Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.
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.
Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA.
María X
MX
Maldonado-Gómez
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.
Inés
I
Martínez
APC Microbiome Institute & School of Microbiology, University College Cork, Cork T12 YN60, Ireland.
Francesca
F
Bottacini
APC Microbiome Institute & School of Microbiology, University College Cork, Cork T12 YN60, Ireland.
Amy
A
O'Callaghan
Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma 43124, Italy.
Marco
M
Ventura
APC Microbiome Institute & School of Microbiology, University College Cork, Cork T12 YN60, Ireland.
Douwe
D
van Sinderen
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
Benjamin
B
Hillmann
Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA.
Pajau
P
Vangay
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.
Dan
D
Knights
Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA.
Robert W
RW
Hutkins
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: jwalter1@ualberta.ca.
Jens
J
Walter
D000284:Administration, Oral; D000069978:Bifidobacterium longum / Q000254:growth & development*; D002353:Carrier State; D000069196:Gastrointestinal Microbiome; D006801:Humans; D064307:Microbiota; D019936:Probiotics / Q000008:administration & dosage*; D013997:Time Factors
Bifidobacterium; ecological theory; gut microbiome; gut microbiota; invasion ecology; live biotherapeutic; metagenomics; microbial ecology; microbiome modulation; probiotic