Abstract
Fecal samples collected for microbiome analyses are typically frozen to avoid postcollection changes in microbial composition. eNAT is a guanidine thiocyanate-based medium that stabilizes microbial DNA and allows safe specimen handling and shipping by inactivating microorganisms. We collected fecal samples (n = 50) from children undergoing hematopoietic stem cell transplantation. We divided samples into three aliquots: (a) stored in RNAlater and immediately transferred to −80°C; (b) stored in eNAT medium and immediately transferred to −80°C; and (c) stored in eNAT medium at ambient temperature (~20°C) for 30 days prior to transfer to −80°C. Mean (standard deviation) Shannon diversity and Chao1 indices in sample aliquots were 2.05 (0.62) and 23.8 (16.6), respectively. Comparing samples frozen immediately in RNAlater to samples frozen immediately in eNAT, there were no differences in Shannon diversity (p =.51), Chao1 richness (p =.66), and overall microbiome composition (p =.99). Comparing eNAT samples frozen immediately to samples stored at ambient temperature, we identified no differences in Shannon diversity (p =.65), Chao1 richness (p =.87), and overall microbiome composition (p =.99). Storage of fecal samples in eNAT at ambient temperature for 30 days did not alter microbiome richness, diversity, or composition. eNAT may be a useful medium for fecal microbiome studies, particularly when cold chain storage is unavailable.
Original language | English (US) |
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Article number | e1046 |
Journal | MicrobiologyOpen |
Volume | 9 |
Issue number | 7 |
DOIs | |
State | Published - Jul 1 2020 |
Funding
M.S.K. was supported by a NIH Career Development Award (K23‐AI135090). The Duke BERD Methods Core's support of this project was made possible (in part) by Grant Number UL1TR002553 from the National Center for Advancing Translational Sciences (NCATS) of the National Institutes of Health (NIH), and NIH Roadmap for Medical Research. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of NCATS or NIH. We offer sincere gratitude to the children and families who participated in this study.
Keywords
- 16S rRNA sequencing
- bacterial inactivation
- biological sample shipping
- stabilization media
ASJC Scopus subject areas
- Microbiology