Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles

Chieh-Chang Chen; Wei-Kai Wu; Chih-Min Chang; Suraphan Panyod; Tzu-Pin Lu; Jyh-Ming Liou; Yu-Jen Fang; Eric Y Chuang; Ming-Shiang Wu

doi:10.1016/j.jfma.2020.01.013

Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles

J Formos Med Assoc. 2020 Dec;119(12):1791-1798. doi: 10.1016/j.jfma.2020.01.013. Epub 2020 Feb 26.

Authors

Chieh-Chang Chen¹, Wei-Kai Wu², Chih-Min Chang³, Suraphan Panyod⁴, Tzu-Pin Lu³, Jyh-Ming Liou⁵, Yu-Jen Fang⁶, Eric Y Chuang⁷, Ming-Shiang Wu⁸

Affiliations

¹ Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
² Department of Internal Medicine, National Taiwan University Hospital Bei-Hu Branch, Taipei, Taiwan; Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan.
³ Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taiwan; Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taiwan.
⁴ Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taiwan.
⁵ Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
⁶ Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yun-Lin, Taiwan.
⁷ Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taiwan; Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
⁸ Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan. Electronic address: mingshiang@ntu.edu.tw.

PMID: 32111519
DOI: 10.1016/j.jfma.2020.01.013

Abstract

Background/purpose: Appropriate storage of fecal samples is a critical step for the unbiased analysis of microbial communities in metagenomic studies. Rapid freezing at -80 °C is usually considered to be best practice, but this approach is challenging. DNA stabilizing kits may provide a more convenient method to preserve and store clinical samples. We evaluated the reliability of two collection kits (Stratec stool collection tube with stabilizer, #1038111200 and OMNIgene.GUT OMR-200) on preserving fecal microbiota.

Methods: Samples were collected from two locations of the fecal specimen, in four healthy volunteers. The samples were sub-aliquoted and stored in a -80 °C freezer, in Stratec and OMNIgene.GUT (incubation at ambient temperature for 0, 3, or 7 days). The fecal microbial composition was assessed by 16S rRNA sequencing.

Results: We found that alpha diversity was not significantly affected by storage conditions. Samples stored in DNA stabilizers were still representative of the original microbial community after 7 days at ambient temperature. Individual differences were found to have a greater contribution to the differences in microbial community composition than storage conditions or sampling location. Samples subjected to stabilizers displayed microbial community shifts compared with immediately frozen samples. A linear discriminant analysis effect size (LEfSe) analysis showed that the relative abundances of Faecalibacterium were significantly higher in samples stored in Stratec kits.

Conclusion: Our study reveals that both Stratec and OMNIgene.GUT kits provide good microbiome preservation for up to 7 days in ambient temperature and would represent good options for fecal sample collection in large scale, population-based studies.

Keywords: 16S rRNA amplicon sequencing; DNA stabilizers; Fecal microbiota; OMNIgene.GUT; Storage condition; Stratec.

MeSH terms

DNA
Feces
Humans
Microbiota* / genetics
RNA, Ribosomal, 16S / genetics
Reproducibility of Results
Sequence Analysis, DNA
Temperature

Substances

RNA, Ribosomal, 16S
DNA