Although there are numerous studies focusing on structure and function of the gut microbiota, very few is known finally regarding the gut microbial colonization and the host homeostasis.  Some studies already focused on the structural dynamics of the early life gut microbiota, but little is known about factor which allows bacteria to establish in the gut and how the host responds to this colonization factors. Recent studies tried to decipher those mechanism using models.

Sarkis Mazmanian group used Bacteroides fragilis strains and mutant with germ free mice to characterize commensal colonization factors. For instance, they observed that a specific locus is upregulated during the colonization in gut mice and help Bacteroides fragilis to penetrate colonic mucus. Others studies led by Sahar El Aidy permit to shed light on homeostasis establishment dynamics between host and its gut microbiota.