Rapid Reconstitution of the Fecal Microbiome after Extended Diet-Induced Changes Indicates a Stable Gut Microbiome in Healthy Adult Dogs

Abstract

The gut microbiome has an important role in health, and diet represents a key lever for shaping the gut microbiome across all stages of life. Maternal milk consumption in neonates leads to long-term health effects, indicating that pliability in the infant gut microbiome in response to diet can drive enduring change. The ability of diet to drive lasting changes in the adult gut microbiome is less understood. We studied the effect of an extreme dietary shift on the fecal microbiome of 46 Labrador retriever dogs (mean age, 4.6 years) over 11 months. Dogs were fed a nutritionally complete, commercially available complex diet (CD) for a minimum of 5 weeks, followed by highly purified diets (PDs) for 36 weeks, and the initial CD for at least a further 4 weeks. Fecal samples were collected at regular intervals for DNA extraction. By analyzing 16S rRNA genes and the metagenomes, we observed minor effects on microbial diversity but significant changes in bacterial taxa and genetic potential when a PD was fed. Specifically, metagenomics identified an enrichment of quinone- and GABA-related pathways on PD, providing insights into dietary effects on cross-feeding strategies impacting community structure. When dogs returned to the CD, no significant differences were found with the initial time point. These findings are consistent with the gut microbiome being rapidly adaptable but capable of being reconstituted when provided with similar diets. These data highlight that long-term changes in the adult dog gut microbiome may only be achieved through long-term maintenance on a specified diet, rather than through feeding a transitionary diet.IMPORTANCE Diet can influence the adult gut microbiome (the community of bacteria) and health outcomes, but the ability to make changes persisting beyond feeding of a particular diet is poorly understood. We investigated whether feeding highly purified diets to adult dogs for 36 weeks would alter bacterial populations sufficiently to result in a persistent change following the dogs' return to a commercial diet. As expected, the microbiome changed when the purified diet was fed, but the original microbiome was reconstituted within weeks of the dogs returning to the commercial diet. The significance of these findings is in identifying an intrinsic stability of the host microbiome in healthy dogs, suggesting that dietary changes to support adult dog health through modifying the gut microbiome may be achieved only through maintenance on a specified diet, rather than through feeding transitionary diets.

Keywords: canine; diet; fecal metagenome; fecal microbiota.

FIG 1

Study design showing timelines, diet changes, and fecal sample collection points, with numbers analyzed for each group, for 16S sequencing and metagenomics.

FIG 2

Principal-component analysis (PCA) score plots of OTU data. Following Illumina sequencing analysis of fecal DNA, PCA was used to assess the variance of samples when fed one of three purified diets (PDs) only, where all dogs were fed diet A at PD4 (A), and variance when also including phases when fed complete diets (CDs) (B). Numbers represent week of study.

FIG 3

The diversity of fecal microbiota was determined at each sampling phase using 6 different approaches. Box plots represent quartiles. Time points that do not share a letter are significantly different by Tukey tests (P < 0.05).

FIG 4

Taxonomic relative abundance distribution of fecal microbiota at each sampling phase, at the phylum level (A), with number of OTUs in each phylum listed in the legend, and at the family level for Bacteroidetes (B), Firmicutes (C), Proteobacteria (D), and Actinobacteria (E).

FIG 5

Multigroup PCA scores of metagenome data at the pathway level, for four time points (data for 8 dogs fed PD “A”).

FIG 6

A comparison of significant changes in pathway abundance between different time points. Following the transition to PD, 178 pathways increased and 31 decreased in abundance (bar chart, left-hand side; CD1 to PD4). Following the transition back to CD, 142 pathways decreased and 6 increased on the return to CD (bar chart, right-hand side; PD36 to CD40). Of the 178 pathways that increased from CD to PD, 124 decreased following the return to CD (top Venn diagram), while 5 of the 31 that decreased from CD to PD increased on return to CD (bottom Venn diagram). The total number of significant changes between time points (described in the time point bar at the bottom of the figure) shows that no pathway had a significant difference between PD4 and PD36 or between CD1 and CD40.