Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

Authors

María X. Maldonado-Gómez, University of Nebraska-Lincoln
Inés Martínez, University of Nebraska-Lincoln
Francesca Bottacini, University College Cork, IrelandFollow
Amy O’Callaghan, University College Cork, Ireland
Marco Ventura, University of Parma, ItalyFollow
Douwe van Sinderen, University College Cork, IrelandFollow
Benjamin Hillmann, University of MinnesotaFollow
Pajau Vangay, University of MinnesotaFollow
Dan Knights, University of MinnesotaFollow
Robert W. Hutkins, University of Nebraska-LincolnFollow
Jens Walter, University of AlbertaFollow

Document Type

Article

Date of this Version

10-2016

Citation

Published in Cell Host & Microbe 20 (October 12, 2016), pp 515–526. doi 10.1016/j.chom.2016.09.001

Comments

Copyright © 2016 Elsevier Inc. Used by permission.

Abstract

Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution.