Sample storage conditions induce post-collection biases in microbiome profiles

BMC Microbiology

Kieng B. Vang¹  Robert J. Griffin²  Allen Gies³  Samir V. Jenkins⁴ 

[1] Center for Integrative Nanotechnology Sciences, University of Arkansas, Little Rock, USA;Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, USA;Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, USA;Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, USA

关键词: Gut microbiome;    16S rRNA;    Alpha diversity;    Fecal microbiome transplantations;    Metabolic function analysis;   

DOI  :  10.1186/s12866-018-1359-5

学科分类：微生物学和免疫学

来源: BioMed Central

【 摘 要 】

Here we investigated the influence of different stabilization and storage strategies on the quality and composition of the fecal microbial community. Namely, same-day isolated murine DNA was compared to samples stored for 1 month in air at ambient temperature, with or without preservative buffers (i.e. EDTA and lysis buffer), different temperatures (i.e. 4 °C, − 20 °C, and − 80 °C), and hypoxic conditions. Only storage in lysis buffer significantly reduced DNA content, yet without integrity loss. Storage in EDTA affected alpha diversity the most, which was also reflected in cluster separation. Distinct changes were also seen in the phyla and bacterial species abundance per storage strategy. Metabolic function analysis showed 22 pathways not significantly affected by storage conditions, whereas the tyrosine metabolism pathway was significantly changed in all strategies except by EDTA. Each long-term storage strategy introduced a unique post-collection bias, which is important to take into account when interpreting data.

【 授权许可】

CC BY