A Novel Fecal Sample Collection Method for Metagenomic Analyses
Condition: Healthy
Study type: Observational

Summary: 
      This is an open-label, one-arm, one-time-point pilot assessing the intra- and inter-group
      variation of gut microbiome collection methods and storage conditions using metagenomic
      sequencing for analysis. This study recruited 6 adult volunteers collecting 12 fecal samples
      from one bowel movement. Subjects were given detailed instructions as to collect and store
      feces samples into the 4 different collection and preservation methods and return samples for
      metagenomic analysis.
    

Detailed description: 
      A total of 6 subjects were enrolled in this pilot study. The inclusion criteria to be
      enrolled in the study included: age >18; Bristol Stool Scale type 3 and 4 (normal), agree to
      collect and donate the feces, and the ability to understand and write English. Exclusion
      criteria included people with constipation, slightly dry, or diarrhea feces (Bristol Stool
      Scale types 1-2, 5-7), pregnant or breastfeeding females, history of alcohol, drug, or
      medication abuse, known allergies to any substance in the study product, current diagnosis of
      inflammatory bowel disease (Crohn's Disease or Ulcerative Colitis), and currently taking any
      medication that may interfere with defecation.

      Fecal collection kits were mailed to subjects with instructions for sample collection. A
      total of 12 samples (3 sites on the bowel movement, 4 collection/preserving methods) were
      collected by each subject yielding a total of 72 samples to be processed. Four preservation
      methods were used to process the samples for metagenomic sequencing: freezing (-20°C), room
      temperature storage, Zymo DNA shield kit (room temperature), and DESS DNA preservation (room
      temperature). All the samples are shipped at room temperature except the samples meant for
      freezing which were shipped on dry ice. At the lab, all the samples were put into a fridge
      (4°C) except the frozen samples which were put in a -20°C freezer.

      Samples underwent DNA extraction and sequencing per previously published methods with the
      objective to understand intra- and inter-sample comparisons for collection methods and
      stability during storage/shipping. Results will include taxonomic abundance metrics,
      metabolic pathway classification, and diversity analysis.
    

Intervention name(s): No intervention
Intervention type(s): Other
Intervention description(s): The single group had no intervention. All followed the same procedures of different collection methods.
Observational model: Case-Only
Time perspective: Prospective
Sampling method: Probability Sample
Study population: 
        In order to account for potential drop-out, 6 participants were enrolled to achieve a
        properly-powered sample size. This target sample size was informed by the literature review
        and power analysis. Both males and females could participate, ages 18+, with no exclusions
        to race or ethnicity.
      
Biospecimen description: 
      Metagenomic (DNA) analysis of (stool) gut microbiome samples
    
Keywords: gut microbiome; metagenomic sequencing; stool collection