TABLE 1.

The characteristics of gut microbiota in COVID-19 patients.

Sample size	Microbiota species	Geographic location	Gut microbiota characteristics in COVID-19	Ref.
15 COVID-19 patients, 6 community acquired pneumonia patients, 15 healthy controls	Bacterial	Hong Kong, China	Enrichment of opportunistic pathogenic bacteria and reduction of beneficial symbiotic bacteria, the baseline abundance of Clostridium ramosum, Coprobacillus, and Clostridium hathewayi was correlated with COVID-19 severity, whilst Alistipes onderdonkii and Faecalibacterium prausnitzii abundance inverse correlated with the disease severity	Zuo et al., 2020b
100 COVID-19 patients, 79 non-COVID-19 controls	Bacterial	Hong Kong, China	Gut microbiota known to have immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectum, and Bifidobacterium were depleted. After adjusting for antibiotic use and patients’ age, F. prausnitzii and Bifidobacterium bifidum were negatively correlated with the severity	Yeoh et al., 2021
9 COVID-19 children aged from 7 to 139 months, 14 age-matched healthy controls	Bacterial	Not provided	At phylum level Bacteroidetes and Firmicutes were significantly more abundant in the gut of children with COVID-19 than healthy controls. Pathogenic bacterium Pseudomonas dominated among the gut microbiota, and persistent exist during the COVID-19.	Xu R. et al., 2021
36 COVID-19 patients, 23 suspected patients, 72 healthy controls	Bacterial	Henan, China	At genus level Akkermansla, Streptococcus, Enterococcus, and Bifidobacterium were enriched in COVID-19 patients whereas Pseudobutyrivibrio, Blautia, Faecalibacterium, and Bacteroides were more abundant in healthy people	Ren et al., 2021
86 COVID-19 patients, 21 post COVID-19 patients, 11 pneumonia controls, 26asymptomatic controls	Bacterial	Germany	Parabacteroides was positively correlated with the severity of COVID-19, Fusicatenibacter was negatively correlated with disease severity. F. prausnitzii was inversely associated with the number of complications and mortality, the relative abundance of the genus Alistipes was increased with the number of complications	Schult et al., 2022
13 COVID-19 patients, 5 healthy controls	Bacterial	Beijing, China	Ruminococcus gnavus, Coprobacillus, Eggerthella, Lachnospiraceae bacterium 2_1_58 FAA, Clostridium ramosum, and Eggerthella lenta were enriched in COVID-19 patients, while Alistipes_sp_AP11, Alistipes indistinctus, Eubacterium hallii, Roseburia intestinalis, Burkholderiales bacterium 1_1_47, Coprobacter fastidiosus, Eubacterium eligens, Bacteroides salyersiae, Odoribacter splanchnicus, Alistipes shahii, Ruminococcus bromii, and Bacteroides massiliensis were significantly depleted	Cao et al., 2021
115 COVID-19 patients, (mild, 19; moderate, 37; or severe 59)	Bacterial	Portuguese	The abundance of Actinobacteria and Lachnospiraceae was lower, and the abundance of Proteobacteria was higher in moderate and severe COVID-19 patients than in mild COVID-19 patients.	Moreira-Rosário et al., 2021
117 patients infected with SARS-CoV-2, 95 SARS-CoV-2 negative patients	Bacterial	German (98% Caucasian ethnicity)	In SARS-CoV-2 positive patients, the abundance of Bacteroidetes and Enterobacteriaceae was higher, and the abundance of several genera such as Bifidobacterium, Streptococcus, and Collinsella was lower.	Reinold et al., 2021
62 COVID-19 patients, 33 seasonal flu patients, 40 healthy controls	Bacterial	Hefei, China	Compared with healthy controls, members of the genera Streptococcus, Lactobacillus, Clostridium, and Bifidobacterium was increased in COVID-19, while members of the general Bacteroidetes, Faecalibacterium, Roseburia, Parabacteroides, and Coprococcus was decreased.	Tao et al., 2020
30 COVID-19 patients, 9 community acquired pneumonia patients, 30 healthy controls	Fungal	Hong Kong, China	Enrichment of opportunistic fungal pathogens, Candida aureus, Candida albicans, and Aspergillus flavus during the disease course	Zuo et al., 2020a
67 COVID-19 patients, 35 H1N1 infected patients, 48 healthy controls	Fungal	Zhejiang, China	Increased fungal load and enrichment of some opportunistic pathogenic fungi. Ascomycota (such as Penicillium polonicum, Penicillium citrinum, and Aspergillus with its five species) and Basidiomycota (such as Malassezia yamatoensis, Rhodotorula mucilaginosa, Moesziomyces aphidis) were depleted	Lv et al., 2021
30 COVID-19 patients (21 non-severe COVID-19, 9 developing severe/critical COVID-19), 23 healthy controls	Fungal	German (mainly Caucasian ethnicity)	Increased abundance of Ascomycota phylum and the genus Bipolaris, and reduced fungal gut microbiota diversity, evenness and richness in severe/critical COVID-19 compared with non-severe COVID-19.	Reinold et al., 2022
13 COVID-19 patients, 5 healthy controls	Virome	Beijing, China	Enrichment of bacteriophages (Inoviridae and Microviridae), plant-RNA virus cucumber green mottle mosaic viruses, and unclassified viruses. 14 Microviridae phages, one Podoviridae phage, one Inoviridae phage, and one unclassified virus were enriched in severe COVID-19 cases	Cao et al., 2021
98 COVID-19 patients, 78 non-COVID-19 controls matched for gender and co-morbidities	Virome	Hong Kong, China	Enrichment of environment-derived eukaryotic DNA viruses, underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses). 10 virus species including 1 RNA virus, 9 DNA virus and pepper chlorotic spot virus were inversely correlated with COVID-19 severity	Zuo et al., 2021b
15 COVID-19 patients, 6 community acquired pneumonia patients, 15 healthy controls	Virome	Hong Kong, China	Gut DNA virome diversity was decreased. The fecal DNA virome of COVID-19 patients was mainly composed of crAss-like phages, Myoviridae, Siphoviridae, Guaphage, Podoviridae, and Microviridae. (the metagenomic data were obtained from a study of Zuo et al., 2020b, available publicly at the National Center for Biotechnology Information Sequence Read. Archive BioProject accession number PRJNA624223)	Lu et al., 2021