*Bamidele, T. A., Fowora, M. A., Raheem, T. Y., Ajayi, A., Adagbada, A., Yisau, J. I., Salau, O. Y., Shaibu, J. O., Amoo, O. S., Aiyedogbon, N., Fesobi, T. W., Akintunde, G., Iwalokun, B. A., Smith, S. I., and Salako, B. L. Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, 6, Edmund Crescent, Yaba-Lagos, Nigeria
*Correspondence to: bamideletj@gmail.com; Tel: +2348038578093; ORCID: https://orcid.org/0000–0003–2155–8639
Abstract:
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), when disseminated to the gastrointestinal tract (GIT), can cause alterations in the composition and diversity of the gastrointestinal tract microbiota. However, there is a paucity of data linking SARS-CoV-2 fecal negativity with the GI microbial balance. This study investigated the association between the GI bacterial composition and clinically defined asymptomatic, mild/moderate COVID-19 fecal-negative individuals.
Methodology: This was a cross sectional, comparative study of GI bacterial composition in COVID-19 nasopharyngeal (NP) -positive (n=7) and negative (n=5) participants at the testing facility of the Nigerian Institute of Medical Research between 6th July and 8th August 2022. Faecal samples were collected from the 12 participants. The RNA extracted from the NP-positive samples was used for RT‒qPCR detection of the nucleocapsid and open reading frame (ORF1ab) genes, while DNA from all the faecal samples was used for 16S rRNA metataxonomic analysis.
Results: The participants comprised males (n=4) and females (n=8), ages 17-74 years. The NP-positive participants reported no (n=2, 28.5%), mild (n=4, 57.1%) and moderate (n=1, 14.3%) clinical symptoms. The viral genes were undetected with uniform or rich bacterial species in the fecal samples. The most abundant bacterial phyla were the Firmicutes, Bacteroidota, and Proteobacteria while Prevotella copri, Phocaeicola vulgatus, and the immuno- modulatory, anti-inflammatory bacterium, Faecalibacterium prausnitzii, were the dominant species. There were no significant differences in alpha diversity, Pielou evenness (p=0.223) and Shannon richness index (p=0.062), or beta taxonomic diversity (PERMANOVA p=0.357) between NP-positive and negative participants.
Conclusion: This study did not reveal any differences in the gut bacterial community between asymptomatic and mild/moderate COVID-19 patients, and apparently healthy controls. The asymptomatic, mild, and moderate COVID19 patients in this study maintained balanced gut bacterial diversity, with undetected viral gene in their stool, which may pose little or no threats to the public health in terms of SARS-CoV-2 shedding to the environment. This may however not be generalizable given the small sample size.
Keywords: Gastrointestinal, eubiosis, microbiome, SARS-CoV-2, fecal, RT‒PCR.
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