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

doi:10.1016/j.chom.2016.09.001

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

Cell Host Microbe. 2016 Oct 12;20(4):515-526. doi: 10.1016/j.chom.2016.09.001. Epub 2016 Sep 29.

Affiliations

¹ Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA.
² Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA; Department of Agricultural, Nutritional and Food Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada.
³ APC Microbiome Institute & School of Microbiology, University College Cork, Cork T12 YN60, Ireland.
⁴ Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma 43124, Italy.
⁵ Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
⁶ Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA.
⁷ Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA; Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108-6106, USA.
⁸ Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA; Department of Agricultural, Nutritional and Food Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada. Electronic address: [email protected].

PMID: 27693307
DOI: 10.1016/j.chom.2016.09.001

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.

Keywords: Bifidobacterium; ecological theory; gut microbiome; gut microbiota; invasion ecology; live biotherapeutic; metagenomics; microbial ecology; microbiome modulation; probiotic.

MeSH terms

Administration, Oral
Bifidobacterium longum / growth & development*
Carrier State*
Gastrointestinal Microbiome*
Humans
Microbiota*
Probiotics / administration & dosage*
Time Factors