Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
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...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Language: | English |
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NATURE PORTFOLIO
2021
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| Subjects: | |
| Online Access: | http://hdl.handle.net/20.500.11937/86462 |
| _version_ | 1848764829671620608 |
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| author | Jones, Jacquelyn Reinke, S.N. Ali, Alishum Palmer, D.J. Christophersen, Claus |
| author_facet | Jones, Jacquelyn Reinke, S.N. Ali, Alishum Palmer, D.J. Christophersen, Claus |
| author_sort | Jones, Jacquelyn |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T11:25:35Z |
| format | Journal Article |
| id | curtin-20.500.11937-86462 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T11:25:35Z |
| publishDate | 2021 |
| publisher | NATURE PORTFOLIO |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-864622021-11-29T09:09:15Z Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations Jones, Jacquelyn Reinke, S.N. Ali, Alishum Palmer, D.J. Christophersen, Claus Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics STOOL FORM FREQUENCY 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. 2021 Journal Article http://hdl.handle.net/20.500.11937/86462 10.1038/s41598-021-93031-z English http://creativecommons.org/licenses/by/4.0/ NATURE PORTFOLIO fulltext |
| spellingShingle | Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics STOOL FORM FREQUENCY Jones, Jacquelyn Reinke, S.N. Ali, Alishum Palmer, D.J. Christophersen, Claus Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations |
| title | Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations |
| title_full | Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations |
| title_fullStr | Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations |
| title_full_unstemmed | Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations |
| title_short | Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations |
| title_sort | fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations |
| topic | Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics STOOL FORM FREQUENCY |
| url | http://hdl.handle.net/20.500.11937/86462 |