BackgroundEffective means are needed to efficiently collect fecal samples for microbiome analysis in large-scale epidemiological studies. Using twenty-four fecal aliquots prepared from three healthy individuals, we compared the following four fecal sample collection methods for assessment of human gut microbiome: 1) fecal occult blood test cards, held at room temperature for three days, 2) Eppendorf tubes, at room temperature for three days, 3) Eppendorf tubes with RNAlater, at room temperature, and 4) as controls, samples immediately frozen at −80°C. The 24 samples were assayed by 16S rRNA gene sequencing to compare overall microbiome structure and taxon distributions according to collection method.ResultsStoring fecal occult blood test card samples at room temperature for three days did not affect total DNA purity and relative 16S rRNA bacterial gene contents, compared with fresh frozen collection. Overall microbiome structure, based on phylogenetic UniFrac index, differed significantly by subject (p = 0.001), but microbiome structure (p = 0.497) and relative abundance of major microbial taxa (phyla) (p > 0.05) did not differ significantly by collection method.ConclusionsOur findings suggest that low-cost fecal occult blood test card collection may be a feasible means of sample collection for fecal microbiome assessment in large-scale population-based studies.
Comparison of methods for fecal microbiome biospecimen collection
Christine Dominianni,Jing Wu,R. Hayes,Jiyoung Ahn
Published 2014 in BMC Microbiology
ABSTRACT
PUBLICATION RECORD
- Publication year
2014
- Venue
BMC Microbiology
- Publication date
2014-04-23
- Fields of study
Biology, Medicine, Environmental Science
- Identifiers
- External record
- Source metadata
Semantic Scholar, PubMed
CITATION MAP
EXTRACTION MAP
CLAIMS
CONCEPTS
- 16s rrna gene sequencing
Sequencing assay used to profile bacterial community composition from the fecal aliquots.
- dna purity
A quality metric describing the cleanliness of extracted fecal DNA.
- eppendorf tubes
Microcentrifuge tubes used here as a fecal sample collection and storage container.
- fecal occult blood test cards
Cards used here to collect and store fecal aliquots for later microbiome profiling.
- fresh frozen collection
The control condition in which fecal samples were immediately frozen at −80°C.
Aliases: immediately frozen at −80°C
- major microbial taxa (phyla)
High-level bacterial taxonomic groups used to compare relative abundance across collection methods.
Aliases: major microbial taxa
- phylogenetic unifrac index
A phylogenetic beta-diversity metric used to compare overall microbiome structure.
- relative 16s rrna bacterial gene contents
The proportion of bacterial 16S rRNA gene signal measured in the extracted fecal DNA.
- rnalater
A nucleic-acid stabilizing reagent added to some fecal samples before room-temperature storage.
REFERENCES
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