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Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundances

View Article: PubMed Central - PubMed

ABSTRACT

Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets. The kittens fed kibbled diets had relatively higher abundances of Lactobacillus (>100-fold), Bifidobacterium (>100-fold), and Collinsella (>9-fold) than kittens fed canned diets. There were relatively few differences in the predicted microbiome functions associated with the pre-weaning diet. Post-weaning diet affected the abundance of functional gene groups. Genes involved in vitamin biosynthesis, metabolism, and transport, were significantly enriched in the metagenomes of kittens fed the canned diet. The impact of post-weaning diet on the metagenome in terms of vitamin biosynthesis functions suggests that modulation of the microbiome function through diet may be an important avenue for improving the nutrition of companion animals.

No MeSH data available.


Scores plot from PCA of kittens’ faecal microbiota composition at the species level.The first letter indicates the mother’s diet during pregnancy and lactation and the second letter indicates the kitten’s diet; canned (C) or kibbled (K). Lines converge at the spatial centroid for each treatment group. Diet K-Diet K (K-K) n = 3 females, n = 2 males. Diet C-Diet K (C-K) n = 3 females, n = 2 males. Diet K-Diet C (K-C) n = 3 females, n = 2 males. Diet C-Diet C (C-C) n = 4 females, n = 1 male.
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f1: Scores plot from PCA of kittens’ faecal microbiota composition at the species level.The first letter indicates the mother’s diet during pregnancy and lactation and the second letter indicates the kitten’s diet; canned (C) or kibbled (K). Lines converge at the spatial centroid for each treatment group. Diet K-Diet K (K-K) n = 3 females, n = 2 males. Diet C-Diet K (C-K) n = 3 females, n = 2 males. Diet K-Diet C (K-C) n = 3 females, n = 2 males. Diet C-Diet C (C-C) n = 4 females, n = 1 male.

Mentions: Consistent with our previous study6, the post-weaning diet had a considerable effect on the composition of faecal microbiota (Fig. 1). Of the 195 taxa identified at the genus or species level, 147 had significantly different mean relative abundances (FDR < 0.05) between kittens fed kibbled and canned diets (i.e. C-K and K-K kittens compared to K-C and C-C kittens; Supplementary Table S1–S5xlsx). Overall, the kittens fed kibbled diets post-weaning had substantially higher relative abundances of bacteria from the Lactobacillus, Bifidobacterium, and Collinsella genera compared to kittens fed the canned diet post-weaning (Table 2). In our previous study using 16S amplicon sequencing, an increase in Lactobacillus of similar magnitude was also observed in kittens fed the kibbed diet6. However, Bifidobacterium was not detected in our previous study and the proportions of Collinsella were <1%6, whereas in our current study, Collinsella made up >10% of the microbiota in kittens fed the kibbled diet. This discrepancy may be explained by the differences in sequencing methods used; reliable detection of Bifidobacterium using V1-V3 primers, such as those used in our previous study, can be problematic20, and PCR amplification biases are avoided by shotgun sequencing methods.


Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundances
Scores plot from PCA of kittens’ faecal microbiota composition at the species level.The first letter indicates the mother’s diet during pregnancy and lactation and the second letter indicates the kitten’s diet; canned (C) or kibbled (K). Lines converge at the spatial centroid for each treatment group. Diet K-Diet K (K-K) n = 3 females, n = 2 males. Diet C-Diet K (C-K) n = 3 females, n = 2 males. Diet K-Diet C (K-C) n = 3 females, n = 2 males. Diet C-Diet C (C-C) n = 4 females, n = 1 male.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120286&req=5

f1: Scores plot from PCA of kittens’ faecal microbiota composition at the species level.The first letter indicates the mother’s diet during pregnancy and lactation and the second letter indicates the kitten’s diet; canned (C) or kibbled (K). Lines converge at the spatial centroid for each treatment group. Diet K-Diet K (K-K) n = 3 females, n = 2 males. Diet C-Diet K (C-K) n = 3 females, n = 2 males. Diet K-Diet C (K-C) n = 3 females, n = 2 males. Diet C-Diet C (C-C) n = 4 females, n = 1 male.
Mentions: Consistent with our previous study6, the post-weaning diet had a considerable effect on the composition of faecal microbiota (Fig. 1). Of the 195 taxa identified at the genus or species level, 147 had significantly different mean relative abundances (FDR < 0.05) between kittens fed kibbled and canned diets (i.e. C-K and K-K kittens compared to K-C and C-C kittens; Supplementary Table S1–S5xlsx). Overall, the kittens fed kibbled diets post-weaning had substantially higher relative abundances of bacteria from the Lactobacillus, Bifidobacterium, and Collinsella genera compared to kittens fed the canned diet post-weaning (Table 2). In our previous study using 16S amplicon sequencing, an increase in Lactobacillus of similar magnitude was also observed in kittens fed the kibbed diet6. However, Bifidobacterium was not detected in our previous study and the proportions of Collinsella were <1%6, whereas in our current study, Collinsella made up >10% of the microbiota in kittens fed the kibbled diet. This discrepancy may be explained by the differences in sequencing methods used; reliable detection of Bifidobacterium using V1-V3 primers, such as those used in our previous study, can be problematic20, and PCR amplification biases are avoided by shotgun sequencing methods.

View Article: PubMed Central - PubMed

ABSTRACT

Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets. The kittens fed kibbled diets had relatively higher abundances of Lactobacillus (&gt;100-fold), Bifidobacterium (&gt;100-fold), and Collinsella (&gt;9-fold) than kittens fed canned diets. There were relatively few differences in the predicted microbiome functions associated with the pre-weaning diet. Post-weaning diet affected the abundance of functional gene groups. Genes involved in vitamin biosynthesis, metabolism, and transport, were significantly enriched in the metagenomes of kittens fed the canned diet. The impact of post-weaning diet on the metagenome in terms of vitamin biosynthesis functions suggests that modulation of the microbiome function through diet may be an important avenue for improving the nutrition of companion animals.

No MeSH data available.