Cell 159, 253–266 (2014)

Identifying the microbes that inhabit a particular environment as well as competition among different cohabitating species can help in understanding microbial invasion mechanisms and in treating diseases associated with dysbiosis of the microbiota in the human gut. To study how microbes colonize a gut environment and to characterize the conditions under which different microbial species can live (their 'fundamental niche'), Seedorf et al. performed several transplantation experiments where they introduced microbiota isolated from different non-mice habitats (xenomicrobiota) into germ-free mice. These xenomicrobiota included those isolated from human and zebrafish gut, human tongue and skin, termite hindgut and a non-animal (soil) community. Subsequent characterization by 16S rRNA sequencing of the colonized microbiomes revealed that the mouse gut is within the fundamental niches of a greater proportion of bacterial taxa from non-mice gut environments compared to those from non-gut habitats. Nevertheless, further experiments examining biomass levels, carbohydrate and bile acid metabolism and co-housing of animals to report on microbiota function showed that most bacterial phylotypes cannot realize this niche in a gut harboring indigenous microbiota. In addition, experiments where the germ-free recipient mice lacked mature T and B immune cells allowed the authors to conclude that there is greater selective pressure on xenomicrobiota upon transplantation into the foreign host compared to the indigenous mouse gut microbiota. These results highlight the dynamic interplay among diverse species that can be exploited for understanding colonization and for generating next-generation probiotics.