Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases

Abstract

Background Dozens of studies have demonstrated gut dysbiosis in COVID-19 patients during the acute and recovery phases. However, a consensus on the specific COVID-19 associated bacteria is missing. In this study, we performed a meta-analysis to explore whether robust and reproducible alterations in the gut microbiota of COVID-19 patients exist across different populations. Methods A systematic review was conducted for studies published prior to May 2022 in electronic databases. After review, we included 16 studies that comparing the gut microbiota in COVID-19 patients to those of controls. The 16S rRNA sequence data of these studies were then re-analyzed using a standardized workflow and synthesized by meta-analysis. Results We found that gut bacterial diversity of COVID-19 patients in both the acute and recovery phases was consistently lower than non-COVID-19 individuals. Microbial differential abundance analysis showed depletion of anti-inflammatory butyrate-producing bacteria and enrichment of taxa with pro-inflammatory properties in COVID-19 patients during the acute phase compared to non-COVID-19 individuals. Analysis of microbial communities showed that the gut microbiota of COVID-19 recovered patients were still in unhealthy ecostates. Conclusions Our results provided a comprehensive synthesis to better understand gut microbial perturbations associated with COVID-19 and identified underlying biomarkers for microbiome-based diagnostics and therapeutics.

The relationship between gut microbiota and COVID-19 progression: new insights into immunopathogenesis and treatment

“…COVID-19 patients exhibited an enrichment of opportunistic pathogenic species including Bacteroides , Corynebacterium , Enterocloster , Enterococcus , Flavonifractor , Parabacteroides and Streptococcus compared with healthy controls. The abundance of anti-inflammatory butyrate-producing bacteria (e.g., Dialister , Faecalibacterium , Lachnospira , Megasphaera , Prevotella , Roseburia and Ruminococcus ) was reduced in COVID-19 patients ( 21 ). COVID-19 patients showed an imbalanced metabolism characterized by enhanced protein metabolism and suppressed carbohydrate-oriented catabolism, which might impel putrefactive gut microbiota dysbiosis in COVID-19 patients ( 19 ).…”

“…↑Blautia, Lactobacillus, RuminococcusPositively correlate with proinflammatory cytokines IFN-g, IL-2, IL-4, IL-6, IL-8, IL-10 and TNF-a Magnify inflammation (35)(Continued)producing bacteria (e.g., Dialister, Faecalibacterium, Lachnospira, Megasphaera, Prevotella, Roseburia and Ruminococcus) was reduced in COVID-19 patients(21). COVID-19…”

Antibiotic cocktail followed by Clostridium butyricum (CBM588) supplementation improves colonic anastomotic healing in mice

“…Since the introduction of the revolutionary method of bacterial characterization by Pace et al 26 , 16S rRNA-based characterization of bacterial species has been universally accepted as an accurate method for bacterial identi cation 27 . 16S rRNA metagenomic analysis has provided an objective tool to explore bacterial diversity and composition under a wide variety of clinical scenarios, in which 16S rRNA amplicon with SMS analysis was widely adopted for economic affordability and rapid microbial detection strategy 28 .To date, the use of 16S ribosomal RNA (rRNA) metagenomic analysis to study GM changes in the clinical setting have demonstrated the capability to analyze associations between GM changes and colorectal diseases 28 , COVID-19 infections 29 , prosthetic joint infections 30 , chronic wound infections after wisdom tooth extraction 31 , detection of postoperative infection sources 32 , and the potential to in uence SSI outcomes in colorectal surgery 14 . In this study, the 16S rRNA amplicon with SMS analysis was utilized to verify gut GM changes in mice.…”

Role of the microbiota-gut-brain axis in postacute COVID syndrome

“…Multiple studies over the course of the COVID-19 pandemic have revealed that the infection impacts the composition of the gut microbiome. A recent systematic review found that gut bacterial diversity was decreased in both patients with acute COVID-19 and those who have recovered from COVID-19, coupled with a decreased abundance of butyrate producers and increases in taxa with proinflammatory properties ( 35 ). This gut perturbation continued into the recovery phase after the resolution of an initial infection, suggesting that it may persist and could conceivably contribute, at least in part, to PASC in some individuals.…”