The intestinal tract is inhabited by a large and diverse community of microbes collectively referred to as the gut microbiota. While the gut microbiota provides important benefits to its host, its disturbance is associated with chronic inflammatory diseases. For example, we previously reported that, in mice, consumption of relatively low concentrations of two commonly used emulsifiers, detergent-like molecules and ubiquitous component of processed foods, induced chronic colitis in susceptible host and low-grade inflammation and obesity/ metabolic syndrome in wild-type hosts. Emulsifier-induced effects was associated with microbiota encroachment, altered species composition and increased pro-inflammatory potential. Follow-up mechanistic studies demonstrated that the intestinal microbiota is the direct target of such additives, and importantly revealed that not all the microbiotas are impacted in the same way by such disturbance, supporting the concept that some individuals might be at higher risk of host–microbiota perturbations. Our current work is revealing important inter-individual variations in microbiota composition and function, opening new therapeutic avenues to treat and prevent chronic inflammatory disorders.