Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groupsOriginal 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?
The study characterized the upper respiratory tract (URT) microbiome, meaning the combined nasal and oral bacterial communities, in patients infected with the SARS-CoV-2 Delta versus Omicron variant compared with healthy controls. The authors aimed to identify variant-specific microbiome signatures, since prior work had compared COVID-19 patients to controls but had not examined how distinct variants shape the URT microbiome.
Who was studied?
The cohort comprised 43 COVID-19 patients (24 Delta and 19 Omicron) and 19 healthy controls from Eastern India, with samples collected in 2021 to 2022 (average age about 36 years in patients and 33 in controls). URT swabs were profiled by next-generation sequencing of the V3 to V4 variable regions of the 16S rRNA gene on the Illumina NovaSeq 6000 platform, yielding 12,172 amplicon sequence variants across 34 phyla, 924 genera, and 1,429 species.
What were the most important findings?
COVID-19 patients showed significantly lower intra-individual (alpha) diversity and higher inter-individual (beta) diversity than controls, with Proteobacteria dominant in patients (73.57 percent versus 22.24 percent) and genera such as Pseudomonas, Klebsiella, Enterobacter, and Acinetobacter enriched, while control-associated commensals including Streptococcus, Veillonella, Prevotella, Neisseria, and Bifidobacterium were depleted. Delta patients had lower diversity and greater dysbiosis than Omicron patients, and nine control-associated species declined in a consistent trend of control greater than Omicron greater than Delta. A random forest classifier built on core species distinguished the three groups with roughly 90 percent (plus or minus 0.5 percent) accuracy (class error 0 percent for controls, 18 percent for Omicron, 14 percent for Delta).
What are the greatest implications of this study?
The authors conclude that different SARS-CoV-2 variants are associated with variant-specific URT microbiome signatures, with the newer Omicron variant more closely resembling the healthy control microbiome than the older Delta variant, which may inform host-microbiome interaction research and future nasal probiotic strategies. Because this is an observational, cross-sectional comparison in a modest sample, the results reflect association rather than causation and, as the authors note, sample size is a limitation.