Effects of dietary fiber on the feline gastrointestinal metagenome.

Four healthy adult cats were used in a crossover design to determine phylogeny and metabolic functional capacity of the cat's gastrointestinal microbiota using a metagenomic approach. Healthy adult cats (1.7 years old) were fed diets containing 4% cellulose, fructooligosaccharides (FOS), or pectin for 30 d, at which time fresh fecal samples were collected. Fecal DNA samples from each cat consuming each diet were subjected to 454 pyrosequencing. Dominant phyla determined using two independent databases (MG-RAST and IMG/M) included Firmicutes (mean=36.3 and 49.8%, respectively), Bacteroidetes (mean=36.1 and 24.1%, respectively), and Proteobacteria (mean=12.4 and 11.1%, respectively). Primary functional categories as determined by KEGG were associated with carbohydrates, clustering-based subsystems, protein metabolism, and amino acids and derivatives. Primary functional categories as determined by COG were associated with amino acid metabolism and transport, general function prediction only, and carbohydrate transport and metabolism. Analysis of carbohydrate-active enzymes revealed modifications in several glycoside hydrolases, glycosyl transferases, and carbohydrate-binding molecules with FOS and pectin consumption. While the cat is an obligate carnivore, its gut microbiome is similar regarding microbial phylogeny and gene content to omnivores.

Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice.

This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503,280 (K9C) and 505,061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised ∼35% of all sequences, followed by Proteobacteria (13-15%) and Fusobacteria (7-8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented ∼1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease.

Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing.

BACKGROUND: Dogs suffer from many of the same maladies as humans that may be affected by the gut microbiome, but knowledge of the canine microbiome is incomplete. This work aimed to use 16S rDNA tag pyrosequencing to phylogenetically characterize hindgut microbiome in dogs and determine how consumption of dietary fiber affects community structure. PRINCIPAL FINDINGS: Six healthy adult dogs were used in a crossover design. A control diet without supplemental fiber and a beet pulp-supplemented (7.5%) diet were fed. Fecal DNA was extracted and the V3 hypervariable region of the microbial 16S rDNA gene amplified using primers suitable for 454-pyrosequencing. Microbial diversity was assessed on random 2000-sequence subsamples of individual and pooled DNA samples by diet. Our dataset comprised 77,771 reads with an average length of 141 nt. Individual samples contained approximately 129 OTU, with Fusobacteria (23-40% of reads), Firmicutes (14-28% of reads) and Bacteroidetes (31-34% of reads) being co-dominant phyla. Feeding dietary fiber generally decreased Fusobacteria and increased Firmicutes, but these changes were not equally apparent in all dogs. UniFrac analysis revealed that structure of the gut microbiome was affected by diet and Firmicutes appeared to play a strong role in by-diet clustering. CONCLUSIONS: Our data suggest three co-dominant bacterial phyla in the canine hindgut. Furthermore, a relatively small amount of dietary fiber changed the structure of the gut microbiome detectably. Our data are among the first to characterize the healthy canine gut microbiome using pyrosequencing and provide a basis for studies focused on devising dietary interventions for microbiome-associated diseases.

Evaluation of nutrient digestibility and fecal characteristics of exotic felids fed horse- or beef-based diets: use of the domestic cat as a model for exotic felids.

The objective of this study was to determine the effects of feeding commercially available beef- and horse-based diets on nutrient digestibility and fecal characteristics of large captive exotic felids and domestic cats. Four species of large exotic felids including cheetahs, Malayan tigers, jaguars, and Amur tigers, and domestic cats were utilized in a crossover design. Raw meat diets included a beef-based diet (57% protein; 28% fat) and a horse-based diet (51% protein; 30% fat). All cats were acclimated to the diet for 16 days followed by a 4 day collection period, where total feces, including one fresh sample, were collected. All feces were scored on collection. Intake did not differ due to diet, but fecal output was greater when cats consumed the horse-based diet. Total tract apparent dry matter (DM) digestibility was higher (P<0.05) and organic matter (OM) and crude protein (CP) digestibilities were lower (P<0.05) when cats were fed the beef-based diet compared with the horse-based diet. CP digestibility was similar in domestic cats and cheetahs, and greater (P<0.05) than Amur tigers. Fecal scores were lower and fecal DM was greater (P<0.05) when cats consumed the horse-based diet compared with the beef-based diet. Domestic cats had lower (P<0.05) fecal ammonia concentrations compared with all other species. Fecal ammonia concentrations were lowest (P<0.05) when cats were fed the horse-based diet. Fecal total short-chain fatty acid (SCFA), branched-chain fatty acid (BCFA), and butyrate concentrations were higher (P<0.05) when cats consumed the beef-based diet. Our results suggest that the domestic cat serves as an appropriate model for large exotic felid species, but differences among the species exist. Decreased nutrient digestibility by tigers and jaguars should be considered when developing feeding recommendations for these species based on domestic cat data.

Carbohydrates blended with polydextrose lower gas production and short-chain fatty acid production in an in vitro system.

Maximizing health benefits of prebiotics, while limiting negative side effects, is of importance to the food industry. This study examined several oligosaccharides and their blends in an in vitro fermentation model. Substrates included medium- and long-chain fructooligosaccharides (FOS), oligofructose-enriched inulin, galactooligosaccharide, polydextrose (POL), and 50:50 substrate blends. Substrates and blends were fermented in vitro using human fecal inoculum, and fermentation characteristics were quantified at 0, 4, 8, and 12 hours. We hypothesized that mixtures of short- and long-chain oligosaccharides would generate less gas than do short-chain oligosaccharides and modulate gut microflora to a greater extent than do long-chain oligosaccharides. Carbohydrates blended with POL had decreased (P < .01) total gas volume and H(2) produced after 4, 8, and 12 hours of fermentation compared with individual carbohydrates. Mixing of 2 oligofructose-enriched inulin products led to less (P < .05) gas produced and a slower (P < .05) rate of production. When mixed with POL, all carbohydrates tested in the present study produced less total short-chain fatty acids (P < .04) and butyrate (P < .0001) after 12 hours of in vitro fermentation, compared with individual carbohydrates. The bifidogenic effect of medium-chain FOS and oligofructose-enriched inulin after 12 hours of in vitro fermentation was lower (P < .05) when mixed with POL. Mixing the pure carbohydrates with galactooligosaccharide increased (P < .05) bifidobacteria counts measured after 12 hours of in vitro fermentation, except when mixed with medium-chain FOS. In general, when mixed with POL, all carbohydrates had lower gas production, gas production rates, butyrate and total short-chain fatty acid production, and bifidobacteria counts than when fermented alone for 12 hours.

Age and diet affect gene expression profile in canine skeletal muscle.

We evaluated gene transcription in canine skeletal muscle (biceps femoris) using microarray analysis to identify effects of age and diet on gene expression. Twelve female beagles were used (six 1-year olds and six 12-year olds) and they were fed one of two experimental diets for 12 months. One diet contained primarily plant-based protein sources (PPB), whereas the second diet contained primarily animal-based protein sources (APB). Affymetrix GeneChip Canine Genome Arrays were used to hybridize extracted RNA. Age had the greatest effect on gene transcription (262 differentially expressed genes), whereas the effect of diet was relatively small (22 differentially expressed genes). Effects of age (regardless of diet) were most notable on genes related to metabolism, cell cycle and cell development, and transcription function. All these genes were predominantly down-regulated in geriatric dogs. Age-affected genes that were differentially expressed on only one of two diets were primarily noted in the PPB diet group (144/165 genes). Again, genes related to cell cycle (22/35) and metabolism (15/19) had predominantly decreased transcription in geriatric dogs, but 6/8 genes related to muscle development had increased expression. Effects of diet on muscle gene expression were mostly noted in geriatric dogs, but no consistent patterns in transcription were observed. The insight these data provide into gene expression profiles of canine skeletal muscle as affected by age, could serve as a foundation for future research pertaining to age-related muscle diseases.

In vitro fermentation profiles, gas production rates, and microbiota modulation as affected by certain fructans, galactooligosaccharides, and polydextrose.

It is of interest to benefit from the positive intestinal health outcomes of prebiotic consumption but with minimal gas production. This study examined gas production potential, fermentation profile, and microbial modulation properties of several types of oligosaccharides. Substrates studied included short-chain, medium-chain, and long-chain fructooligosaccharides, oligofructose-enriched inulin, galactooligosaccharide, and polydextrose. Each substrate was fermented in vitro using human fecal inoculum, and fermentation characteristics were quantified at 0, 4, 8, and 12 h. Gas and short-chain fatty acid (SCFA) production data showed that short-chain oligosaccharides were more rapidly fermented and produced more SCFA and gas than substrates with greater degrees of polymerization. Lactobacilli increased similarly among substrates. Short-chain oligosaccharides fermentation resulted in the greatest increase in bifidobacteria concentrations. Mixing short- and long-chain oligosaccharides attenuated short-chain oligosaccharide fermentation rate and extent. This study provides new information on the fermentation characteristics of some oligosaccharides used in human nutrition.

Effects of dietary supplementation of DL-methionine or 2-hydroxy-4-(methylthio)-butanoic acid on food intake, nutrient digestibility, nitrogen balance, and urinary and blood metabolites in healthy, growing dogs.

The aim of this study was to evaluate effects on nutritional responses of supplemental DL-methionine and 2-hydroxy-4-(methylthio) butanoic acid (HMTBA) in a commercial-type diet in growing dogs. A nitrogen balance study was conducted as a randomized complete block design using 30 Pointer puppies (72-d-old; 5.5 kg). A corn and poultry byproduct meal based diet was supplemented with 0.1 or 0.2% DL-methionine or HMTBA on an equimolar basis. Organic matter and gross energy tended (p < 0.10) to be less digestible by dogs fed the 0.1% HMTBA diet compared with the 0.2% DL-methionine diet, but other nutrients were unaffected. Postprandial urinary calcium tended (p < 0.10) to be lower for the basal and HMTBA treatments. Fecal ammonia tended (p < 0.10) to be lower for the 0.1% HMTBA diet than for the 0.2% DL-methionine diet. At the levels tested, DL-methionine and HMTBA appear to act similarly when included in a corn and poultry by-product meal diet fed to young dogs.