Longitudinal fecal microbiome and metabolite data demonstrate rapid shifts and subsequent stabilization after an abrupt dietary change in healthy adult dogs

Abstract

Background Diet has a large influence on gut microbiota diversity and function. Although previous studies have investigated the effect of dietary interventions on the gut microbiome, longitudinal changes in the gut microbiome, microbial functions, and metabolite profiles post dietary interventions have been underexplored. How long these outcomes require to reach a steady-state, how they relate to one another, and their impact on host physiological changes are largely unknown. To address these unknowns, we collected longitudinal fecal samples following an abrupt dietary change in healthy adult beagles (n = 12, age: 5.16 ± 0.87 year, BW: 13.37 ± 0.68 kg) using a crossover design. All dogs were fed a kibble diet (control) from d1-14, and then fed that same diet supplemented with fiber (HFD) or a protein-rich canned diet (CD) from d15-27. Fresh fecal samples were collected on d13, 16, 20, 24, and 27 for metabolite and microbiome assessment. Fecal microbial diversity and composition, metabolite profiles, and microbial functions dramatically diverged and stabilized within a few days (2 d for metabolites; 6 d for microbiota) after dietary interventions. Fecal acetate, propionate, and total short-chain fatty acids increased after change to HFD, while fecal isobutyrate, isovalerate, total branched-chain fatty acids, phenol, and indole increased after dogs consumed CD. Relative abundance of ~ 100 bacterial species mainly belonging to the Firmicutes, Proteobacteria, and Actinobacteria phyla increased in HFD. These shifts in gut microbiome diversity and composition were accompanied by functional changes. Transition to HFD led to increases in the relative abundance of KEGG orthology (KO) terms related to starch and sucrose metabolism, fatty acid biosynthesis, and amino sugar and nucleotide sugar metabolism, while transition to CD resulted in increased relative abundance of KO terms pertaining to inositol phosphate metabolism and sulfur metabolism. Significant associations among fecal microbial taxa, KO terms, and metabolites were observed, allowing for high-accuracy prediction of diet group by random forest analysis. Conclusions Longitudinal sampling and a multi-modal approach to characterizing the gastrointestinal environment allowed us to demonstrate how drastically and quickly dietary changes impact the fecal microbiome and metabolite profiles of dogs following an abrupt dietary change and identify key microbe-metabolite relationships that allowed for treatment prediction.

Effect of Yeast Saccharomyces cerevisiae as a Probiotic on Diet Digestibility, Fermentative Metabolites, and Composition and Functional Potential of the Fecal Microbiota of Dogs Submitted to an Abrupt Dietary Change

“…Surprisingly, based on the results found, it seems that the gastrointestinal tract of dogs can have the capability to quickly adapt to a new diet. Similar results were reported by [ 22 ], who described that in general fecal consistency and most fecal metabolites and microbiota changed in a few days (2–6 days) after an abrupt dietary change in dogs, with complete stabilization after two weeks. However, these findings must be extrapolated carefully to pet dogs, considering that laboratory dogs may be more used to dietary changes and there are a lot of individual factors that may affect the gastrointestinal response to dietary change.…”

Comparison of the fecal microbiota of adult healthy dogs fed a plant-based (vegan) or an animal-based diet

“…Fecal collections from the dogs were only done at baseline (after the adaption period where all dogs were fed the MEAT diet) and exit (after feeding either the PLANT or MEAT diet exclusively for 3 months) timepoints. Based on recent research, the gut microbiota in dogs is very resilient meaning microbiota shifts and stabilization following a dietary intervention can be seen in just 2 weeks ( Lin et al, 2022 ). In the current study changes may have occurred soon after introducing the MEAT or PLANT diet however, the pattern of change was indeterminable due to the data collection timepoints.…”

Abrupt Dietary Change and Gradual Dietary Transition Impact Diarrheal Symptoms, Fecal Fermentation Characteristics, Microbiota, and Metabolic Profile in Healthy Puppies

“…Moreover, AC rather than GT significantly lowered fecal pH. Lin et al found that diarrhea in beagle dogs decreased on the second day following a rapid dietary transition [ 23 ].…”