Joseph F. Petrosin’s research while affiliated with Baylor College of Medicine and other places

What is this page?


This page lists works of an author who doesn't have a ResearchGate profile or hasn't added the works to their profile yet. It is automatically generated from public (personal) data to further our legitimate goal of comprehensive and accurate scientific recordkeeping. If you are this author and want this page removed, please let us know.

Publications (1)


a) and b). Bland Altman plots of observed OTUs (1a) and Shannon index (1b) for the four different methods of sample collection compared to the frozen standard of immediate freezing.
a) Relative abundance of the four main phyla for each sampling method (immediate freezing in a plain sterile tube (frozen), immediate freezing on a swab (swab frozen), using the OMNIgene•GUT kit (OMNIgene•GUT), collecting into a plain sterile tube in the post (plain post) and collecting onto a swab which is sent in the post (swab post). b) Relative Abundance of the ten main genera for each sampling method.
Methodology compared to frozen standard (average difference, (95% limits of agreement))
Methodology compared to frozen standard (average difference, (95% limit of agreement)
Methodology compared to frozen standard (average difference, (95% limit of agreement)
Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study
  • Article
  • Full-text available

June 2019

·

135 Reads

·

21 Citations

·

Sam D. Leary

·

·

[...]

·

Kathleen M. Gillespie

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.

Download

Citations (1)


... A corresponding kit for the microbiome (OMNIgene•GUT) has been used in several studies. 17,18 To our knowledge, only a few studies compared feces collection methods for simultaneous gut microbiota profiling and fecal metabolomics. 10 Notably, studies comparing collection with that of 95% EtOH and commercial fecal collection kits are lacking. ...

Reference:

Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization
Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study