Correlation between Targeted qPCR Assays and Untargeted DNA Shotgun Metagenomic Sequencing for Assessing the Fecal Microbiota in Dogs.

Autor: Sung CH; Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA., Pilla R; Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA., Chen CC; Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA., Ishii PE; Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA., Toresson L; Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, Helsinki University, 00014 Helsinki, Finland.; Evidensia Specialist Animal Hospital, 25466 Helsingborg, Sweden., Allenspach-Jorn K; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA., Jergens AE; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA., Summers S; Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA., Swanson KS; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA., Volk H; Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, 30545 Hannover, Germany., Schmidt T; Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, 30545 Hannover, Germany., Stuebing H; Clinic of Small Animal Medicine, Ludwig-Maximilians University, 80539 Munich, Germany., Rieder J; Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, 30545 Hannover, Germany., Busch K; Clinic of Small Animal Medicine, Ludwig-Maximilians University, 80539 Munich, Germany., Werner M; Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, 8057 Zurich, Switzerland., Lisjak A; Small Animal Clinic of Veterinary Faculty Ljubljana, University of Ljubljana, 1000 Ljubljana, Slovenia., Gaschen FP; Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA., Belchik SE; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA., Tolbert MK; Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA., Lidbury JA; Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA., Steiner JM; Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA., Suchodolski JS; Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA.
Jazyk: angličtina
Zdroj: Animals : an open access journal from MDPI [Animals (Basel)] 2023 Aug 11; Vol. 13 (16). Date of Electronic Publication: 2023 Aug 11.
DOI: 10.3390/ani13162597
Abstrakt: 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.
Databáze: MEDLINE
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