In Silico Analysis of Probiotic Bacteria Changes Across COVID-19 Severity Stages

The gut microbiota plays a crucial role in modulating the immune response during COVID-19, with several studies reporting significant alterations in specific bacterial genera, including <i>Akkermansia</i>, <i>Bacteroides</i>, <i>Bifidobacterium</i>, <i>Faecalibacterium</i>, <i>Lactobacillus</i>, <i>Oscillospira</i>, and <i>Ruminococcus</i>. These genera are symbionts of the gut microbiota and contribute to host health. However, comparing results across studies is challenging due to differences in analysis methods and reference databases. We screened 16S rRNA raw datasets available in public databases on COVID-19, focusing on the V3-V4 region of the bacterial genome. In total, seven studies were included. All samples underwent the same bioinformatics pipeline, evaluating the differential abundance of these seven bacterial genera at each level of severity. The reanalysis identified significant changes in differential abundance. <i>Bifidobacterium</i> emerged as a potential biomarker of disease severity and a therapeutic target. <i>Bacteroides</i> presented a complex pattern, possibly related to disease-associated inflammation or opportunistic pathogen growth. <i>Lactobacillus</i> showed significant changes in abundance across the COVID-19 stages. On the other hand, <i>Akkermansia</i> and <i>Faecalibacterium</i> did not show significant differences, while <i>Oscillospira</i> and <i>Ruminococcus</i> produced statistically significant results but with limited relevance to COVID-19 severity. Our findings reveal new insights into the differential abundance of key bacterial genera in COVID-19, particularly <i>Bifidobacterium</i> and <i>Bacteroides</i>.