The majority of fecal microbiota transplantation (FMT) peer-review publications suggest that 28 days is sufficient to assess the effect of human microbes because studies in healthy mice (C57BL/6J) indicate that transplanted human gut microbiome is ‘stable’. On the contrary, we present data that illustrates that microbiome stability is a relative concept, that vary across donors and that their functional effect on intestinal health should only be assessed beyond such period to cover innate and adaptive immunity relevant in chronic inflammatory diseases, including Crohn’s Disease.