Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota Katti R Horng Corresp., 1 2 3 4 5
1, 2
, Holly H Ganz
3, 4
, Jonathan A Eisen
3
, Stanley L Marks
5
Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, United States William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, Davis, California, United States Department of Evolution and Ecology, University of California, Davis, Davis, California, United States AnimalBiome, Inc., Oakland, California, United States Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
Corresponding Author: Katti R Horng Email address:
[email protected]
Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25°C, 4°C, and -80°C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value= 6.87, DF= 3, P
