Table 1.

Studies exploring the role of gut microbiota in COVID-19.

Authors	Study design	Study population	Analyses/methods	Salient findings	Limitations
Zuo et al. (62)	Single center, prospective	15 COVID-19 patients in Hong Kong compared against 6 subjects with community-acquired pneumonia and 15 healthy individuals	Shotgun metagenomic sequencing for profiling of GI microbiota	Significant alterations in GI microbiota (dysbiosis) in COVID-19 patients Persistent dysbiosis despite clearance of SARS-CoV-2 Positive correlation between dysbiosis and severity of COVID-19	Small sample size. Only hospitalized patients with moderate to severe COVID-19. >50% patients with COVID-19 had received antibiotics.
Gu et al. (61)	Single-center, cross-sectional	30 COVID-19 patients compared against 24 H1N1 patients and 30 matched healthy controls	16S ribosomal RNA gene sequencing for profiling of GI microbiota	Significantly reduced bacterial diversity (dysbiosis) with COVID-19, a significantly higher relative abundance of opportunistic pathogens, and a lower relative abundance of beneficial symbionts. Patients with H1N1 displayed lower diversity and different overall microbial composition compared with COVID-19 patients.	Small sample size. Healthy controls matched for age, sex, and BMI but not for diet and lifestyle factors. H1N1 cohort had been hospitalized for severe illness, compared to COVID-19 cohort which had disease severity classified as “general” and “severe”.
Yeoh et al. (63)	Prospective cohort study from two centers	100 COVID-19 compared against healthy controls	Shotgun sequencing of stool DNA for profiling of GI microbiota. Assessment of serum levels of inflammatory markers.	Significant alterations in the GI microbiota (dysbiosis) in COVID-19 patients. Dysbiosis persisted even after 30 disease post illness. Significant correlation of dysbiosis with severity of COVID-19 illness and with various serum pro-inflammatory markers.	Heterogeneous clinical management of patients. 30-day changes were studied in 27 (out of 100) patients
Zuo et al. (66)	Prospective cohort study from two centers	15 hospitalized patients with COVID-19	RNA shotgun metagenomics for profiling of GI microbiota. Assessment of functionality of GI microbiota and detection of replicative activity of SARS-CoV-2 virus in the GI tract.	Detection of alterations in GI microbiota (dysbiosis) with high markers of bacterial cellular building. 46.7% patients had stool positivity for SARS-CoV-2, even in the absence of GI manifestations. High replicative activity of SARS-CoV-2 in the GI tract suggesting.	Small sample size. Exact role of various microbiota profiles in determining severity of COVID-19 infection needs further studies
Tsikala et al. (67)	Cross-sectional (A statement across 122 countries)	42 low- or low-middle-income countries compared against 80 high- or upper-middle-income countries	Statistical analysis comparing deaths per million secondary to COVID-19 infection, against population health indicators like water current score, health efficiency, percentage rural population, proportion of diarrhoea cases secondary to inadequate sanitation and healthy life expectancy (HALE) at birth.	A statistically significant negative correlation was observed between COVID-19 mortality and populations that had a high percentage of rural residents, and a high proportion of diarrhea secondary to inadequate sanitation. As a result, a high microbial exposure to gram-negative bacteria was proposed to confer protective effects against COVID 19, possibly due to increased interferon type I levels.	Cross-sectional data based on national population health indicators. Inferential hypothesis based on effect of environmental microbiological prevalence rather than direct sequencing of human GI microbiota samples. No analysis of interferon type-I levels in study populations.
Prasad et al. (60)	Prospective cohort study from one center	30 hospitalized patients with COVID-19 and 16 healthy subjects.	Microbial DNA extraction and 16S rRNA sequencing in the plasma samples. Levels of gut permeability markers were also measured.	In the plasma samples of about 65% patients with COVID-19, abnormal signatures of gut microbes were seen. As compared with the healthy controls, patients with COVID-19 had significantly elevated plasma levels of gut permeability markers (such as FABP2, PGN, and LPS).	Small sample size. One-time collection of the plasma. Absence of demonstration of gut dysbiosis in the stools.
Newsome et al. (64)	Prospective cohort study from one center	50 hospitalized COVID-19 patients, 9 recovered patients and 34 uninfected subjects.	16S rRNA sequencing and qPCR analysis was performed on fecal DNA/RNA.	The fecal microbial composition was significantly different in the currently infected COVID-19 patients. The COVID-19 patients had increased relative abundance of Campylobacter and Klebsiella, two genera associated with GI disease. The microbiota composition was similar between recovered and uninfected patients.	Small sample size. Cross-sectional sampling.
Lv et al. (65)	Prospective cohort study from one center	56 hospitalized COVID-19 patients and 47 age- and sex-matched healthy subjects.	Stool samples were analyzed for various microbial biochemical products (or metabolome) using gas chromatography–mass spectrometry.	Differences in the metabolomes of COVID-19 patients were observed compared with healthy controls.	Small sample size. Absence of demonstration of gut dysbiosis in the stools. No control for diet and anti-microbial agents.