Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19Original paper
Karen Pendergrass is a microbiome researcher specializing in microbiome-targeted interventions (MBTIs). She systematically analyzes scientific literature to identify microbial patterns, develop hypotheses, and validate interventions. As the founder of the Microbiome Signatures Database, she bridges microbiome research with clinical practice. In 2012, based on her own investigative research, she became the first documented case of FMT for Celiac Disease, four years before the first published case study.
Read MoreWhat was studied?
This study asked whether the pharyngeal microbiome differs in COVID-19 and whether enriched bacteria could influence SARS-CoV-2 infection. The throat was chosen because the virus enters via the upper respiratory tract. Pharyngeal swabs underwent shotgun metagenomic sequencing, compared against public healthy-person data. Selected enriched strains were then cocultured with Vero cells to measure their effect on ACE2, the viral receptor, by RT-qPCR.
Who was studied?
The clinical sample was 22 suspected COVID-19 patients in Wuhan, China, all with fever and cough. RT-qPCR split them into 11 SARS-CoV-2 positive and 11 negative cases. Seven healthy pharyngeal metagenomes from a public database served as a third comparison group. The experimental arm used Vero cells, an African green monkey kidney line, challenged with cultured bacterial strains in vitro.
What were the most important findings?
Across all samples 6502 species were identified. The COVID-19 group showed lower community evenness than the non-COVID-19 group by the Pielou index (p = 0.019), while both patient groups had lower diversity than healthy people. A generalized linear model found 81 bacterial species enriched in COVID-19 and none depleted, with 51 species up at least 8 fold. The top three enriched genera were Streptococcus, Prevotella and Campylobacter. Two Streptococcus strains, S. suis and S. agalactiae, significantly raised ACE2 expression in Vero cells at 8 hours, while three control species did not.
What are the greatest implications of this study?
Enriched pharyngeal opportunistic pathogens may participate in virus-host interactions, potentially by raising ACE2 and easing SARS-CoV-2 entry or by seeding secondary bacterial infection. The throat microbiome could thus be a modifiable factor. The ACE2 result offers a plausible mechanism linking specific Streptococcus strains to infection. With only 11 positive cases and in-vitro assays in monkey cells, these findings are exploratory and do not establish that these bacteria worsen COVID-19 in people.