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

DNA Feces Humans Microbiota / genetics RNA, Ribosomal, 16S / genetics Reproducibility of Results Sequence Analysis, DNA Temperature
16S rRNA amplicon sequencing DNA stabilizers Fecal microbiota OMNIgene.GUT Storage condition Stratec

Journal

Journal of the Formosan Medical Association = Taiwan yi zhi
ISSN: 0929-6646
Titre abrégé: J Formos Med Assoc
Pays: Singapore
ID NLM: 9214933

Informations de publication

Date de publication:
Dec 2020
Historique:
received: 01 07 2019
revised: 04 12 2019
accepted: 22 01 2020
pubmed: 1 3 2020
medline: 20 2 2021
entrez: 1 3 2020
Statut: ppublish

Résumé

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. 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. 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. 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.

Sections du résumé

BACKGROUND/PURPOSE OBJECTIVE
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 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 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 CONCLUSIONS
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.

Identifiants

DOI: 10.1016/j.jfma.2020.01.013 PMID: 32111519
pubmed: 32111519
pii: S0929-6646(20)30017-6
doi: 10.1016/j.jfma.2020.01.013
pii:
doi:

Substances chimiques

RNA, Ribosomal, 16S 0
DNA 9007-49-2

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1791-1798

Informations de copyright

Copyright © 2020 Formosan Medical Association. Published by Elsevier B.V. All rights reserved.

Auteurs

Chieh-Chang Chen (CC)

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.

Wei-Kai Wu (WK)

Department of Internal Medicine, National Taiwan University Hospital Bei-Hu Branch, Taipei, Taiwan; Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan.

Chih-Min Chang (CM)

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.

Suraphan Panyod (S)

Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taiwan.

Tzu-Pin Lu (TP)

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.

Jyh-Ming Liou (JM)

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.

Yu-Jen Fang (YJ)

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.

Eric Y Chuang (EY)

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.

Ming-Shiang Wu (MS)

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.

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Classifications MeSH

questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Comparison of DNA stabilizers and storage...
questionsmedicales.fr › Liquides et sécrétions biologiques › Fèces › Comparison of DNA stabilizers and storage...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Comparison of DNA stabilizers and storage...
questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › Biodiversité › Biote › Microbiote › Comparison of DNA stabilizers and storage...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN ribosomique › ARN ribosomique 16S › Comparison of DNA stabilizers and storage...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Méthodologie en recherche épidémiologique › Reproductibilité des résultats › Comparison of DNA stabilizers and storage...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Comparison of DNA stabilizers and storage...
questionsmedicales.fr › Environnement et santé publique › Environnement › Concepts météorologiques › Atmosphère › Temps (météorologie) › Température › Comparison of DNA stabilizers and storage...