An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants
Abstract Background Stool metabolites provide essential insights into the function of the gut microbiome. The current gold standard for storage of stool samples for metabolomics is flash-freezing at − 80 °C which can be inconvenient and expensive. Ambient temperature storage of stool is more practic...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-02-01
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| Series: | BMC Microbiology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12866-021-02104-6 |
| _version_ | 1818582863759540224 |
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| author | Sivapriya Ramamoorthy Shira Levy Masouma Mohamed Alaa Abdelghani Anne M. Evans Luke A. D. Miller Lopa Mehta Sean Moore Elizaveta Freinkman Suchitra K. Hourigan |
| author_facet | Sivapriya Ramamoorthy Shira Levy Masouma Mohamed Alaa Abdelghani Anne M. Evans Luke A. D. Miller Lopa Mehta Sean Moore Elizaveta Freinkman Suchitra K. Hourigan |
| author_sort | Sivapriya Ramamoorthy |
| collection | DOAJ |
| description | Abstract Background Stool metabolites provide essential insights into the function of the gut microbiome. The current gold standard for storage of stool samples for metabolomics is flash-freezing at − 80 °C which can be inconvenient and expensive. Ambient temperature storage of stool is more practical, however no available methodologies adequately preserve the metabolomic profile of stool. A novel sampling kit (OMNImet.GUT; DNA Genotek, Inc.) was introduced for ambient temperature storage and stabilization of feces for metabolomics; we aimed to test the performance of this kit vs. flash-freezing. To do this stool was collected from an infant’s diaper was divided into two aliquots: 1) flash-frozen and 2) stored in an OMNImet.GUT tube at ambient temperature for 3–4 days. Samples from the same infant were collected at 2 different time points to assess metabolite changes over time. Subsequently, all samples underwent metabolomic analysis by liquid chromatography – tandem mass spectrometry (LC-MS/MS). Results Paired fecal samples (flash-frozen and ambient temperature) from 16 infants were collected at 2 time points (32 individual samples, 64 aliquots). Similar numbers of metabolites were detected in both the frozen and ambient temperature samples (1126 in frozen, 1107 in ambient temperature, 1064 shared between sample types). Metabolite abundances were strongly correlated between storage methods (median Spearman correlation Rs = 0.785 across metabolites). Hierarchical clustering analysis and principal component analysis showed that samples from the same individuals at a given time point clustered closely, regardless of the storage method. Repeat samples from the same individual were compared by paired t-test, separately for the frozen and OMNImet.GUT. The number of metabolites in each biochemical class that significantly changed (p < 0.05) at timepoint 2 relative to timepoint 1 was similar in flash-frozen versus ambient temperature storage. Changes in microbiota modified metabolites over time were also consistent across both methodologies. Conclusion Ambient temperature storage and stabilization of stool in the OMNImet.GUT device yielded comparable metabolomic results to flash freezing in terms of 1) the identity and abundance of detected biochemicals 2) the distinct metabolomic profiles of subjects and 3) changes in metabolites over time that are plausibly microbiota-induced. This method potentially provides a more convenient, less expensive home collection and storage option for stool metabolomic analysis. |
| first_indexed | 2024-12-16T07:56:09Z |
| format | Article |
| id | doaj.art-10db1355326c4899bcb0816039dc4230 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-16T07:56:09Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-10db1355326c4899bcb0816039dc42302022-12-21T22:38:42ZengBMCBMC Microbiology1471-21802021-02-0121111010.1186/s12866-021-02104-6An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infantsSivapriya Ramamoorthy0Shira Levy1Masouma Mohamed2Alaa Abdelghani3Anne M. Evans4Luke A. D. Miller5Lopa Mehta6Sean Moore7Elizaveta Freinkman8Suchitra K. Hourigan9MetabolonInova Children’s HospitalInova Children’s HospitalInova Children’s HospitalMetabolonMetabolonInova Health SystemDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of VirginiaMetabolonInova Children’s HospitalAbstract Background Stool metabolites provide essential insights into the function of the gut microbiome. The current gold standard for storage of stool samples for metabolomics is flash-freezing at − 80 °C which can be inconvenient and expensive. Ambient temperature storage of stool is more practical, however no available methodologies adequately preserve the metabolomic profile of stool. A novel sampling kit (OMNImet.GUT; DNA Genotek, Inc.) was introduced for ambient temperature storage and stabilization of feces for metabolomics; we aimed to test the performance of this kit vs. flash-freezing. To do this stool was collected from an infant’s diaper was divided into two aliquots: 1) flash-frozen and 2) stored in an OMNImet.GUT tube at ambient temperature for 3–4 days. Samples from the same infant were collected at 2 different time points to assess metabolite changes over time. Subsequently, all samples underwent metabolomic analysis by liquid chromatography – tandem mass spectrometry (LC-MS/MS). Results Paired fecal samples (flash-frozen and ambient temperature) from 16 infants were collected at 2 time points (32 individual samples, 64 aliquots). Similar numbers of metabolites were detected in both the frozen and ambient temperature samples (1126 in frozen, 1107 in ambient temperature, 1064 shared between sample types). Metabolite abundances were strongly correlated between storage methods (median Spearman correlation Rs = 0.785 across metabolites). Hierarchical clustering analysis and principal component analysis showed that samples from the same individuals at a given time point clustered closely, regardless of the storage method. Repeat samples from the same individual were compared by paired t-test, separately for the frozen and OMNImet.GUT. The number of metabolites in each biochemical class that significantly changed (p < 0.05) at timepoint 2 relative to timepoint 1 was similar in flash-frozen versus ambient temperature storage. Changes in microbiota modified metabolites over time were also consistent across both methodologies. Conclusion Ambient temperature storage and stabilization of stool in the OMNImet.GUT device yielded comparable metabolomic results to flash freezing in terms of 1) the identity and abundance of detected biochemicals 2) the distinct metabolomic profiles of subjects and 3) changes in metabolites over time that are plausibly microbiota-induced. This method potentially provides a more convenient, less expensive home collection and storage option for stool metabolomic analysis.https://doi.org/10.1186/s12866-021-02104-6MetabolomicsStoolMicrobiomeInfantsAmbient temperature |
| spellingShingle | Sivapriya Ramamoorthy Shira Levy Masouma Mohamed Alaa Abdelghani Anne M. Evans Luke A. D. Miller Lopa Mehta Sean Moore Elizaveta Freinkman Suchitra K. Hourigan An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants BMC Microbiology Metabolomics Stool Microbiome Infants Ambient temperature |
| title | An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants |
| title_full | An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants |
| title_fullStr | An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants |
| title_full_unstemmed | An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants |
| title_short | An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants |
| title_sort | ambient temperature storage and stabilization device performs comparably to flash frozen collection for stool metabolomics in infants |
| topic | Metabolomics Stool Microbiome Infants Ambient temperature |
| url | https://doi.org/10.1186/s12866-021-02104-6 |
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