The fecal microbiome refers specifically to the microorganisms present in fecal matter. This is in contrast to the widely used term, ‘gut microbiome’ that refers to the microorganisms that live along the entire digestive tract.
While the fecal microbiome is technically derived from the gut microbiome, the two terms are used interchangeably. This is due to standard practices in gut microbiome research, which use feces as a proxy for studying the broader microbial community of the gastrointestinal tract.
Many factors lead to fluctuations in the microbial makeup of the fecal microbiome, such as transit time and dietary changes. However, disease-states and dysbiosis of the gut microbiome are detectable regardless of fluctuations. For this reason, we use ‘gut microbiome analysis’ and ‘gut health test’ as surrogate terms for fecal microbiome analysis.