Untargeted fecal metabolome analysis in obese dogs after weight loss achieved by feeding a high-fiber-high-protein diet.

INTRODUCTION: In humans and companion animals, obesity is accompanied by metabolic derangements. Studies have revealed differences in the composition of the fecal microbiome between obese dogs and those with an ideal body weight. OBJECTIVES: We have previously reported that the fecal microbiome in obese dogs changes after controlled weight reduction, induced by feeding a diet high in fiber and protein. Despite these findings, it is unclear if taxonomic differences infer differences at the functional level between obese dogs and those with an ideal body weight. METHODOLOGY: Untargeted fecal metabolome analysis was performed on dogs with obesity before and after weight loss achieved by feeding a high-fiber-high-protein diet. RESULTS: Fecal metabolome analysis revealed a total of 13 compounds that changed in concentration in obese dogs after weight loss. Of these compounds, metabolites associated with bacterial metabolism decreased after weight loss including purine, L-(-)-methionine, coumestrol, and the alkaloids 1-methylxanthine and trigonelline. Conversely, the polyphenols (-)-epicatechin and matairesinol and the quinoline derivatives 1,5-isoquinolinediol and 2-hydroxiquinoline increased after weight loss. CONCLUSION: These results suggest differences in intestinal microbiome at the functional level after weight loss, but further studies are needed to determine the role of these compounds in the etiology of obesity and weight loss.

Untargeted metabolomic analysis in cats with naturally occurring inflammatory bowel disease and alimentary small cell lymphoma.

Feline chronic enteropathy (CE) is a common gastrointestinal disorder in cats and mainly comprises inflammatory bowel disease (IBD) and small cell lymphoma (SCL). Differentiation between IBD and SCL can be diagnostically challenging. We characterized the fecal metabolome of 14 healthy cats and 22 cats with naturally occurring CE (11 cats with IBD and 11 cats with SCL). Principal component analysis and heat map analysis showed distinct clustering between cats with CE and healthy controls. Random forest classification revealed good group prediction for healthy cats and cats with CE, with an overall out-of-bag error rate of 16.7%. Univariate analysis indicated that levels of 84 compounds in cats with CE differed from those in healthy cats. Polyunsaturated fatty acids held discriminatory power in differentiating IBD from SCL. Metabolomic profiles of cats with CE resembled those in people with CE with significant alterations of metabolites related to tryptophan, arachidonic acid, and glutathione pathways.

Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet.

BACKGROUND: The fecal microbiota from obese individuals can induce obesity in animal models. In addition, studies in humans, animal models and dogs have revealed that the fecal microbiota of subjects with obesity is different from that of lean subjects and changes after weight loss. However, the impact of weight loss on the fecal microbiota in dogs with obesity has not been fully characterized. METHODS: In this study, we used 16S rRNA gene sequencing to investigate the differences in the fecal microbiota of 20 pet dogs with obesity that underwent a weight loss program. The endpoint of the weight loss program was individually tailored to the ideal body weight of each dog. In addition, we evaluated the qPCR based Dysbiosis Index before and after weight loss. RESULTS: After weight loss, the fecal microbiota structure of dogs with obesity changed significantly (weightedANOSIM; p = 0.016, R = 0.073), showing an increase in bacterial richness (p = 0.007), evenness (p = 0.007) and the number of bacterial species (p = 0.007). The fecal microbiota composition of obese dogs after weight loss was characterized by a decrease in Firmicutes (92.3% to 78.2%, q = 0.001), and increase in Bacteroidetes (1.4% to 10.1%, q = 0.002) and Fusobacteria (1.6% to 6.2%, q = 0.040). The qPCR results revealed an overall decrease in the Dysbiosis Index, driven mostly due to a significant decrease in E. coli (p = 0.030), and increase in Fusobacterium spp. (p = 0.017). CONCLUSION: The changes observed in the fecal microbiota of dogs with obesity after weight loss with a weight loss diet rich in fiber and protein were in agreement with previous studies in humans, that reported an increase of bacterial biodiversity and a decrease of the ratio Firmicutes/Bacteroidetes.

Evaluation of the bacterial ocular surface microbiome in ophthalmologically normal dogs prior to and following treatment with topical neomycin-polymyxin-bacitracin.

The ocular surface microbiome of veterinary species has not been thoroughly characterized using molecular-based techniques, such as next generation sequencing (NGS), as the vast majority of studies have utilized traditional culture-based techniques. To date, there is one pilot study evaluating the ocular surface of healthy dogs using NGS. Furthermore, alterations in the ocular surface microbiome over time and after topical antibiotic treatment are unknown. The objectives of this study were to describe the bacterial composition of the ocular surface microbiome in clinically normal dogs, and to determine if microbial community changes occur over time or following topical antibiotic therapy. Topical neomycin-polymyxin-bacitracin ophthalmic ointment was applied to one eye each of 13 adult dogs three times daily for seven days, while contralateral eyes served as untreated controls. The inferior conjunctival fornix of both eyes was sampled via swabbing at baseline prior to antibiotic therapy (day 0), after 1 week of treatment (day 7), and 4 weeks after discontinuing treatment (day 35). Genomic DNA was extracted from the conjunctival swabs and primers targeting the V4 region of bacterial 16S rRNA genes were used to generate amplicon libraries, which were then sequenced on an Illumina platform. Data were analyzed using Quantitative Insights Into Molecular Ecology (QIIME 2.0). At baseline, the most relatively abundant phyla sequenced were Proteobacteria (49.7%), Actinobacteria (25.5%), Firmicutes (12%), Bacteroidetes (7.5%), and Fusobacteria (1.4%). The most common families detected were Pseudomonadaceae (13.2%), Micrococcaceae (12%), Pasteurellaceae (6.9%), Microbacteriaceae (5.2%), Enterobacteriaceae (3.9%), Neisseriaceae (3.5%), and Corynebacteriaceae (3.3%). Alpha and beta diversity measurements did not differ in both control and treatment eyes over time. This report examines the temporal stability of the canine ocular surface microbiome. The major bacterial taxa on the canine ocular surface remained consistent over time and following topical antibiotic therapy.

Reproductive Senescence and Ischemic Stroke Remodel the Gut Microbiome and Modulate the Effects of Estrogen Treatment in Female Rats.

Our previous work has shown that reproductively senescent (or middle-aged; 10-12-month-old) Sprague-Dawley female rats, that are naturally estrogen-deficient, have worse stroke outcomes as compared to normally estrous-cycling adult (5-6-month-old) females. Paradoxically, estrogen replacement to this middle-aged group exacerbates stroke outcomes, while it is neuroprotective in adult females. Recent studies reveal an important role for the gut microbiome and gut metabolites in cardiovascular health, including stroke outcomes. To determine whether gut dysbiosis underlies stroke severity in reproductive senescent females, and underlies the anomalous effects of estrogen on stroke, we compared the gut microbiota and gut metabolites pre and post stroke in (a) gonadally intact adult and middle-aged females, (b) in ovariectomized and estrogen-treated (OVX+E) adult and OVX+E middle-aged females, and (c) in middle-aged OVX+E females after fecal microbiome transfer. Our data show significant gut dysbiosis in reproductive senescent females at baseline and after stroke as indicated by an elevated ratio of the major phyla, Firmicutes/Bacteroidetes (F:B), reduced alpha diversity, and significant shifts in beta diversity as compared with adult females. Specific bacterial families were also altered as a result of reproductive aging, as well as gut metabolites, including elevated serum endotoxin levels and decreased short-chain fatty acids (SCFAs), with a concomitant increase in IL-17A, indicating that reproductive senescence significantly affects gut communities under pathologic conditions. Despite the differences in gonadally intact adult and middle-aged females, estrogen-treated ovariectomized (OVX+E) females of either age group displayed no differences in the major phyla, but there was increased abundance in specific bacterial taxa, including Prevotella and Lactobacillus. The SCFA butyrate was significantly reduced at baseline in the middle-aged OVX+E females, while circulating endotoxin LPS were elevated in this group after stroke, suggesting that gut metabolites were differently affected by estrogen treatment in the two age groups. A fecal transfer from adult OVX+E females to middle-aged OVX+E females significantly reduced infarct volume, improved behavioral recovery and transiently reduced IL-17A expression. These data provide the first evidence that microbial gut communities and metabolites are altered by reproductive senescence in female rats at baseline and after stroke, and suggest that estrogen may impact stroke recovery differently in adult and reproductive senescent females due to an age-specific effect on gut microbiota and metabolites.

Characterization of the fecal microbiome in cats with inflammatory bowel disease or alimentary small cell lymphoma.

Feline chronic enteropathy (CE) is a common gastrointestinal disorder in cats and mainly comprises inflammatory bowel disease (IBD) and small cell lymphoma (SCL). Both IBD and SCL in cats share features with chronic enteropathies such as IBD and monomorphic epitheliotropic intestinal T-cell lymphoma in humans. The aim of this study was to characterize the fecal microbiome of 38 healthy cats and 27 cats with CE (13 cats with IBD and 14 cats with SCL). Alpha diversity indices were significantly decreased in cats with CE (OTU p = 0.003, Shannon Index p = 0.008, Phylogenetic Diversity p = 0.019). ANOSIM showed a significant difference in bacterial communities, albeit with a small effect size (P = 0.023, R = 0.073). Univariate analysis and LEfSE showed a lower abundance of facultative anaerobic taxa of the phyla Firmicutes (families Ruminococcaceae and Turicibacteraceae), Actinobacteria (genus Bifidobacterium) and Bacteroidetes (i.a. Bacteroides plebeius) in cats with CE. The facultative anaerobic taxa Enterobacteriaceae and Streptococcaceae were increased in cats with CE. No significant difference between the microbiome of cats with IBD and those with SCL was found. Cats with CE showed patterns of dysbiosis similar to those in found people with IBD.