Food Science and Technology Department


Department of Food Science and Technology: Faculty Publications

Document Type


Date of this Version



Martínez et al. eLife 2018;7:e36521.

doi 10.7554/eLife.36521


Copyright Martínez et al. This article is distributed under the terms of the Creative Commons Attribution License,


The factors that govern assembly of the gut microbiota are insufficiently understood. Here, we test the hypothesis that inter-individual microbiota variation can arise solely from differences in the order and timing by which the gut is colonized early in life. Experiments in which mice were inoculated in sequence either with two complex seed communities or a cocktail of four bacterial strains and a seed community revealed that colonization order influenced both the outcome of community assembly and the ecological success of individual colonizers. Historical contingency and priority effects also occurred in Rag1-/- mice, suggesting that the adaptive immune system is not a major contributor to these processes. In conclusion, this study established a measurable effect of colonization history on gut microbiota assembly in a model in which host and environmental factors were strictly controlled, illuminating a potential cause for the high levels of unexplained individuality in host-associated microbial communities.

Supplemental figures attached below.

Ramer elife-36521-figures-v1.pdf (2358 kB)
Figures and figure supplements