학술논문
Correlation between Targeted qPCR Assays and Untargeted DNA Shotgun Metagenomic Sequencing for Assessing the Fecal Microbiota in Dogs
Document Type
article
Author
Chi-Hsuan Sung; Rachel Pilla; Chih-Chun Chen; Patricia Eri Ishii; Linda Toresson; Karin Allenspach-Jorn; Albert E. Jergens; Stacie Summers; Kelly S. Swanson; Holger Volk; Teresa Schmidt; Helene Stuebing; Johanna Rieder; Kathrin Busch; Melanie Werner; Anja Lisjak; Frederic P. Gaschen; Sara E. Belchik; M. Katherine Tolbert; Jonathan A. Lidbury; Joerg M. Steiner; Jan S. Suchodolski
Source
Animals, Vol 13, Iss 16, p 2597 (2023)
Subject
Language
English
ISSN
2076-2615
Abstract
DNA shotgun sequencing is an untargeted approach for identifying changes in relative abundances, while qPCR allows reproducible quantification of specific bacteria. The canine dysbiosis index (DI) assesses the canine fecal microbiota by using a mathematical algorithm based on qPCR results. We evaluated the correlation between qPCR and shotgun sequencing using fecal samples from 296 dogs with different clinical phenotypes. While significant correlations were found between qPCR and sequencing, certain taxa were only detectable by qPCR and not by sequencing. Based on sequencing, less than 2% of bacterial species (17/1190) were consistently present in all healthy dogs (n = 76). Dogs with an abnormal DI had lower alpha-diversity compared to dogs with normal DI. Increases in the DI correctly predicted the gradual shifts in microbiota observed by sequencing: minor changes (R = 0.19, DI < 0 with any targeted taxa outside the reference interval, RI), mild-moderate changes (R = 0.24, 0 < DI < 2), and significant dysbiosis (R = 0.54, 0.73, and 0.91 for DI > 2, DI > 5, and DI > 8, respectively), compared to dogs with a normal DI (DI < 0, all targets within the RI), as higher R-values indicated larger dissimilarities. In conclusion, the qPCR-based DI is an effective indicator of overall microbiota shifts observed by shotgun sequencing in dogs.