Collection Methods for Fecal Samples

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Overview

The human gut microbiome is made up of trillions of bacterial cells. Interest in its composition and function is increasing as evidence emerges of its potential role in health and disease. To facilitate human microbiome research, in prospective cohort studies, researchers need to collect samples, including stool samples, that can be used to assess the role of the microbiome in disease etiology. Stool samples are representative of the distal gut microbiome.

Principles for Fresh Fecal Sample Collection

  • Avoid Repeated Temperature Fluctuation

Sharp temperature changes are major stress for many bacteria in stool samples, which can kill microorganisms and exacerbate DNA degradation.

  • Avoid Frozen-thaw Cycles

It is well known that freeze-thaw cycles are key factors leading to DNA degradation in fecal samples, which can lead to poor metagenomic DNA quality and skewed downstream analysis.

  • Shorten the Transportation Time

Transport time should be shortened to prevent undesirable microbial growth and decline. Cold storage may extend transportation times.

Different Fecal Sampling Methods

The relative abundance of phyla changes when samples are subjected to different conditions during sampling and transport that either promote or inhibit microbial proliferation. The ideal fecal specimen collection method preserves the original microbial characteristics of the fecal specimen, stabilizes the microbial DNA, and keeps it at room temperature for multiple days to prevent bacterial growth, as is typical under field conditions.

  • Sampling Without DNA Stabilizer
  • Sampling With DNA Stabilizer

DNA stabilizer is a widely used sample preservation tool in field studies. These DNA stabilization buffers are designed to protect DNA and/or RNA molecules from degradation after collection. One of the best-known stabilization buffers is RNALaterR, which protects RNA from rapid degradation in field studies.

  • Dry Swab

It is recommended to use two swabs to maximize DNA content per sampling session. Samples should be stored in the -80℃ (preferably not the -20℃) and shipped to the lab on dry ice, overnight or two-day shipping.

Overview of methods recommended for sample collection and storage before DNA extraction. Fig.1 Overview of methods recommended for sample collection and storage before DNA extraction. (Wu, 2019)

Stool Subsampling and Storage

Once the sample arrives at the laboratory, it should be frozen for long-term storage at -80℃. Studies were showing that the stool sample can maintain a stable microbial community for up to 2 years after being frozen at -80℃. Sample storage in -20℃ might also be assured for at least for few months. Before freezing a sample, we recommend separating the feces into equal parts for later use, which prevents further unnecessary freeze-thaw cycles.

Stool DNA Extraction

The fecal DNA extraction process usually consists of steps such as sample homogenization, cell lysis, removal of non-DNA material, and DNA purification. To efficiently release bacterial DNA from complex fecal biomass, chemical and mechanical cell lysis is required to break down thick or waxy cell walls.

Services for Fecal Samples Research at Creative Biolabs

Creative Biolabs, one of the world's leading live biotherapeutics CRO services companies, has been at the forefront of next-generation probiotics research for over 10 years. You can rely on our expertise, understanding, experience, and passion to provide the best quality solutions reliably with a fast turnaround time. If you are interested in our stool sample analysis services, please feel free to contact us for more.

Reference

  1. Wu, W.K.; et al. Optimization of fecal sample processing for microbiome study-The journey from the bathroom to bench. Journal of the Formosan Medical Association. 2019, 118(2): 545-555.

For Research Use Only. Not intended for use in food manufacturing or medical procedures (diagnostics or therapeutics). Do Not Use in Humans.

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