Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal

Abstract

Summary: Interest in manipulating the gut microbiota to treat disease has led to a need for understanding how organisms can establish themselves when introduced into a host with an intact microbial community. Here, we employ the concept of orthogonal niche engineering: a resource typically absent from the diet, seaweed, creates a customized niche for an introduced organism. In the short term, co-introduction of this resource at 1% in the diet along with an organism with exclusive access to this resource, Bacteroides plebeius DSM 17135, enables it to colonize at a median abundance of 1% and frequently up to 10 or more percent, both on pulsed and constant seaweed diets. In a two-month follow-up after the initial treatment period, B. plebeius stops responding to seaweed in mice initially on the constant seaweed diet, suggesting treatment regime will affect controllability. These results offer potential for diet-based intervention to introduce and control target organisms. : Kearney et al. show that co-introducing a bacterial commensal along with a resource to which it has exclusive access enables it to grow to high abundances in the mouse gut microbiota. Long-term response of the commensal to substrate depends on the frequency of substrate exposure during an initial diet period. Keywords: bacteroides, gut microbiome, gut microbiota, orthogonal niche, seaweed, microbial ecology, microbiome modulation, microbial engraftment