High-resolution microbiome profiling of 16SrRNA sequencing data, Microbiome Arrays, and expression arrays identifies differential bacterial communities in head and neck cancer patients treated with surgery, chemo-radiation, and PD-1 checkpoint blockade therapy

We have previously shown altered microbiota in saliva from head and neck squamous cell carcinoma (HNSCC) patients, when compared to controls. We now applied high-resolution microbiome profiling (Resphera Insight) to analyze 16S rRNA sequencing and Axiom Microbiome Array (Affymetrix) data in tissue samples from HNSCC patients and healthy controls. DNA from HNSCC (n=43) and controls (n=12) tissue samples was processed for 16SrRNA sequencing and microarray analyses. Raw sequences were processed for quality and length, screened for chimeras and filtered for contaminant human and chloroplast DNA. High-quality passing sequences were submitted to for species-level taxonomic assignments, followed by differential abundance analysis. Compositional arrangement was obtained with the R microbiome package, using a 25% compositional filtration of differentially significant Resphera OTUs, obtained with the Negative Binomial Wald test (p value Citation Format: Rafael E. Guerrero-Preston, Kelvin Navarro, Filipa Godoy-Vitorino, James White, Anne Jedlicka, Gustavo Rivera-Alvarez, Barbara Mora-Lagos, Winston Timp, William Westra, Wayne Koch, Luigi Marchionni, Young Kim, David Sidransky. High-resolution microbiome profiling of 16SrRNA sequencing data, Microbiome Arrays, and expression arrays identifies differential bacterial communities in head and neck cancer patients treated with surgery, chemo-radiation, and PD-1 checkpoint blockade therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 570.