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. 2021 Jun 30:9:e11648.
doi: 10.7717/peerj.11648. eCollection 2021.

Heterogeneity of gut microbial responses in healthy household dogs transitioning from an extruded to a mildly cooked diet

Jirayu Tanprasertsuk  1 , Justin Shmalberg  1   2 , Heather Maughan  1   3 , Devon E Tate  1 , LeeAnn M Perry  1 , Aashish R Jha  1   4 , Ryan W Honaker  1
Affiliations

Heterogeneity of gut microbial responses in healthy household dogs transitioning from an extruded to a mildly cooked diet

Jirayu Tanprasertsuk et al. PeerJ. .

Abstract

Background: The gut microbiota (GM) is associated with canine health and can be impacted by diet. Dog owners in the U.S. have increasingly shown an interest in feeding their dogs a mildly cooked (MC) diet. However, its impact on canine GM and health remains largely unknown.

Methods: Healthy household dogs were tracked upon switching from various brands of extruded to MC diets for four weeks. A health assessment was completed and stool samples were collected by each owner before (day 0) and after the diet transition (day 28). Shotgun metagenomic sequencing was performed at both time points to characterize the GM.

Results: Dogs completed the study by either completing the health assessments (n = 31) or providing stool samples at both time points (n = 28). All owners reported either better or no change in overall health at the end of the study (61% and 39%, respectively), and none reported worse overall health. Defecation frequency was also reported to be lower (58%) or about the same (35%). Principal coordinate (PCo) analysis showed a significant shift (p = 0.004) in the β-diversity of the GM upon diet transition (34.2% and 10.3% explained by the first two axes). The abundances of 70 species increased after the diet change (adjusted p < 0.05), 67% and 24% of which belonged to the Lactobacillales and the Enterobacterales orders respectively. The abundances of 28 species decreased (adjusted p < 0.05), 46%, 18%, and 11% of which belonged to the Clostridiales, Bacillales, and Bacteroidales orders, respectively. Lower Lactobacillales and Enterobacterales, and higher Bacteroidales at baseline were associated with a greater shift along the PCo1 axis. Protein content of the baseline diet was correlated with the shift along the PCo1 axis (ρ = 0.67, p = 0.006).

Conclusion: Owners reported either improvement or no change in health in dogs transitioning from extruded kibble to MC diets for 4 weeks, but this report of health perception requires further exploration in a controlled trial. Diet change also led to a significant shift in the GM profile of healthy dogs. The magnitude of shift was associated with baseline GM and dietary protein, and warrants further examination of individualized responses and personalized nutrition in companion dogs. These results also support future investigation of the impact of a MC diet on health maintenance given its increasing popularity.

Keywords: Canine microbiome; Canine nutrition; Diet processing; Dog kibble; Fresh food; Pet food.

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Conflict of interest statement

Jirayu Tanprasertsuk, Justin Shmalberg, LeeAnn M. Perry, Ryan W. Honaker are employees of and/or hold stocks or stock options in NomNomNow, Inc. Aashish R. Jha, Heather Maughan, Devon E. Tate consult for NomNomNow, Inc.

Figures

Figure 1
Figure 1. Trial flowchart.
Figure 2
Figure 2. Species level principal coordinate analysis (PCoA).
(A) PCo1 (Axis 1) and PCo2 (Axis 2) respectively explain 34.2% and 10.3% of species abundance variance (56 samples from 28 dogs). PERMANOVA using Bray–Curtis distance shows significant spatial separation between baseline (red) and week 4 (blue) (p = 0.004). (B) A significant shift along the PCo1 axis from baseline (red) to week 4 (blue) is observed (p = 1.72E−04, Wilcoxon signed rank test). (C) Varying degrees of shift along the PCo1 axis are observable from baseline to week 4. Subjects were divided into tertiles based on the degree of PCo4 changes between baseline and week 4, with subjects in the first tertile labeled high-responders (HR, maximal PCo1 score increase, red, n = 9), those in the second tertile mid-responders (MR, blue, n = 9), and those in the third tertile low-responders (LR, PCo1 score decrease or minimal PCo1 score increase, gray, n = 10).
Figure 3
Figure 3. Relative abundances at phylum level at baseline and week 4.
The phyla Firmicutes (baseline: 59.18 (36.39–77.09)%, week 4: 49.59 (31.00–77.05)%), Proteobacteria (baseline: 2.12 (0.06–46.75)%, week 4: 33.67 (11.35–61.92)%), Actinobacteria (baseline: 12.59 (0.34–19.35)%, week 4: 1.67 (0.05–9.23)%), and Bacteroidetes (baseline: 0.39 (0.03–3.79)%, week 4: 0.05 (0.00–0.88)%) dominated the GM at baseline and at week 4. Data are displayed separately for high- (HR, n = 9), mid- (MR, n = 9), and low-responders (LR, n = 10) (see section Identification of high-, mid- and low-responders for the definition of HR, MR and LR).
Figure 4
Figure 4. Volcano plot demonstrating fold-change (FC) in species abundance at week 4 compared to baseline.
Vertical dashed lines represent log2FC at 1 and −1 (i.e. FC at 2 and −2), horizontal dashed line adjusted p = 0.05. Adjustments of p values were performed with false discovery rate. Points are colored by phylum.
Figure 5
Figure 5. Principal coordinate analysis (PCoA) of the Kyoto Encyclopedia of Genes and Genomes Orthology (KO) terms.
(A) PCo1 (Axis 1) and PCo2 (Axis 2) respectively explain 67.1% and 11.3% of abundance variance (56 samples from 28 dogs). PERMANOVA using Bray–Curtis distance shows significant spatial separation between baseline (red) and week 4 (blue) (p = 0.007). (B) A significant shift along the PCo1 axis from baseline (red) to week 4 (blue) is observed (p = 0.013, Wilcoxon signed rank test).
Figure 6
Figure 6. Volcano plots demonstrating fold-change (FC) of species abundance between high-responders (HR, n = 9) and low-responders (LR, n = 10) at (A) baseline and (B) week 4.
FC is calculated from HR/LR. Vertical dashed lines show log2FC at 1 and −1 (i.e. FC at 2 and −2). Horizontal dashed line shows adjusted p = 0.05. Adjustment of p values is performed with false discovery rate. Points are colored by phylum.
Figure 7
Figure 7. Volcano plots demonstrating fold-change (FC) of species abundance between week 4 and baseline in (A) high-responders (n = 9) and (B) low-responders (n = 10).
Vertical dashed lines show log2FC at 1 and −1 (i.e. FC at 2 and −2). Horizontal dashed line shows adjusted p = 0.05. Adjustment of p values is performed with false discovery rate. Points are colored by phylum.
Figure 8
Figure 8. Volcano plot demonstrating fold-change (FC) of species abundance between week 4 and baseline in those reporting better overall health (n = 16) compared to those reporting about the same overall health (n = 10).
Vertical dashed lines show log2FC at 1 and −1 (i.e. FC at 2 and −2). Horizontal dashed line shows adjusted p = 0.05. Adjustment of p values is performed with false discovery rate. Points are colored by phylum.
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NomNomNow, Inc. provided monetary support for this research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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