Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study.
<h4>Background</h4>Understanding the role of the gut microbiome is pivotal for the future development of therapies for the prevention and management of autoimmune conditions such as type 1 diabetes when sampling during early life may be particularly important. The current standard method...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0216557 |
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| author | Georgina M Williams Sam D Leary Nadim J Ajami Saranna Chipper Keating Joseph F Petrosin Julian P Hamilton-Shield Kathleen M Gillespie |
| author_facet | Georgina M Williams Sam D Leary Nadim J Ajami Saranna Chipper Keating Joseph F Petrosin Julian P Hamilton-Shield Kathleen M Gillespie |
| author_sort | Georgina M Williams |
| collection | DOAJ |
| description | <h4>Background</h4>Understanding the role of the gut microbiome is pivotal for the future development of therapies for the prevention and management of autoimmune conditions such as type 1 diabetes when sampling during early life may be particularly important. The current standard methods for collecting gut microbiome samples for research is to extract fresh samples or freeze samples immediately after collection. This is often impractical however for population-based studies. The aim of this study was to determine the optimal method for the stabilization of stool bacterial DNA obtained from nappies and transported by post in ambient conditions to the research centre for a national birth cohort study.<h4>Methods</h4>Four methods to collect samples were compared to immediate freezing of samples: 1) collecting faeces onto a swab which was immediately frozen, 2) using a commercially available kit with stabilisation solution (OMNIgene•GUT kit) at ambient temperature, 3) collecting onto a swab and 4) collecting into a sterile plain tube. Samples 3) and 4) were returned to the laboratory by post at ambient temperatures. A Bland Altman analysis was used to assess the agreement between the different methods and the frozen standard.<h4>Results</h4>Stool samples were collected by parents. For samples transported in ambient conditions, the limits of agreement showed that the OMNIgene•GUT kit had the narrowest 95% limits of agreement with the frozen standard as measured by the number of operational taxonomic units and the Shannon diversity index.<h4>Conclusions</h4>All methods assessed for preserving samples collected from nappies at a distance and delivered by post for gut microbiome analysis showed variation / disagreement from the frozen standard. Overall, the OMNIgene•GUT kit preserved the samples with minimal changes compared to other methods and was practical for parents to use. |
| first_indexed | 2024-12-17T21:34:57Z |
| format | Article |
| id | doaj.art-ec0ad79d5954421abd48e056fedec249 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-17T21:34:57Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-ec0ad79d5954421abd48e056fedec2492022-12-21T21:31:46ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-01146e021655710.1371/journal.pone.0216557Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study.Georgina M WilliamsSam D LearyNadim J AjamiSaranna Chipper KeatingJoseph F PetrosinJulian P Hamilton-ShieldKathleen M Gillespie<h4>Background</h4>Understanding the role of the gut microbiome is pivotal for the future development of therapies for the prevention and management of autoimmune conditions such as type 1 diabetes when sampling during early life may be particularly important. The current standard methods for collecting gut microbiome samples for research is to extract fresh samples or freeze samples immediately after collection. This is often impractical however for population-based studies. The aim of this study was to determine the optimal method for the stabilization of stool bacterial DNA obtained from nappies and transported by post in ambient conditions to the research centre for a national birth cohort study.<h4>Methods</h4>Four methods to collect samples were compared to immediate freezing of samples: 1) collecting faeces onto a swab which was immediately frozen, 2) using a commercially available kit with stabilisation solution (OMNIgene•GUT kit) at ambient temperature, 3) collecting onto a swab and 4) collecting into a sterile plain tube. Samples 3) and 4) were returned to the laboratory by post at ambient temperatures. A Bland Altman analysis was used to assess the agreement between the different methods and the frozen standard.<h4>Results</h4>Stool samples were collected by parents. For samples transported in ambient conditions, the limits of agreement showed that the OMNIgene•GUT kit had the narrowest 95% limits of agreement with the frozen standard as measured by the number of operational taxonomic units and the Shannon diversity index.<h4>Conclusions</h4>All methods assessed for preserving samples collected from nappies at a distance and delivered by post for gut microbiome analysis showed variation / disagreement from the frozen standard. Overall, the OMNIgene•GUT kit preserved the samples with minimal changes compared to other methods and was practical for parents to use.https://doi.org/10.1371/journal.pone.0216557 |
| spellingShingle | Georgina M Williams Sam D Leary Nadim J Ajami Saranna Chipper Keating Joseph F Petrosin Julian P Hamilton-Shield Kathleen M Gillespie Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study. PLoS ONE |
| title | Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study. |
| title_full | Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study. |
| title_fullStr | Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study. |
| title_full_unstemmed | Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study. |
| title_short | Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study. |
| title_sort | gut microbiome analysis by post evaluation of the optimal method to collect stool samples from infants within a national cohort study |
| url | https://doi.org/10.1371/journal.pone.0216557 |
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