TABLE 2.

Stool sample collection methods

Method of collection	Stability	Advantages	Disadvantages	Modalities that can be assessed
Immediate cooling
Flash‐frozen	Freeze immediately	Preserves microbial signature	Cold chain management necessary Need for freezer Batch processing not possible	Metagenomics, 16S Amplicon sequencing, metatranscriptomics, metaproteomics, metabolomics
Refrigeration (4°C)	2–24 h	Slowed bacterial growth Slowed down fermentation	Cold chain management necessary Need for refrigerator Deviation from the original sample Batch processing not possible	Metagenomics, 16S Amplicon sequencing, metatranscriptomics, metabolomics (may be affected)
Stabilizing solution (room temperature)
Omnigene GUT	60 days	It can be done at home and shipped back Immediate homogenization No PCR inhibition No preprocessing before DNA extraction High DNA/RNA recovery	Expensive (compared to freezing)	Metagenomics, 16S Amplicon sequencing, metatranscriptomics (may be skewed), metabolomics (may be affected)
RNAlater	Seven days	It can be done at home and shipped back High DNA/RNA recovery	Large container needed A large volume of liquid needed (5:1 ratio) Preprocessing needed for DNA extraction Expensive (compared to freezing)	Metagenomics, 16S Amplicon sequencing, metatranscriptomics
Ethanol (95–99%)	Two days	It can be done at home and shipped back Inexpensive	Large container needed Flammable liquid Preprocessing needed for DNA extraction A large volume of liquid needed (5:1 ratio) Quality of DNA affected	Metagenomics, 16S Amplicon sequencing
Minimal collection
Swab	Variable by solution	It can be done at home and shipped back Inexpensive Reduce deviations from the original sample	Overgrowth of gram‐negative bacteria Highly diluted sample DNA yield poor A small amount of sample Modified DNA extraction method needed	Metagenomics, 16S Amplicon sequencing
Card	Stable once dry	It can be done at home and shipped back Reduce deviations from the original sample	DNA yield poor A small amount of sample Modified DNA extraction method needed Increased contamination risk during the drying process	Metagenomics, 16S Amplicon sequencing

Abbreviation: PCR, polymerase chain reaction.