Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients

Abstract

Over the last decade, it has become increasingly apparent that the microbiome is a central component in human well-being and illness. However, to establish innovative therapeutic methods, it is crucial to learn more about the microbiota. Thereby, the area of metagenomics and associated bioinformatics methods and tools has become considerable in the study of the human microbiome biodiversity. The application of these metagenomics approaches to studying the gut microbiome in COVID-19 patients could be one of the promising areas of research in the fight against the SARS-CoV-2 infection and disparity. Therefore, understanding how the gut microbiome is affected by or could affect the SARS-CoV-2 is very important. Herein, we present an overview of approaches and methods used in the current published studies on COVID-19 patients and the gut microbiome. The accuracy of these researches depends on the appropriate choice and the optimal use of the metagenomics bioinformatics platforms and tools. Interestingly, most studies reported that COVID-19 patients’ microbiota are enriched with opportunistic microorganisms. The choice and use of appropriate computational tools and techniques to accurately investigate the gut microbiota is therefore critical in determining the appropriate microbiome profile for diagnosis and the most reliable antiviral or preventive microbial composition.

Gut microbial profiling of COVID-19 patients in Uganda

“…Distinct microbial signatures were identified, with the prevalence of specific OTUs in COVID-19 patients and a particular abundance of Prevotella in severe cases. This was similar to findings from a recent study [30] which highlighted a protective role of the Prevotella genus in the long-term recovery process while other investigations [31,32] reported varied results. The variation could be attributed to various factors like sample collection methods, patient demographics, or even geographic variations in microbial populations.…”

The Role of Gut Microbiota Dysbiosis as a Potential Factor in Early Diagnosis, Prognosis and Therapeutic Strategy of COVID-19 Patients

“…Faecalibacterium prausnitzii and Clostridium leptum had a positive correlation with neutrophil count in severe patients, as did Eubacterium rectale with IL-6 and Enterobacteriaceae with aspartate aminotransferase (AST). 14,16,17 Bacteroides ovatus, Lachnospiraceae bacterium, and Eubacterium ventriosum had a positive correlation with CD4 and CD8 lymphocytes and other T-cells. Meanwhile, Faecalibacterium prausnitzii had a positive correlation with natural killer (NK) cells and a negative correlation with Coprobacillus spp., Clostridium ramosum, and Clostridium symbiosum.…”

“…15 In healthy individuals, gut microbiota may offer a better understanding of individuals' susceptibility to COVID-19. 16 Changes in the standard composition and function of intestinal microbiota may predispose healthy individuals to an atypical inflammatory response, such as the one seen in COVID-19 cases. 17…”

The triangle relationship between human genome, gut microbiome, and COVID-19: opening of a Pandora’s box

“…In contrast, the richness of beneficial bacterium was negatively correlated with the severity of the disease (Zuo et al, 2020a, b;Sehli et al, 2021). These discrepancies were independent of the antibiotic treatments, strengthening that GM might be a sufficient predictor of disease severity (Wang et al, 2016;Lai et al, 2020;Sehli et al, 2021). Population-level studies suggested that the inflammatory modulated bacteria was likely to be the signature of disease severity.…”