In general all kind of (DNA) samples can be used for metagenome profiling such as:

• samples of human origin (swaps, feces, lavage) 
• food samples for quality control of microorganisms and pathogen detection in an industrial setting (dairies, breweries, meat-processing and agricultural facilities)
• environmental samples

Eurofins Genomics is particularly well-experienced in DNA isolation and sequencing of stool samples.