Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
| Autor: | Claus T. Christophersen, Alishum Ali, Debra J. Palmer, Stacey N. Reinke, Jacquelyn Jones |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Sample (material) Science Microbial communities Biology Article Specimen Handling 03 medical and health sciences Feces 0302 clinical medicine Time of day Cluster Analysis Humans Sequencing Microbiome Food science Multidisciplinary Microbial Viability Short-chain fatty acid Biodiversity Fatty Acids Volatile Gastrointestinal Microbiome 030104 developmental biology Medicine Metagenome Composition (visual arts) Sample collection Metagenomics 030217 neurology & neurosurgery Homogenization (biology) |
| Zdroj: | Scientific Reports Scientific Reports, Vol 11, Iss 1, Pp 1-13 (2021) |
| ISSN: | 2045-2322 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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