Microbiome Responses to Fecal Microbiota Transplantation in Cats with Chronic Digestive Issues

Abstract

There is growing interest in the application of fecal microbiota transplants (FMTs) in small animal medicine, but there are few published studies that have tested their effects in the domestic cat (Felis catus). Here we use 16S rRNA gene sequencing to examine fecal microbiome changes in 46 domestic cats with chronic digestive issues that received FMTs using lyophilized stool that was delivered in oral capsules. Fecal samples were collected from FMT recipients before and two weeks after the end of the full course of 50 capsules, as well as from their stool donors (N = 10), and other healthy cats (N = 113). The fecal microbiomes of FMT recipients varied with host clinical signs and dry kibble consumption, and shifts in the relative abundances of Clostridium, Collinsella, Megamonas, Desulfovibrio and Escherichia were observed after FMT. Overall, donors shared 13% of their bacterial amplicon sequence variants (ASVs) with FMT recipients and the most commonly shared ASVs were classified as Prevotella 9, Peptoclostridium, Bacteroides, and Collinsella. Lastly, the fecal microbiomes of cats with diarrhea became more similar to the microbiomes of age-matched and diet-matched healthy cats compared to cats with constipation. Overall, our results suggest that microbiome responses to FMT may be modulated by the FMT recipient's initial presenting clinical signs, diet, and their donor's microbiome.

Keywords: FMT; antibiotics; diarrhea; domestic cats; dysbiosis; fecal microbiome; fecal transplant; gut microbiome; vomiting.

Figure 1

Three main fecal microbiome comparisons were conducted in this study. (A) We investigated shifts in the fecal microbiomes of FMT recipients by testing whether four host predictors were significantly associated with microbiome composition, alpha-diversity, and beta-diversity. (B) We identified which ASVs ‘engrafted’ in FMT recipients by comparing the fecal microbiomes of FMT recipients to those of their FMT stool donors, and determining which ASVs were shared. (C) Lastly, we examined whether the fecal microbiomes of FMT recipients became more similar to the microbiomes of healthy cats after FMT.

Figure 2

Fecal microbiome composition before and after FMT for twelve of the forty-six cats. Plots showing the relative frequencies of 16S rRNA gene sequences assigned to bacterial genera with mean relative abundances > 1.65%, while all other genera are clumped into an “Other” category. Twelve of the forty-six cats were selected at random for plotting. For plots of the microbiome compositions of all 46 cats, see Figure S1.

Figure 3

Host predictors of fecal microbiome alpha- and beta-diversity in FMT recipients. Boxplots of microbiome evenness (Pielou’s Evenness) by (A) clinical signs and (B) dry kibble consumption for pre-FMT samples. PCoA ordinations based on Aitchison distances showing the clustering of post-FMT samples by (C) Clinical signs, and (D) Dry kibble consumption.

Figure 4

Changes in the relative abundances of bacterial genera in cats receiving oral FMTs. Linear mixed models indicated that the changes in the relative abundance of 10 bacterial genera were significantly associated with (A–E) host clinical signs, (F–J) response to FMT, (K–M) recent antibiotic use, or (N,O) dry kibble consumption. For the statistical output of post-hoc testing using Tukey linear contrasts, see Figure S4.

Figure 5

ASVs shared between FMT recipients and their stool donors. Plots of ASV engraftment or sharing rates across (A) FMT recipients or (B) stool donors (asterisks indicate where the fecal material of two cohabiting cats constituted one donor). ASV sharing rates were calculated by dividing the number of ASVs shared between postFMT samples of FMT recipients and their stool donors (excluding taxa shared between preFMT samples and donors) by the total number of ASVs in the donor sample (excluding any taxa shared with the preFMT samples of FMT recipients). (C) Taxonomic breakdown of ASVs shared between FMT recipients and their stool donors.

Figure 6

Do the fecal microbiomes of cats receiving FMT become similar to the microbiomes of healthy cats? We examined shifts in the fecal microbiome of FMT recipients by quantifying how similar their fecal microbiomes were (before and after FMT) to those from an age-matched and diet-matched healthy reference set. We computed the difference between the two similarity scores (postFMT similarity–preFMT similarity) to generate the change in similarity (Δ) for each FMT recipient–healthy animal dyad. We then correlated these Δ values with host characteristics using generalized linear models. (A–D) Average Δ in similarity scores for each group (±St.Error). A value of 0 indicates no shift in similarity. Bray–Curtis distances were used. See Table S13 for model statistics.