Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseasesOriginal 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?
Researchers compared the microbiomes of COVID-19, chronic obstructive pulmonary disease (COPD), and upper respiratory tract infection (URTI) samples. They asked whether microbiome diversity, composition, and genomic features differ across these respiratory conditions.
How was it studied?
The team analyzed 21 RNASeq metagenomic datasets: eleven COVID-19 samples (from Bangladesh and China), six COPD samples (UK), and four URTI samples (USA). Sequences were mapped against bacterial, archaeal, and viral reference genomes, then functionally annotated for metabolic and resistance genes.
What did they find?
Reads mapped to 534 bacterial, 60 archaeal, and 61 viral genomes, with diversity greatest in COVID-19 samples, then COPD, then URTI. Most bacterial (94.57%) and archaeal (80.0%) genera were shared between COVID-19 and non-COVID samples, but only 24.59% of viral genera overlapped, and COVID-19 samples uniquely carried 16 non-SARS-CoV-2 viral genera. Strain-level virome analysis found 660 strains in COVID-19 and 729 in non-COVID samples, with 34.50% shared; COVID-19 metagenomes also showed higher abundance of cobalt-zinc-cadmium resistance and multidrug efflux-pump resistance genes.
Why it matters
Distinct microbiome and resistance-gene profiles across COVID-19 and non-COVID respiratory diseases could inform microbiome-based diagnostics and therapeutics, though the authors note larger, more diverse sample sets are needed.