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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 biplot from partial least squares discriminant analysis (PLS-DA) of kittens’ faecal metagenome COG-predicted functional classifications.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. Grey spheres show the COG functions that best discriminate the groups from each other. The size of the spheres are proportional to the relative abundance of that COG function. The spatial position of each COG function is plotted as a weighted average of the coordinates of all samples. 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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f2: Scores biplot from partial least squares discriminant analysis (PLS-DA) of kittens’ faecal metagenome COG-predicted functional classifications.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. Grey spheres show the COG functions that best discriminate the groups from each other. The size of the spheres are proportional to the relative abundance of that COG function. The spatial position of each COG function is plotted as a weighted average of the coordinates of all samples. 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: While the maternal diet during pregnancy and lactation had some observable effects on the microbial community composition in the kittens at 17 weeks of age, they had less impact on the predicted metagenome function composition (Supplementary Table S6xlsx). Comparisons of the kitten’s faecal metagenomes, classified using the Clusters of Orthologous Groups (COG) of proteins database and analysed using permutation MANOVA, showed a significant effect of post-weaning diet (P = 0.001). Although no effect from the maternal diet was observed (P = 0.687), there was a significant interaction between maternal diet and post-weaning diet (P = 0.031). This observation was supported by discriminant analyses which showed that the kitten’s faecal metagenomes could be differentiated based on the mother’s diet (Fig. 2). Comparisons of the metagenome gene functions with community taxonomic compositions via Procrustes rotation analysis also showed good agreement between the two analyses (correlation = 0.76, P = 0.001; Fig. 3). The lesser differences observed on the composition of the metagenome compared to the microbial taxonomic composition is a well reported phenomenon42, suggesting that a high degree of genetic redundancy exists in the microbial community. Nevertheless, in our study, the post-weaning diet clearly impacted the kitten’s metagenome composition.


Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundances
Scores biplot from partial least squares discriminant analysis (PLS-DA) of kittens’ faecal metagenome COG-predicted functional classifications.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. Grey spheres show the COG functions that best discriminate the groups from each other. The size of the spheres are proportional to the relative abundance of that COG function. The spatial position of each COG function is plotted as a weighted average of the coordinates of all samples. 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

f2: Scores biplot from partial least squares discriminant analysis (PLS-DA) of kittens’ faecal metagenome COG-predicted functional classifications.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. Grey spheres show the COG functions that best discriminate the groups from each other. The size of the spheres are proportional to the relative abundance of that COG function. The spatial position of each COG function is plotted as a weighted average of the coordinates of all samples. 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: While the maternal diet during pregnancy and lactation had some observable effects on the microbial community composition in the kittens at 17 weeks of age, they had less impact on the predicted metagenome function composition (Supplementary Table S6xlsx). Comparisons of the kitten’s faecal metagenomes, classified using the Clusters of Orthologous Groups (COG) of proteins database and analysed using permutation MANOVA, showed a significant effect of post-weaning diet (P = 0.001). Although no effect from the maternal diet was observed (P = 0.687), there was a significant interaction between maternal diet and post-weaning diet (P = 0.031). This observation was supported by discriminant analyses which showed that the kitten’s faecal metagenomes could be differentiated based on the mother’s diet (Fig. 2). Comparisons of the metagenome gene functions with community taxonomic compositions via Procrustes rotation analysis also showed good agreement between the two analyses (correlation = 0.76, P = 0.001; Fig. 3). The lesser differences observed on the composition of the metagenome compared to the microbial taxonomic composition is a well reported phenomenon42, suggesting that a high degree of genetic redundancy exists in the microbial community. Nevertheless, in our study, the post-weaning diet clearly impacted the kitten’s metagenome composition.

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.