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Sample storage conditions induce post-collection biases in microbiome profiles

Samir V Jenkins1, Kieng B Vang2, Allen Gies3

  • 1Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.

BMC Microbiology
|December 29, 2018
PubMed
Abstract

Insights

Fecal microbial DNA storage methods impact community quality and composition. Storage in lysis buffer reduced DNA content, while EDTA storage most affected diversity, highlighting unique biases for each strategy.

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Fecal microbial community analysis is crucial for understanding host health.
  • Standardization of sample collection and storage is essential for reliable results.
  • Investigating the impact of various storage conditions on fecal DNA quality is necessary.

Purpose of the Study:

  • To evaluate the influence of different stabilization and storage strategies on fecal microbial DNA quality and composition.
  • To identify optimal storage conditions that minimize post-collection bias.
  • To provide guidance for researchers handling fecal samples for microbial analysis.

Main Methods:

  • Murine DNA samples were subjected to various storage conditions for one month.
  • Conditions included ambient temperature, different temperatures (-80°C, -20°C, 4°C), and hypoxic conditions.
  • Samples were stored with or without preservative buffers (EDTA, lysis buffer).

Main Results:

  • Storage in lysis buffer reduced DNA content but maintained integrity.
  • EDTA storage significantly impacted alpha diversity and community structure.
  • Distinct changes in bacterial phyla and species abundance were observed across strategies.
  • Metabolic function analysis revealed condition-specific alterations, notably in tyrosine metabolism.

Conclusions:

  • Each long-term storage strategy introduces unique post-collection biases.
  • Researchers must consider these biases when interpreting fecal microbial community data.
  • Careful selection of storage methods is critical for accurate microbiome research.
Keywords:
16S rRNAAlpha diversityFecal microbiome transplantationsGut microbiomeMetabolic function analysis

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