BackgroundDogs 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 FindingsSix 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.ConclusionsOur 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.

The relative contribution of novel fibers such as polydextrose and soluble corn fiber (SCF) to the human gut microbiome and its association with host physiology has not been well studied. This study was conducted to test the impact of polydextrose and SCF on the composition of the human gut microbiota using 454 pyrosequencing and to identify associations among fecal microbiota and fermentative end-products. Healthy adult men (n = 20) with a mean dietary fiber (DF) intake of 14 g/d were enrolled in a randomized, double-blind, placebo-controlled crossover study. Participants consumed 3 treatment snack bars/d during each 21-d period that contained no supplemental fiber (NFC), polydextrose (PDX; 21 g/d), or SCF (21 g/d) for 21 d. There were no washout periods. Fecal samples were collected on d 16-21 of each period; DNA was extracted, followed by amplification of the V4-V6 region of the 16S rRNA gene using barcoded primers. PDX and SCF significantly affected the relative abundance of bacteria at the class, genus, and species level. The consumption of PDX and SCF led to greater fecal Clostridiaceae and Veillonellaceae and lower Eubacteriaceae compared with a NFC. The abundance of Faecalibacterium, Phascolarctobacterium, and Dialister was greater (P < 0.05) in response to PDX and SCF intake, whereas Lactobacillus was greater (P < 0.05) only after SCF intake. Faecalibacterium prausnitzii, well known for its antiinflammatory properties, was greater (P < 0.05) after fiber consumption. Principal component analysis clearly indicated a distinct clustering of individuals consuming supplemental fibers. Our data demonstrate a beneficial shift in the gut microbiome of adults consuming PDX and SCF, with potential application as prebiotics.

High-protein, low-carbohydrate (HPLC) diets are common in cats, but their effect on the gut microbiome has been ignored. The present study was conducted to test the effects of dietary protein:carbohydrate ratio on the gut microbiota of growing kittens. Male domestic shorthair kittens were raised by mothers fed moderate-protein, moderate-carbohydrate (MPMC; n 7) or HPLC (n 7) diets, and then weaned at 8 weeks onto the same diet. Fresh faeces were collected at 8, 12 and 16 weeks; DNA was extracted, followed by amplification of the V4 -V6 region of the 16S rRNA gene using 454 pyrosequencing. A total of 384 588 sequences (average of 9374 per sample) were generated. Dual hierarchical clustering indicated distinct clustering based on the protein:carbohydrate ratio regardless of age. The protein:carbohydrate ratio affected faecal bacteria. Faecal Actinobacteria were greater (P, 0·05) and Fusobacteria were lower (P, 0·05) in MPMC-fed kittens. Faecal Clostridium, Faecalibacterium, Ruminococcus, Blautia and Eubacterium were greater (P, 0·05) in HPLC-fed kittens, while Dialister, Acidaminococcus, Bifidobacterium, Megasphaera and Mitsuokella were greater (P,0·05) in MPMC-fed kittens. Principal component analysis of faecal bacteria and blood metabolites and hormones resulted in distinct clusters. Of particular interest was the clustering of blood TAG with faecal Clostridiaceae, Eubacteriaceae, Ruminococcaceae, Fusobacteriaceae and Lachnospiraceae; blood ghrelin with faecal Coriobacteriaceae, Bifidobacteriaceae and Veillonellaceae; and blood glucose, cholesterol and leptin with faecal Lactobacillaceae. The present results demonstrate that the protein:carbohydrate ratio affects the faecal microbiome, and highlight the associations between faecal microbes and circulating hormones and metabolites that may be important in terms of satiety and host metabolism.

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.

The objective of the present study was to evaluate digestive physiological outcomes elicited by functional fibres fed to healthy adult men. A total of twenty-one healthy adult men were utilised in a cross-over design. Each subject received polydextrose (PDX) or soluble maize fibre (SCF) (21 g/d) or no supplemental fibre (no fibre control; NFC) in a snack bar. Periods were 21 d and faeces were collected during the last 5 d of each period. Food intake, including fibre intake, did not differ among treatments. Flatulence (P¼ 0·001) and distention (P¼ 0·07) were greatest when subjects consumed PDX or SCF. Reflux was greater (P¼ 0·04) when subjects consumed SCF compared with NFC. All tolerance scores were low (, 2·5), indicating only slight discomfort. Faecal ammonia, 4-methylphenol, indole and branchedchain fatty acid concentrations were decreased (P,0·01) when subjects consumed the functional fibre sources compared with NFC. Faecal acetate, propionate and butyrate concentrations were lower (P, 0·05) when subjects consumed PDX compared with SCF and NFC. Faecal pH was lower (P¼0·01) when subjects consumed SCF compared with NFC, while PDX was intermediate. Faecal wet weight was greatest (P¼ 0·03) when subjects consumed SCF compared with NFC. Faecal dry weight tended to be greater (P¼0·07) when subjects consumed PDX compared with NFC. The functional fibres led to 1·4 and 0·9 g (PDX and SCF, respectively) increases in faecal dry mass per g supplemental fibre intake. Bifidobacterium spp. concentrations were greater (P,0·05) when subjects consumed SCF compared with NFC. These functional fibres appear to be beneficial to gut health while leading to minimal gastrointestinal upset.

The objectives of this study were to determine differences in apparent total tract energy and macronutrient digestibility, fecal and urine characteristics, and serum chemistry of domestic cats fed raw and cooked meat-based diets and extruded diet. Nine adult female domestic shorthair cats were utilized in a replicated 3 × 3 Latin square design. Dietary treatments included a high-protein extruded diet (EX; 57% CP), a raw beef-based diet (RB; 53% CP), and a cooked beef-based diet (CB; 52% CP). Cats were housed individually in metabolic cages and fed to maintain BW. The study consisted of three 21-d periods. Each period included diet adaptation during d 0 to 16; fecal and urine sample collections during d 17 to 20; and blood sample collection at d 21. Food intake was measured daily. Total feces and urine were collected for determination of nutrient digestibility. In addition, a fresh urine sample was collected from each cat for urinalysis, and a fresh fecal sample was collected from each cat for determination of DM percentage and ammonia, short-chain fatty acid (SCFA), and branched-chain fatty acid (BCFA) concentrations. All feces were scored after collection using a scale ranging from 1 (hard, dry pellets) to 5 (watery, liquid that can be poured). Blood was analyzed for serum metabolites. Apparent total tract DM, OM, CP, fat, and GE digestibilities were greater (P ≤ 0.05) in cats fed RB and CB than those fed EX. Total fecal SCFA concentrations did not differ among dietary treatments; however, molar ratios of SCFA were modified by diet, with cats fed RB and CB having an increased (P ≤ 0.05) proportion of fecal propionate and decreased (P ≤ 0.05) proportion of fecal butyrate compared with cats fed EX. Fecal concentrations of ammonia, isobutyrate, valerate, isovalerate, and total BCFA were greater (P ≤ 0.05) in cats fed EX compared with cats fed RB and CB. Our results indicated that cooking a raw meat diet does not alter apparent total tract energy and macronutrient digestibility and may also minimize risk of microbial contamination. Given the increasing popularity of feeding raw diets and the metabolic differences noted in this experiment, further research focused on the adequacy and safety of raw beef-based diets in domestic cats is justified.

Short-chain fructooligosaccharides (scFOS) and galactooligosaccharides (GOS) are nondigestible oligosaccharides that result in a prebiotic effect in some animal species; however, the cat has not been well studied in this regard. This experiment evaluated scFOS and GOS supplementation on nutrient digestibility, fermentative end product production, and fecal microbial ecology of cats. Eight healthy adult cats were fed diets containing no prebiotic, 0.5% scFOS, 0.5% GOS, or 0.5% scFOS + 0.5% GOS (scFOS + GOS) in a replicated 4 × 4 Latin square design. Apparent total tract CP digestibility was decreased (P < 0.05) when cats were fed a diet containing scFOS + GOS compared with the other treatments. Dry matter, OM, acid hydrolyzed fat, and GE digestibilities were not different (P > 0.05) among treatments. Cats fed scFOS-, GOS-, and scFOS + GOS-supplemented diets had greater (P < 0.05) fecal Bifidobacterium spp. populations compared with cats fed the control diet. Fecal pH was less (P < 0.05) for cats fed the scFOS + GOS-supplemented diet compared with the control. Butyrate (P = 0.05) and valerate (P < 0.05) concentrations were greater when cats consumed the scFOS + GOS diet. Acetate tended (P = 0.10) to be greater when cats were fed the scFOS + GOS diet. Total short-chain fatty acid (P = 0.06) and total branched-chain fatty acid (P = 0.06) concentrations also tended to be greater when cats consumed the scFOS + GOS treatment. Fecal protein catabolites, including ammonia, 4-methylphenol, indole, and biogenic amines, blood lymphocytes, neutrophils, total white blood cell counts, or fecal DM concentration and output did not differ (P > 0.05) among treatments. Low level supplementation of scFOS, GOS, and their combination exert positive effects on select indices of gut health in cats.

During the development of obesity, adipose tissue undergoes major expansion and remodeling, but the biological processes involved in this transition are not well understood. The objective of this study was to analyze global gene expression profiles of adipose tissue in dogs, fed a high-fat diet, during the transition from a lean to obese phenotype. Nine female beagles (4.09 ± 0.64 yr; 8.48 ± 0.35 kg) were randomized to ad libitum feeding or body weight maintenance. Subcutaneous adipose tissue biopsy, blood, and dual x-ray absorptiometry measurements were collected at 0, 4, 8, 12, and 24 wk of feeding. Serum was analyzed for glucose, insulin, fructosamine, triglycerides, free fatty acids, adiponectin, and leptin. Formalin-fixed adipose tissue was used for determination of adipocyte size. Adipose RNA samples were hybridized to Affymetrix Canine 2.0 microarrays. Statistical analysis, using repeated-measures ANOVA, showed ad libitum feeding increased (P < 0.05) body weight (0 wk, 8.36 ± 0.34 kg; 24 wk, 14.64 ± 0.34 kg), body fat mass (0 wk, 1.36 ± 0.24 kg; 24 wk, 6.52 ± 0.24 kg), adipocyte size (0 wk, 114.66 ± 17.38 μm(2); 24 wk, 320.97 ± 0.18.17 μm(2)), and leptin (0 wk, 0.8 ± 1.0 ng/ml; 24 wk, 12.9 ± 1.0 ng/ml). Microarrays displayed 1,665 differentially expressed genes in adipose tissue as weight increased. Alterations were seen in adipose tissue homeostatic processes including metabolism, oxidative stress, mitochondrial homeostasis, and extracellular matrix. Adipose transcriptome changes highlight the dynamic and adaptive response to ad libitum feeding and obesity development.