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Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a
Georgina M Williams1,2, Sam D Leary1, Nadim J Ajami3
1The NIHR Bristol Biomedical Research Centre, Nutrition Theme, University of Bristol, Bristol, United Kingdom.
Insights
The OMNIgene•GUT kit is the most effective method for stabilizing stool samples collected from nappies for gut microbiome analysis. This method allows for postal transport at ambient temperatures with minimal changes to bacterial DNA, proving practical for large birth cohort studies.
Area of Science:
- Microbiology
- Immunology
- Genetics
Background:
- The gut microbiome plays a crucial role in autoimmune diseases like type 1 diabetes.
- Early-life gut microbiome sampling is vital for understanding disease development.
- Current sample collection methods (fresh or immediate freezing) are impractical for population-based studies.
Purpose of the Study:
- To identify the optimal method for stabilizing stool bacterial DNA from nappies for postal transport.
- To evaluate sample preservation methods for a national birth cohort study.
Main Methods:
- Four sample collection methods were compared against immediate freezing.
- Methods included swabs (frozen and ambient), a commercial stabilization kit (OMNIgene•GUT), and plain tubes.
- Samples were transported by post at ambient temperatures.
- Bland Altman analysis assessed agreement with the frozen standard.
Main Results:
- All ambient transport methods showed variation compared to the frozen standard.
- The OMNIgene•GUT kit demonstrated the narrowest 95% limits of agreement.
- Agreement was measured by operational taxonomic units and Shannon diversity index.
Conclusions:
- The OMNIgene•GUT kit offers the best preservation of stool bacterial DNA for gut microbiome analysis among tested methods.
- This kit is practical for parents and suitable for large-scale studies involving postal sample delivery.
- Minimal changes in bacterial DNA were observed with the OMNIgene•GUT kit compared to other methods.
Background:
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.
Methods:
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.
Results:
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.
Conclusions:
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.
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