑↑, Prevotella spp.↓, Ezakiella spp.↓, Murdochiella spp.↓, Porphyromonas spp.↓ COVID-19 dominated by: Streptococcus spp., Rothia spp., Veillonella spp., Erysipelato clostridium spp., Actinomyces spp. HC dominated by: Bifidobacterium spp., Romboutsia spp., Faecalibacterium spp., Fusicatenibacter spp., Eubacterium hallii group, Blautia spp., Collinsella spp. H1N1 dominated by: Enterococcus spp., Prevotella spp., Finegoldia spp., Peptoniphilus spp.Richness, diversity, and structure of the gut microbiota were not significantly different between general and severe COVID-19 patients. |
| d’Ettorre et al. (2020) | The formulation administered in this study contained: Streptococcus thermophilus DSM 32345, Lactobacillus acidophilus DSM 32241, Lactobacillus helveticus DSM 32242, Lactobacillus paracasei DSM 32243, Lactiplantibacillus plantarum DSM 32244, Lactobacillus brevis DSM 27961, Bifidobacterium lactis DSM 32246, Bifidobacterium lactis DSM 32247. |
| Tang et al. (2020) | Lactobacillus spp.↓, Bifidobacterium spp.↓, Faecalibacterium prausnitzii↓, Clostridium butyricum↓, Clostridium leptum↓, Eubacterium rectale↓, Enterobacteriaceae ↓, Bacteroides spp.↓ bEnterococcus spp.↑ (It was increased with disease severity) |
| Zuo et al. (2020b) | Candida albicans↑, Aspergillus flavus↑, Aspergillus niger↑ |
| Zuo et al. (2020a) |
Antibiotic negative COVID-19 group:
Clostridium hathewayi↑, Actinomyces viscosus↑, Bacteroides nordii↑ Antibiotic positive COVID-19 group: Faecalibacterium prausnitzii↓, Lachnospiraceae bacterium↓, Eubacterium rectale↓, Ruminococcus obeum↓, Dorea formicigenerans↓ |
| Zuo et al. (2021a) |
Enriched in fecal samples in high infectivity:
Collinsella aerrofaciens↑, Morganella morganii↑, Streptococcus infantis↑ Enriched in fecal samples in low to non infectivity: Parabacteroides merdae↑, Bacteroides stercoris↑, Alistipes onderdonkii ↑, Lachnospiraceae bacterium↑ |
| Cao et al. (2021) |
COVID-19 vs. HC:Bacteria:
Ruminococcus gnavus↑, Eggerthella spp.↑, Coprobacillus spp.↑, Lachnospiraceae bacterium 2_1_58FAA↑, Clostridium ramosum↑, Eggerthella lenta↑, Lachnospiraceae bacterium 1_4_56FAA↑, Alistipes_sp_AP11↓, Roseburia intestinalis↓, Burkholderiales bacterium 1_1_47↓, Eubacterium_hallii↓, Parasutterella_excrementihominis↓, Alistipes indistinctus↓, Coprobacter fastidiosus↓, Eubacterium eligens↓, Bacterioidales bacterium ph8↓, Bacterioides salyersiae↓, Odoribacter splanchnicus↓, Alistipes shahii↓, Ruminococcus bromii↓, Bacteroides massiliensis↓ Virome: Inviridae↑, Microviridae↑, virgaviridae↑ Antibiotic positive vs. antibiotic negative COVID-19 patients:Bacteria: Subdoligranulum↓, Roseburia inulinivorans↓, Roseburia hominis↓, Parasutterella excrementihominis↓, Lachnospiraceae bacterium 2_1_46FAA↓, Faecalibacterium prausnitzii↓,Dorea formicigenerans↓, Coprococcus catus↓, Collinsella aerofaciens↓, Bacteroides vulgatus↓,Veillonella parvula↑, Coprobacillus spp.↑, Clostridium ramosum↑ Virome: No virus was identified as a differential species. Effect of disease severity on gut microbiome: Virome: Severe cases: Fourteen Microviridaephages, one Inoviridae phage, one Podoviridae phage and one unclassified virus↑ Mild cases: No viral community increased Bacteria: Severe cases: Corynebacterium durum↑, Rothia mucilaginosa↑, Enterococcus faecium↑, Campylobacter gracilis↑, Corynebacterium spp.↑, Enterococcus spp.↑, Rothia spp.↑, Megasphaera spp.↑, Campylobacter spp.↑, Eubacterium spp.↓ Mild cases: Eubacterium rectale↑ |
| Liu et al. (2021) | After intervention(FMT): Proteobacteria ↓, Actinobacteria ↑, Bifidobacterium spp.↑, Faecalibacterium spp.↑, Collinsella spp.↑ |
| Lv et al. (2021b) | COVID-19 vs. others: Candida glabrata↓, Candida parapsilosis↓, Five unclassified species separately belonging to Helotiales↓, Pleosporales↓, Sordariales↓, Microscypha spp.↓,Emericellopsis spp.↓, Cystobasidium spp.↑, An unclassified species of Exidiaceae↓, Trebouxiadecolorans↓, An unclassified species belonging to the kingdom Chromista↓ |
| Lv et al. (2021a) | COVID-19 vs. others: Ruminococcaceae↓, Eubacteriumhallii group↓, Family XIII AD3011 group↓, Anaerostipes spp.↓, Fusicatenibacter spp.↓, Roseburia spp.↓, Faecalibacterium spp.↓, Ruminococcus spp. 5139BFAA↓, Aspergillus rugulosus↓, Aspergillus tritici↓,Penicillium spp.↓, Penicillium citrinum ↓, Actinomyces spp.↑, Sphingomonas spp.↑, Rothia spp.↑, Actinomyces odontolyticus↑, Streptococcus parasanguinis↑, Aspergillus penicillioide↓ |
| Yeoh et al. (2021) | Ruminococcus gnavus↑, Bacteroides dorei↑, Ruminococcus torques↑, Bacteroides vulgates↑, Bacteroides ovatus↑, Bacteroides caccae↑,Akkermansia muciniphila↑, Bifidobacterium adolescentis↑, Eubacterium rectal↑, Ruminococcus bromii↑, Subdoligranulum unclassified↑, Bifidobacterium pseudocatenulatum↑, Faecalibacterium prausnitzii↑, Collinsella aerofaciens↑, Ruminococcus obeum↑, Dorea longicatena↑, Coprococcus comes↑, Dorea formicigenerans↑ |
| Prasad et al. (2021) | Plasma samples: Proteobacteria↑, Firmicutes ↑, Actinobacteria ↑, Acinetobacter spp.↑, Nitrospirillum spp.↑, Cupriavidus spp.↑, Pseudomonas spp.↑, Aquabacterium spp.↑, Burkholderia spp.↑, Caballeronia spp.↑, Paraburkholderia spp.↑, Bravibacterium spp.↑, Sphingomonas spp.↑, Staphylococcus spp.↓, Lactobacillus spp.↓ |
| He et al. (2021) | Ruminococcus gnavus↓, Lachnospiraceae↓, Tyzzerella spp.↓, Blautia spp.↓, Eubacterium spp.↓, Peptostreptococcaceae↓,Butyrivibrio spp.↓, Ruminococcus spp.↓, Lachnoclostridium spp.↓, Bacteroides uniformis↑, Bacteoides graminisolvens↑, Bacteroides coprophilus↑ |
| Zhou et al. (2021) | Phylum (Actinobacteria↑), Family (Lachnospiraceae↓, Desulfovibrionaceae↓), Faecalibacterium spp.↓, Roseburia spp.↓, Fusicatenibacter spp.↓, Ruminococcus spp.↓, Clostridium XVIII↓, Dorea spp.↓, Butyricicoccus spp.↓, Romboutsia spp.↓, Intestinimonas spp.↓, Bilophila spp.↓, Escherichia spp.↑, Flavonifractor spp.↑, Intestinibacter spp.↑, Intestinibacter bartlettii↑, Clostridium aldenense↑, Clostridium bolteae↑, Flavonifractor plautii↑, Clostridium ramosum↑, Faecalibacterium prausnitzii↓, Roseburia inulinivorans↓, Fusicatenibacter saccharivorans↓, Ruminococcus bromii↓, Blautia faecis↓, Butyricicoccus pullicaecorum↓, Intestinimonas butyriciproducens↓ |
| Moreira-Rosário et al. (2021) | Severe cases: Proteobacteria↑, Firmicutes/Bacteroidetes ratio↓, Roseburia spp.↓, Lachnospira spp.↓ |
| Wu et al. (2021) |
Blautia spp.↓, Coprococcus spp.↓, Collinsella spp.↓, Streptococcus spp.↑, Weissella spp.↑, Enterococcus spp.↑, Rothia spp.↑, Lactobacillus spp.↑, Actinomyces spp.↑, Granulicatella spp.↑, Bacteroides caccae↓, Bacteroides coprophilus↓, Blautia obeum↓, Clostridium colinum↓, Clostridium citroniae↑, Bifidobacterium longum↑, Rothia mucilaginosa↑ Associations between gut microbiota disturbance and SARS-CoV-2 viral loads: Prevotella copri and Eubacterium dolichum were positively correlated and Streptococcus anginosus, Dialister spp., Alistipes spp., Ruminococcus spp., Clostridium citroniae, Bifidobacterium spp., Haemophilus spp., and Haemophilus parainfluenzae were negatively correlated with the viral load of SARS-CoV-2. |
| Gaibani et al. (2021) |
Study1
c
: Enterococcaceae↑, Coriobacteriaceae↑, Lactobacillaceae↑, Veillonellaceae↑, Porphyromonadaceae↑, Staphylococcaceae↑, Bacteroidaceae↓, Lachnospiraceae↓, Ruminococcaceae↓,Prevotellaceae↓, Clostridiaceae↓ Study2 c : Enterococcus spp.↑, Klebsiella spp.↓, Ruminococcus spp.↑ |
| Kim et al. (2021) | Escherichia spp.↑, Citrobacter spp.↑, Collinsella spp.↑, Bifidobacterium spp.↑, Bacteroides spp.↓, Butyricimonas spp.↓, Odoribacter spp.↓ |
| Zuo et al. (2021b) | Pepper Mild Mottle Virus (PMMoV)↓, Eukaryotic viruses particularly environment-derived eukaryotic viruses with unknown host↑, Streptococcus phage↑, Escherichia phage↑, Homavirus↑, Lactococcus phage↑, Ralstonia phage↑, Solumvirus↑, Microcystis phage↑ Severe cases: plant-derived RNA virus↓, Pepper Chlorotic Spot Virus (PCSV)↓, Myxococcus phage↓, Rheinheimera phage↓, Microcystis virus↓, Bacteroides phage↓, Murmansk poxvirus↓, Saudi moumouvirus↓, Sphaerotilus phage↓, Tomelloso virus↓, Ruegeria phage↓ |
| Khan et al. (2021) | Firmicutes↓, Bacteroidetes↑, Proteobacteria↑, Actinobacteria↑Severe cases: Bacteroides plebeius↓, Faecalibacterium prausnitzii↓, Roseburia faecis↓, Bifidobacterium spp.↑, Bacteroides caccae↑, Bacteroides ovatus↑, Bacteroides fragilis↑, Ruminococcus gnavus↑, Clostridium bolteae↑, Clostridium citroniae↑, Clostridium hathewayi↑, Parabacteroides distasonis↑ |
| Hegazy et al. (2021) | The formulation used in this study was a yogurt containing Bifidobacterium spp. and Lactobacillus spp. |
| Wang et al. (2021b) | Probiotic administration protocol: Bifidobacterium lactobacillus triplex live tablet; each tablet contained no less than 0.5×107 CFU of live Bifidobacterium longum; live Lactobacillus bulgaricus and Streptococcus thermophilus that was not lower than 0.5×106 CFU, 4 pieces at a time, 3 times a day. |
aHealthy control.
bBacteroides spp. was decreased in all groups, but the decrease was within the lower normal limits. There was no significant difference between the groups.
cStudy1: comparison between COVID-19 patients and healthy controls, Study2: comparison between COVID-19 patients and non-COVID-19 ICU admitted control.