Abstract
Studies of the gut microbiome have become increasingly common with recent technological advances. Gut microbes play an important role in human and animal health, and gut microbiome analysis holds great potential for evaluating health in wildlife, as microbiota can be assessed from non-invasively collected fecal samples. However, many common fecal preservation protocols (e.g. freezing at - 80. °C) are not suitable for field conditions, or have not been tested for long-term (greater than 2. weeks) storage. In this study, we collected fresh fecal samples from captive spider monkeys (Ateles geoffroyi) at the Columbian Park Zoo (Lafayette, IN, USA). The samples were pooled, homogenized, and preserved for up to 8. weeks prior to DNA extraction and sequencing. Preservation methods included: freezing at - 20 °C, freezing at - 80 °C, immersion in 100% ethanol, application to FTA cards, and immersion in RNAlater. At 0 (fresh), 1, 2, 4, and 8 weeks from fecal collection, DNA was extracted and microbial DNA was amplified and sequenced. DNA concentration, purity, microbial diversity, and microbial composition were compared across all methods and time points. DNA concentration and purity did not correlate with microbial diversity or composition. Microbial composition of frozen and ethanol samples were most similar to fresh samples. FTA card and RNAlater-preserved samples had the least similar microbial composition and abundance compared to fresh samples. Microbial composition and diversity were relatively stable over time within each preservation method. Based on these results, if freezers are not available, we recommend preserving fecal samples in ethanol (for up to 8 weeks) prior to microbial extraction and analysis.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 16-26 |
| Number of pages | 11 |
| Journal | Journal of Microbiological Methods |
| Volume | 113 |
| DOIs | |
| State | Published - Jun 1 2015 |
Funding
We would like to thank the Columbian Park Zoo for kindly providing us with spider monkey fecal samples. Krista Nichols, Ching Ching Wu, and Tsang-Long Lin generously provided laboratory space for the molecular work. We also thank Richard D. Howard for his support of this project, and review of this manuscript. Bong Suk-Kim's guidance and Gaenna Rogers' assistance in the laboratory were greatly appreciated. This project was funded by Morris Animal Foundation , Purdue University College of Veterinary Medicine Veterinary Scholars Program , San Diego Zoo Global , the Offield Family Foundation , and the Earth Microbiome Project . We also thank the Howard Hughes Medical Institute for their support. VLH was supported by a Purdue University Andrews Fellowship and a Purdue Research Foundation Research Grant .
Keywords
- Ateles geoffroyi
- Fecal microbial community
- Fecal preservation method
- Gut microbiota
- Primate
ASJC Scopus subject areas
- Microbiology (medical)
- Molecular Biology
- Microbiology