Document Type
Journal Article
Publication Title
Scientific Reports
Volume
11
Issue
1
PubMed ID
34234185
Publisher
Nature
School
School of Medical and Health Sciences / School of Science/ Centre for Integrative Metabolomics and Computational Biology
RAS ID
36259
Abstract
Associations between the human gut microbiome and health outcomes continues to be of great interest, although fecal sample collection methods which impact microbiome studies are sometimes neglected. Here, we expand on previous work in sample optimization, to promote high quality microbiome data. To compare fecal sample collection methods, amplicons from the bacterial 16S rRNA gene (V4) and fungal (ITS2) region, as well as short chain fatty acid (SCFA) concentrations were determined in fecal material over three timepoints. We demonstrated that spot sampling of stool results in variable detection of some microbial members, and inconsistent levels of SCFA; therefore, sample homogenization prior to subsequent analysis or subsampling is recommended. We also identify a trend in microbial and metabolite composition that shifts over two consecutive stool collections less than 25 h apart. Lastly, we show significant differences in bacterial composition that result from collecting stool samples in OMNIgene·Gut tube (DNA Genotec) or Stool Nucleic Acid Collection and Preservation Tube (NORGEN) compared to immediate freezing. To assist with planning fecal sample collection and storage procedures for microbiome investigations with multiple analyses, we recommend participants to collect the first full bowel movement of the day and freeze the sample immediately after collection.
DOI
10.1038/s41598-021-93031-z
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Life Sciences Commons, Medicine and Health Sciences Commons, Physical Sciences and Mathematics Commons
Comments
Jones, J., Reinke, S. N., Ali, A., Palmer, D. J., & Christophersen, C. T. (2021). Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations. Scientific Reports, 11, Article 13964.
https://doi.org/10.1038/s41598-021-93031-z