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. 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.
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.
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.
Authors: Hajara Aslam; Wolfgang Marx; Tetyana Rocks; Amy Loughman; Vinoomika Chandrasekaran; Anu Ruusunen; Samantha L Dawson; Madeline West; Eva Mullarkey; Julie A Pasco; Felice N Jacka Journal: Gut Microbes Date: 2020-11-09