Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA SequencingOriginal 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 examined the nasal and oropharyngeal (NOP) microbial community using 16S rRNA gene sequencing. Researchers compared the microbiota composition and diversity across groups differing in COVID-19 status and severity. The goal was to characterize how SARS-CoV-2 infection alters the local respiratory microbiome, since no reliable markers exist to predict disease prognosis in these patients.
Who was studied?
The cohort included 21 patients affected by COVID-19, some paucisymptomatic and others admitted to the Intensive Care Unit (ICU). They were compared against 10 controls who tested negative for COVID-19, as well as 8 patients infected with other human coronaviruses (HKU1, NL63, and OC43). All samples were drawn from nasal/oropharyngeal swabs analyzed by 16S rRNA sequencing.
What were the most important findings?
Chao1 index, a measure of microbial richness, was significantly lower in ICU COVID-19 patients compared to paucisymptomatic patients. Chao1 was also decreased across ICU, paucisymptomatic, and other-coronavirus groups relative to controls. Shannon diversity index, which accounts for both richness and evenness, was significantly reduced only in ICU patients compared to controls and paucisymptomatic patients. At the phylum level, Deinococcus-Thermus was detected only in controls and was absent in SARS-CoV-2 and other-coronavirus patient groups.
What are the greatest implications of this study?
The progressive loss of microbial diversity in the nasal/oropharyngeal tract, most pronounced in ICU patients, suggests that upper respiratory microbiome disruption tracks with COVID-19 severity. These findings raise the possibility that 16S rRNA-based diversity indices, such as Chao1 and Shannon, could serve as candidate biomarkers to help stratify disease severity. Further research could clarify whether restoring microbial diversity or targeting specific taxa like Deinococcus-Thermus has prognostic or therapeutic relevance in COVID-19 management.