Table 1.

Intestinal microbial alterations and their effect in COVID-19.

(Refs.)	Intestinal Microbial Alterations	Effect in COVID-19
[24]	Faecalibacterium prausnitzii ↓	Anti-inflammatory. Inverse correlation between abundance and disease severity.
	Alistipes onderdonkii ↓	Involving in the serotonin precursor tryptophan metabolism and maintaining gut immune homeostasis. Negative correlation with COVID-19 severity.
	Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides massiliensis, Bacteroides ovatus ↓	Downregulating the expression of angiotensin-converting enzyme 2 (ACE2). Correlated inversely with SARS-CoV-2 load in fecal samples.
	Coprobacillus, Clostridium ramosum, Clostridium hathewayi ↑	Correlating positively with COVID-19 severity. Coprobacillus bacterium upregulates the expression of ACE2.
[68]	Streptococcus, Rothia, Veillonella, Actinomyces ↑	Opportunistic pathogens. Significantly increased relative abundances in COVID-19 patients compared with those in healthy controls.
	Fusicatenibacter, Anaerostipes, Agathobacter, unclassified Lachnospiraceae, Eubacterium hallii ↓	Butyrate-producing bacteria. The abundances are dramatically reduced in COVID-19 patients compared with those in healthy controls.
[61]	Candida albicans, Candida auris, Aspergillus flavus, Aspergillus niger ↑	Significantly higher relative abundances in hospitalized COVID-19 patients compared with those in healthy controls.
[25]	Faecalibacterium prausnitzii, Eubacterium rectale, Bifidobacterium adolescentis ↓	Anti-inflammatory. These bacteria are depleted in COVID-19 patients.
	Bacteroides dorei, Akkermansia muciniphila ↑	Correlating positively with IL-1β, IL-6, and CXCL8. Enriched in COVID-19 patients.
[26]	Faecalibacterium prausnitzii, Clostridium butyricum, Clostridium leptum, Eubacterium rectale ↓	Butyrate-producing bacteria. The abundances decreased significantly in COVID-19 patients.
	Lactobacillus, Bifidobacterium ↓	Producing lactic acid, regulating immunity, and maintaining intestinal barrier function. Correlating negatively with COVID-19 severity.
	Enterococcus (Ec), Enterobacteriaceae (E) ↑	Opportunistic pathogens. Correlating positively with COVID-19 severity and the Ec/E ratio can predict death in critically ill patients.
[71]	Faecalibacterium ↓	An immunosupportive Clostridiales genus. Correlating negatively with bloodstream infection (BSI).
[72]	Bilophila, Citrobacter ↓	Correlating negatively with COVID-19 severity.
	Genus: Streptococcus, Clostridium, Lactobacillus, Bifidobacterium, ↑	The abundances increased significantly in COVID-19 patients compared with those in healthy controls.
[76]	Genus: Escherichia/Shigella, Citrobacter, Collinsella, Bifidobacterium ↑	Correlating positively with COVID-19.
	Genus: Bacteroides, Butyricimonas, Odoribacter ↓	Short-chain fatty acid (SCFA)-producing bacteria. Markedly reduced in patients with COVID-19 compared to healthy controls.
[75]	Butyricicoccus pullicaecorum, Clostridium ruminatium, Lachnospira pectinoschiza, Pseudobutyrivibrio xylanivorans, ↓	Completely absent in the guts of COVID-19-infected patients.
	Roseburia faecis, Lachnospira pectinoschiza, Faecalibacterium prausnitzii ↓	Short-chain fatty acid-producing bacteria. Correlating negatively with COVID-19 severity.
	Clostridium hathewayi, arabacteroides distasonis, Ruminococcus gnavus ↑	Correlating positively with COVID-19 severity.
[85]	Bacteroidaceae, Lachnospiraceae, Ruminococcaceae ↓	Producing short-chain fatty acids (SCFAs). The abundances decreased significantly in COVID-19 patients compared to those in healthy controls.
	Enterococcus ↑	Far overrepresented in COVID-19 patients developing bloodstream infections (BSIs) and admitted to the intensive care unit.
	Enterococcaceae, Coriobacteriaceae, Lactobacillaceae, Veillonellaceae, Porphyromonadaceae Staphylococcaceae ↑	The abundance increased significantly in COVID-19 patients compared to those in healthy controls.
[69]	Ruminococcus gnavus, Bacteroides vulgatus ↑	The abundances increased significantly in patients with post-acute COVID-19 syndrome (PACS) than in non-COVID-19 controls.
	Bifidobacterium pseudocatenulatum, Faecalibacterium prausnitzii ↓	Butyrate-producing bacteria. Correlating negatively with the development of PACS.
[86]	Genus: Roseburia, Megasphaer Species: Roseburia inulinivorans, Bacteroides faecis, Bifidobacterium bifidum, Parabacteroides goldsteinii, Lachnospiraceae bacterium 9143BFAA, Megasphaera sp. ↓	Correlating negatively with COVID-19 severity.
	Genus: Paraprevotella, Lachnospiraceae, Erysipelotrichaceae Species: Paraprevotella sp., Streptococcus thermophilus, Clostridium ramosum, Bifidobacterium animalis ↑	Correlating positively with COVID-19 severity.
[87]	Genus: Collinsella ↓	Inhibiting the binding of SARS-CoV-2 to ACE2, suppressing proinflammatory cytokine secretion, antioxidant, and anti-apoptotic. Correlating negatively with the mortality rates of COVID-19.
	Genus: Dorea, Fusicatenibacter ↓	Short-chain fatty acid (SCFA)-producing bacteria. Correlating negatively with the mortality rates of COVID-19

Notes: ↑, significantly increased; ↓, significantly decreased.