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

María X. Maldonado-Gómez, Inés Martínez, Francesca Bottacini, Amy O'Callaghan, Marco Ventura, Douwe van Sinderen, Benjamin Hillmann, Pajau Vangay, Dan Knights, Robert W. Hutkins, Jens Walter

Research output: Contribution to journalArticlepeer-review

235 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)515-526
Number of pages12
JournalCell Host and Microbe
Issue number4
StatePublished - Oct 12 2016

Bibliographical note

Funding Information:
We thank the subjects of the human trial for their determination and compliance. This study was funded by Mead Johnson Nutrition, while D.v.S., A.O’C., and F.B. are members of the APC Microbiome Institute funded by Science Foundation Ireland (SFI) through the Irish Government’s National Development Plan (grant number SFI/12/RC/2273). AH1206 and 1206 are trademarks of Alimentary Health (Cork, Republic of Ireland), who provided probiotic powders, primer sequences, and critical feedback on the manuscript. We thank Jon Vanderhoof (Boston Children’s Hospital, Boston, MA; Boys Town National Research Hospital, Omaha, NE; and Mead Johnson Nutrition, Glenview, IL) for the initiation of this study and Rosemary Pauley-Hunter (Boys Town National Research Hospital, Omaha, NE) for support with the IRB application.

Publisher Copyright:
© 2016 Elsevier Inc.


  • Bifidobacterium
  • ecological theory
  • gut microbiome
  • gut microbiota
  • invasion ecology
  • live biotherapeutic
  • metagenomics
  • microbial ecology
  • microbiome modulation
  • probiotic


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