Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16S rRNA gene analysis

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.

Phylogenetic analysis of 16S rRNA gene sequences reveals distal gut bacterial diversity in wild wolves (Canis lupus)

The aim of this study was to describe the microbial communities in the distal gut of wild wolves (Canis lupus). Fecal samples were collected from three healthy unrelated adult wolves captured at the nearby of Dalai Lake Nature Reserve in Inner Mongolia of China. The diversity of fecal bacteria was investigated by constructing PCR-amplified 16S rRNA gene clone libraries using the universal bacterial primers 27 F and 1493 R. A total of 307 non-chimeric near-full-length 16S rRNA gene sequences were analyzed and 65 non-redundant bacteria phylotypes (operational taxonomical units, OTUs) were identified. Seventeen OTUs (26%) showed less than 98% sequence similarity to 16S rRNA gene sequences were reported previously. Five different bacterial phyla were identified, with the majority of OTUs being classified within the phylum Firmicutes (60%), followed by Bacteroidetes (16.9%), Proteobacteria (9.2%), Fusobacteria (9.2%) and Actinobacteria (4.6%). The majority of clones fell within the order Clostridiales (53.8% of OTUs). It was predominantly affiliated with five families: Lachnospiraceae was the most diverse bacterial family in this order, followed by Ruminococcaceae, Clostridiaceae, Peptococcaceae and Peptostreptococcaceae.

Characterization of fecal microbiota in cats using universal 16S rRNA gene and group-specific primers for Lactobacillus and Bifidobacterium spp

The diversity of the feline intestinal microbiota has not been well elucidated. The aim of this study was to characterize fecal microbiota of cats by comparative sequence analysis with universal bacterial 16S rRNA gene and group-specific primers for Bifidobacterium and Lactobacillus spp. Using universal bacterial primers, a total of 133 non-redundant 16S rRNA gene sequences were identified in fecal samples obtained from 15 healthy pet cats. The majority of these sequences were assigned to the phylum Firmicutes, followed by Proteobacteria and Bacteroidetes. Further classification showed that Firmicutes were predominantly affiliated with Clostridium clusters XI, XIVa, and I. Using group-specific primers for Bifidobacterium and Lactobacillus spp., 364 clones were analyzed in fecal samples obtained from 12 additional cats and these bacterial genera were observed in 100% and 92% of cats, respectively. These detection rates differed from those obtained using universal bacterial primers, where Bifidobacterium and Lactobacillus spp. were each detected in 2 cats (13.3%). Overall, 23 different Lactobacillus-like and 11 Bifidobacterium-like sequences were identified. We observed marked differences in the prevalence of the various lactic acid bacteria in individual cats. In conclusion, the use of a combination of universal and group-specific primers allows a more detailed characterization of lactic acid bacteria in the feline intestine. While Bifidobacterium and Lactobacillus spp. are prevalent in feline fecal samples, individual animals show a unique species distribution.

Investigation of the faecal microbiota associated with canine chronic diarrhoea

Diarrhoea is a common problem in dogs and can result in disturbance of the normal intestinal microbiota. However, little is known about the gastrointestinal microbiota of dogs with chronic diarrhoea and controlled canine studies of dietary management are scarce. The aims of this study were to investigate the predominant faecal microbiota of chronic diarrhoea dogs and to examine the effect(s) of a fibre blend on the canine faecal microbiota. A 3-week fibre supplementation feeding study was performed in nine chronic diarrhoea and eight control dogs. Atopobium cluster, Lactobacillus-Enterococcus group and Clostridium cluster XIV were the predominant bacterial groups in all dogs. Chronic diarrhoea dogs had significantly higher Bacteroides counts at baseline and significantly lower Atopobium cluster counts following fibre supplementation compared with control dogs. Atopobium cluster levels increased significantly in control dogs, while counts of sulphate-reducing bacteria decreased significantly and Clostridium clusters I and II counts increased significantly in chronic diarrhoea dogs during fibre supplementation. Microbial profiles (detected by denaturing gradient gel electrophoresis) demonstrated interindividual variation, with greater similarity seen between the chronic diarrhoea and control dogs' profiles after fibre supplementation compared with baseline. In conclusion, fibre supplementation induced changes in the canine faecal microbiota, with greater resemblance between the microbiota of chronic diarrhoea and control dogs after this dietary modulation.

Molecular analysis of the bacterial microbiota in duodenal biopsies from dogs with idiopathic inflammatory bowel disease

An association between mucosa-adherent commensal bacteria and inflammatory bowel disease (IBD) has been proposed for humans. There are no reports characterizing the mucosa-adherent duodenal microbiota in dogs with idiopathic IBD using molecular methods. The aim of this study was to investigate differences in the mucosa-adherent duodenal microbiota between dogs with idiopathic IBD and healthy dogs. Duodenal biopsy samples were collected from seven dogs with IBD and seven healthy control dogs. DNA was extracted, 16S ribosomal RNA genes were amplified and 16S rRNA gene clone libraries were constructed and compared between groups. A total of 1035 clones were selected, and based on a 98% similarity criterion, 133 unique phylotypes were identified across all dogs. These phylotypes belonged to seven bacterial phyla: Proteobacteria (52.9%), Firmicutes (26.1%), Bacteroidetes (7.7%), Actinobacteria (8.6%), Fusobacteria (4.4%), Tenericutes (0.2%) and Verrucomicrobia (0.1%). Significant differences were identified in the relative abundance of several bacterial groups between dogs with IBD and healthy dogs (p<0.001). Healthy dogs and dogs with IBD clustered according to their disease status. Dogs with IBD had a significantly higher abundance of clones belonging to Alpha-, Beta-, and Gamma-proteobacteria (p<0.0001 for all classes), and a significantly lower abundance of Clostridia (p<0.0001). Bacteria of the genera Pseudomonas, Acinetobacter, Conchiformibious, Achromobacter, Brucella, and Brevundimonas, were significantly more abundant in dogs with IBD. In conclusion, significant differences of the mucosa-adherent duodenal microbiota were observed between dogs with idiopathic IBD and healthy dogs in this study. These results warrant further investigations into the role of the intestinal microbiota in the pathophysiology of canine IBD.

The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing

Background

Recent studies have shown that the fecal microbiota is generally resilient to short-term antibiotic administration, but some bacterial taxa may remain depressed for several months. Limited information is available about the effect of antimicrobials on small intestinal microbiota, an important contributor to gastrointestinal health. The antibiotic tylosin is often successfully used for the treatment of chronic diarrhea in dogs, but its exact mode of action and its effect on the intestinal microbiota remain unknown. The aim of this study was to evaluate the effect of tylosin on canine jejunal microbiota. Tylosin was administered at 20 to 22 mg/kg q 24 hr for 14 days to five healthy dogs, each with a pre-existing jejunal fistula. Jejunal brush samples were collected through the fistula on days 0, 14, and 28 (14 days after withdrawal of tylosin). Bacterial diversity was characterized using massive parallel 16S rRNA gene pyrosequencing.

Results

Pyrosequencing revealed a previously unrecognized species richness in the canine small intestine. Ten bacterial phyla were identified. Microbial populations were phylogenetically more similar during tylosin treatment. However, a remarkable inter-individual response was observed for specific taxa. Fusobacteria, Bacteroidales, and Moraxella tended to decrease. The proportions of Enterococcus-like organisms, Pasteurella spp., and Dietzia spp. increased significantly during tylosin administration (p < 0.05). The proportion of Escherichia coli-like organisms increased by day 28 (p = 0.04). These changes were not accompanied by any obvious clinical effects. On day 28, the phylogenetic composition of the microbiota was similar to day 0 in only 2 of 5 dogs. Bacterial diversity resembled the pre-treatment state in 3 of 5 dogs. Several bacterial taxa such as Spirochaetes, Streptomycetaceae, and Prevotellaceae failed to recover at day 28 (p < 0.05). Several bacterial groups considered to be sensitive to tylosin increased in their proportions.

Conclusion

Tylosin may lead to prolonged effects on the composition and diversity of jejunal microbiota. However, these changes were not associated with any short-term clinical signs of gastrointestinal disease in healthy dogs. Our results illustrate the complexity of the intestinal microbiota and the challenges associated with evaluating the effect of antibiotic administration on the various bacterial groups and their potential interactions.

Estimation of intestinal permeability in healthy dogs using the contrast medium iohexol

BACKGROUND

Iohexol is a nonradioactive marker that has been used successfully to test intestinal permeability in humans with inflammatory bowel disease. There is evidence in dogs that iohexol shares a similar permeability pathway as (51)chromium-EDTA, the gold standard marker.

OBJECTIVE

The objective of this study was to determine an optimal oral iohexol dosage for an intestinal permeability serum test (IPST) and to use the test to estimate intestinal permeability in healthy dogs.

METHODS

Eight clinically healthy dogs free of gastrointestinal, liver, and pancreatic disease were used in the study. Dosages of 0.25, 0.5, 1.0, 2.0, and 4.0 mL/kg of Omnipaque-350 (iohexol) were administered to 2 dogs at weekly intervals. Iohexol concentration was determined in serum samples obtained hourly for 6 hours after administration by high-performance liquid chromatography. Using the optimal dosage, iohexol was administered to 8 dogs twice, 6-36 days (mean 10 days) apart, and coefficients of variation (CVs) for iohexol concentration were calculated.

RESULTS

A dosage of 2.0 mL/kg was chosen as optimal for the IPST, based on ease of iohexol detection in serum, intestinal contrast, and clinical effects of iohexol. Following administration of this dose to healthy dogs, mean (+/-SD) serum iohexol concentrations were 8.74+/-4.38, 11.89+/-5.67, 12.40+/-5.47, 9.23+/-5.54, 7.61+/-5.13, and 5.27+/-2.67 microg/mL at 1, 2, 3, 4, 5, and 6 hours after iohexol administration, respectively. CVs between the 2 test days were 28-45%.

CONCLUSIONS

Using the iohexol dosage established in this study, the iohexol IPST was easy to perform as a marker for intestinal permeability in dogs. Further studies to establish reference intervals and evaluate the diagnostic value of the iohexol IPST in dogs with gastrointestinal disease are warranted.

Ecological characterization of the colonic microbiota of normal and diarrheic dogs

We used terminal restriction fragment polymorphism (T-RFLP) analysis to assess (1) stability of the fecal microbiota in dogs living in environments characterized by varying degrees of exposure to factors that might alter the microbiota and (2) changes in the microbiota associated with acute episodes of diarrhea. Results showed that the healthy canine GI tract harbors potential enteric pathogens. Dogs living in an environment providing minimal exposure to factors that might alter the microbiota had similar microbiotas; the microbiotas of dogs kept in more variable environments were more variable. Substantial changes in the microbiota occurred during diarrheic episodes, including increased levels of Clostridium perfringens, Enterococcus faecalis, and Enterococcus faecium. When diet and medications of a dog having a previously stable microbiota were changed repeatedly, the microbiota also changed repeatedly. Temporal trend analysis showed directional changes in the microbiota after perturbation, a return to the starting condition, and then fluctuating changes over time.

Assessment of microbial diversity along the feline intestinal tract using 16S rRNA gene analysis

The aim of this study was to describe the microbial communities along the gastrointestinal tract in healthy cats based on analysis of the 16S rRNA gene. Gastrointestinal content (i.e. content from the stomach, duodenum, jejunum, ileum, and colon) was collected from four healthy conventionally raised colony cats and one healthy specific pathogen-free (SPF) cat. Bacterial 16S rRNA genes were amplified using universal bacterial primers and analyzed by comparative sequence analysis. A total of 1008 clones were analyzed and 109 nonredundant 16S rRNA gene sequences were identified. In the four conventionally raised cats, five different bacterial phyla were observed, with sequences predominantly classified in the phylum Firmicutes (68%), followed by Proteobacteria (14%), Bacteroidetes (10%), Fusobacteria (5%), and Actinobacteria (4%). The majority of clones fell within the order Clostridiales (54%), followed by Lactobacillales, Bacteroidales, Campylobacterales, and Fusobacteriales (14%, 11%, 10%, and 6%, respectively). Clostridiales were predominantly affiliated with Clostridium clusters I (58%) and XIVa (27%). The intestinal microbiota of the SPF cat displayed a reduced bacterial diversity, with 98% of all clones classified in the phylum Firmicutes. Further classification showed that the Firmicutes clones belonged exclusively to the class Clostridiales and were predominantly affiliated with Clostridium cluster I.

Molecular-phylogenetic characterization of microbial communities imbalances in the small intestine of dogs with inflammatory bowel disease

An association between luminal commensal bacteria and inflammatory bowel disease (IBD) has been suggested in humans, but studies investigating the intestinal microbial communities of dogs with IBD have not been published. The aim of this study was to characterize differences of the small intestinal microbial communities between dogs with IBD and healthy control dogs. Duodenal brush cytology samples were endoscopically collected from 10 dogs with IBD and nine healthy control dogs. DNA was extracted and 16S rRNA gene was amplified using universal bacterial primers. Constructed 16S rRNA gene clone libraries were compared between groups. From a total of 1240 selected clones, 156 unique 16S rRNA gene sequences were identified, belonging to six phyla: Firmicutes (53.4%), Proteobacteria (28.4%), Bacteroidetes (7.0%), Spirochaetes (5.2%), Fusobacteria (3.4%), Actinobacteria (1.1%), and Incertae sedis (1.5%). Species richness was significantly lower in the IBD group (P=0.038). Principal component analysis indicated that the small intestinal microbial communities of IBD and control dogs are composed of distinct microbial communities. The most profound difference involved enrichment of the IBD dogs with members of the Enterobacteriaceae family. However, differences involving members of other families, such as Clostridiaceae, Bacteroidetes and Spirochaetes, were also identified. In conclusion, canine IBD is associated with altered duodenal microbial communities compared with healthy controls.