Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly

• Published in: eLife Vol. 7
• Main Authors: Martínez, Inés, Maldonado-Gomez, Maria X, Gomes-Neto, João Carlos, Kittana, Hatem, Ding, Hua, Schmaltz, Robert, Joglekar, Payal, Cardona, Roberto Jiménez, Marsteller, Nathan L, Kembel, Steven W, Benson, Andrew K, Peterson, Daniel A, Ramer-Tait, Amanda E, Walter, Jens
• Format: Journal Article
• Language: English
• Published: England eLife Science Publications, Ltd 18.09.2018; eLife Sciences Publications Ltd; eLife Sciences Publications, Ltd
• Subjects: Adaptive Immunity; Analysis; Animal experimentation; Animals; Bacteria; Bacteria - growth & development; Biodiversity; Cecum - microbiology; Chronic diseases; colonisation history; Colonization; Colony Count, Microbial; community ecology; Coral reefs; Diet; Ecology; Ecosystems; Environmental factors; Experiments; Gastrointestinal Microbiome; Gastrointestinal system; Genetics; gut microbiota; historical contingency; Homeodomain Proteins - metabolism; Immune system; Infants; Intestinal microflora; Lactobacillus; Marine ecosystems; Metabolism; Mice, Inbred C57BL; Microbiota; Microbiota (Symbiotic organisms); Microorganisms; Models, Animal; Multivariate analysis; Physiological aspects; Physiology; priority effect; RAG1 protein; Rain forests; Reefs; Scientists; Taxonomy; Time Factors; Twins; Variance analysis; Canada; United States > US; historical contingency; mouse; priority effect; ecology; community ecology; colonisation history; gut microbiota; Lactobacillus
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.36521

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 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.