Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome
Summary: Practical considerations in fecal sample collection for microbiome research include time to sample storage, time of collection, and hindgut position during terminal collections. Here, parallel experiments were performed to investigate the relative effect of these factors on microbiome compo...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004224003110 |
| _version_ | 1797317131073748992 |
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| author | Kevin L. Gustafson Zachary L. McAdams Amber L. Russell Rebecca A. Dorfmeyer Giedre M. Turner Aaron C. Ericsson |
| author_facet | Kevin L. Gustafson Zachary L. McAdams Amber L. Russell Rebecca A. Dorfmeyer Giedre M. Turner Aaron C. Ericsson |
| author_sort | Kevin L. Gustafson |
| collection | DOAJ |
| description | Summary: Practical considerations in fecal sample collection for microbiome research include time to sample storage, time of collection, and hindgut position during terminal collections. Here, parallel experiments were performed to investigate the relative effect of these factors on microbiome composition in mice colonized with two different vendor-origin microbiomes. 16S rRNA amplicon sequencing of immediately flash-frozen feces showed no difference in alpha or beta diversity compared to samples incubated up to 9 h at room temperature. Samples collected in the morning showed greater alpha diversity compared to samples collected in the afternoon. While a significant effect of time was detected in all hindgut regions, the effect increased from cecum to distal colon. This study highlights common scenarios in microbiome research that may affect outcome measures of microbial community analysis. However, we demonstrate a relatively low effect size of these technical factors when compared to a primary experimental factor with large intergroup variability. |
| first_indexed | 2024-03-08T03:29:27Z |
| format | Article |
| id | doaj.art-8952db83593e4fd885f252024e7b25d6 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-08T03:29:27Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-8952db83593e4fd885f252024e7b25d62024-02-11T05:11:51ZengElsevieriScience2589-00422024-03-01273109090Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiomeKevin L. Gustafson0Zachary L. McAdams1Amber L. Russell2Rebecca A. Dorfmeyer3Giedre M. Turner4Aaron C. Ericsson5University of Missouri (MU) Comparative Medicine Program, Columbia, MO 65201, USA; Department of Veterinary Pathobiology, MU, Columbia, MO 65201, USAMolecular Pathogenesis and Therapeutics Program, MU, Columbia, MO 65201, USADepartment of Veterinary Pathobiology, MU, Columbia, MO 65201, USAMU Metagenomics Center (MUMC), Mutant Mouse Resource and Research Center at the University of Missouri (MU MMRRC), Columbia, MO 65201, USAMU Metagenomics Center (MUMC), Mutant Mouse Resource and Research Center at the University of Missouri (MU MMRRC), Columbia, MO 65201, USAUniversity of Missouri (MU) Comparative Medicine Program, Columbia, MO 65201, USA; Department of Veterinary Pathobiology, MU, Columbia, MO 65201, USA; Molecular Pathogenesis and Therapeutics Program, MU, Columbia, MO 65201, USA; MU Metagenomics Center (MUMC), Mutant Mouse Resource and Research Center at the University of Missouri (MU MMRRC), Columbia, MO 65201, USA; Corresponding authorSummary: Practical considerations in fecal sample collection for microbiome research include time to sample storage, time of collection, and hindgut position during terminal collections. Here, parallel experiments were performed to investigate the relative effect of these factors on microbiome composition in mice colonized with two different vendor-origin microbiomes. 16S rRNA amplicon sequencing of immediately flash-frozen feces showed no difference in alpha or beta diversity compared to samples incubated up to 9 h at room temperature. Samples collected in the morning showed greater alpha diversity compared to samples collected in the afternoon. While a significant effect of time was detected in all hindgut regions, the effect increased from cecum to distal colon. This study highlights common scenarios in microbiome research that may affect outcome measures of microbial community analysis. However, we demonstrate a relatively low effect size of these technical factors when compared to a primary experimental factor with large intergroup variability.http://www.sciencedirect.com/science/article/pii/S2589004224003110MicrobiologyMicrobiome |
| spellingShingle | Kevin L. Gustafson Zachary L. McAdams Amber L. Russell Rebecca A. Dorfmeyer Giedre M. Turner Aaron C. Ericsson Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome iScience Microbiology Microbiome |
| title | Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome |
| title_full | Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome |
| title_fullStr | Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome |
| title_full_unstemmed | Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome |
| title_short | Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome |
| title_sort | effect size of delayed freezing diurnal variation and hindgut location on the mouse fecal microbiome |
| topic | Microbiology Microbiome |
| url | http://www.sciencedirect.com/science/article/pii/S2589004224003110 |
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