Browsing by Subject "microbiota"
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Item Characterization of the Fecal Microbiota in Dogs with Chronic Enteropathies and Acute Hemorrhagic Diarrhea(2012-10-19) Markel, MelissaRecent 16S rRNA gene sequencing studies of the duodenal and fecal microbiota have revealed alterations in the abundance of specific bacterial groups in dogs with gastrointestinal (GI) disorders. The aim of this study was to establish a panel of quantitative real-time PCR (qPCR) assays for the evaluation of specific bacterial groups in fecal samples of healthy dogs, dogs with chronic enteropathies (CE), and dogs with acute hemorrhagic diarrhea (AHD). Fecal samples from 242 healthy dogs, 118 dogs with CE, and 57 dogs with AHD were analyzed using qPCR assays targeting Faecalibacterium spp., Turicibacter spp., Bifidobacterium spp., Lactobacillus spp., Streptococcus spp., Ruminococcaceae, C. perfringens, E. coli, gamma-Proteobacteria, Bacteroidetes, and Firmicutes). Differences in bacterial abundance among the three groups were evaluated using a Kruskal-Wallis test followed by a Dunn's post-test. A Bonferroni correction was used to correct for multiple comparisons and an adjusted p<0.05 was considered for statistical significance. Faecalibacterium spp., Turicibacter spp., and Ruminococcaceae were significantly decreased in CE and AHD compared to healthy dogs (p<0.001 for all). Lactobacillus spp. and Streptococcus spp. were significantly increased in dogs with CE (p<0.001 for both) when compared to the healthy dogs. In contrast, Lactobacillus spp. and Streptococcus spp. were significantly decreased in dogs with AHD compared to healthy dogs (p<0.01 and p<0.05, respectively) and also when compared to the dogs with CE (p<0.001 for both). C. perfringens and E. coli were significantly increased in dogs with AHD (p<0.001 and p<0.01, respectively), when compared to healthy dogs. E. coli was also significantly increased in dogs with CE when compared to the healthy dogs (p<0.001). Bacteroidetes were significantly lower in dogs with CE compared to healthy dogs (<0.001). Firmicutes were significantly higher in healthy dogs in comparison to dogs with AHD (p<0.05). Bifidobacterium spp. and gamma-Proteobacteria were not significantly different among all three groups of dogs. In conclusion, the qPCR panel employed here revealed a fecal dysbiosis in dogs with CE and AHD when compared to healthy dogs. These results are similar to recently reported findings using molecular sequencing approaches. Quantification of these bacterial groups by qPCR may be a useful adjunct for the diagnosis or monitoring of gastrointestinal disease in dogs.Item Diet, Disease State, and the Space Environment Modify the Intestinal Microbiota and Mucosal Environment via Microbiota-directed Alterations in Colonocyte Signalling(2013-11-25) Ritchie, Lauren EMicrobial dysbiosis and toll-like receptor (TLR) signaling play a role in colonic injury and inflammation. Ulcerative colitis and radiation are known to alter microbiota, and diets containing polyphenols impact bacterial populations. We hypothesized that diet can mitigate dextran sodium sulfate (DSS) colitis (sorghum bran diets containing polyphenols) and space environment-induced alterations (normal iron content) in colonic microbiota and TLR signaling. To test this we utilized two experimental paradigms; DSS-induced colitis (3% DSS, 48-hr, 3 exposures, 2 wk separation), and three models to emulate the space environment: 1) fractionated low linear energy transfer (LET) ? radiation (RAD) (3 Gy) and high Fe diet (IRON) (650 mg/kg), 2) high LET Si particle exposure (50 cGy) and 1/6 G hind limb unloading (HLU), and 3) 13 d spaceflight. Bran diets upregulated proliferation, and repair protein (TFF3 and TGF?) and short chain fatty acid (SCFA) transporter (Slc16a1 and Slc5a8) expression post-DSS. Diet significantly affected 24-hr fecal butyrate production, with Cellulose and Black bran having numerically higher concentrations. Two predominant phyla were identified, Firmicutes and Bacteroidetes, and this ratio was higher in Cellulose DSS. Post DSS#3 the proportion of Bacteroidales, Clostridiales, and Lactobacillales was reduced compared to post DSS#2 for all diets. Black bran non-DSS rats had the highest richness and diversity. Colonic injury negatively correlated with the proportion of Firmicutes, Actinobacteria, and Lactobacillales, and positively correlated with Unknown and Unclassified groups. Bran diets reduced the severity of epithelial injury, maintained fecal butyrate, and prevented microbial dysbiosis and depletion during DSS-induced colitis. IRON+RAD decreased SCFA concentrations. Low and high LET radiation, HLU, IRON and spaceflight increased Bacteroidetes and decreased Firmicutes. HLU and spaceflight increased Clostridiales and decreased Lactobacillales. RAD and IRON+RAD animals had increased Lactobacillales and significantly lower Clostridiales compared to CON and IRON. TLR9 and IL-6 were downregulated by RAD. TLR4, TFF3 and TGF? differentially changed with IRON and spaceflight. Microgravity independently affected the microbiota, regardless of radiation energy or dose. Each environmental insult differentially altered the microbiota and mucosal gene expression, with distinct diet, microgravity, and radiation effects observed. Bran diets mitigated deleterious effects of colitis, maintained barrier integrity, and prevented microbiota dysbiosis.Item Fecal Microbiome in Dogs with Acute Diarrhea(2013-11-07) Guard, Blake CrosbyRecent molecular studies have revealed that the canine gastrointestinal tract (GIT) harbors a highly complex microbial ecosystem. Gut microbes play a very important role in the development and regulation of the immune system of the host, mediated in-part through the production of immunomodulatory metabolites (e.g., butyrate, propionate, indole). Limited information is available about potential changes in the predominant bacterial groups in dogs with acute diarrhea, and characterizing the functional gene content of the microbiome may help to understand relationships between microbiota, endogenous metabolites, and gastrointestinal disease. Therefore, the aim of this study was (1) to characterize the fecal microbiome in healthy dogs, dogs with acute non-hemorrhagic diarrhea (NHD), and dogs with acute hemorrhagic diarrhea (AHD) using 16S rRNA gene sequencing and qPCR analysis; (2) to measure fecal concentrations of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs); and (3) to describe the functional gene content of the fecal microbiome. Fecal samples were collected from healthy dogs (n=13), dogs with NHD (n=5), and dogs with AHD (n=6). The fecal microbiota were analyzed by 454-pyrosequencing of 16S rRNA genes and qPCR assays. SCFAs were quantified by gas chromatography/mass spectrometry (GC/MS). Functional genes present in the microbiome were predicted from the 16S rRNA gene data using the software PICRUSt. The Shannon Index for bacterial diversity was significantly decreased in dogs with acute diarrhea (AD; both NHD and AHD groups combined) compared to healthy dogs (p=0.0020). Sequences belonging to Bacteroidetes were significantly decreased in dogs with AD compared to healthy dogs (p=0.0280). Sequences belonging to the genus Faecalibacterium and an unclassified genus within the family Ruminococcaceae were both significantly decreased in dogs with AD compared to healthy dogs (p=0.0319 and 0.0368, respectively). Also, a significant decrease in Blautia spp. were observed in dogs with AD compared to healthy dogs (p=0.0472). The proportions of butyric acid were significantly increased and proportions of propionic acid were significantly decreased in dogs with AD compared to healthy dogs (p<0.05 for both). Significant differences were not observed in functional categories among all dogs after adjustment for multiple comparisons. Results of this study revealed a bacterial dysbiosis in fecal samples of dogs with NHD and dogs with AHD compared to healthy dogs. The bacterial groups that were commonly decreased during acute diarrhea are considered to be important SCFA producers and may be important for canine intestinal health. Future studies to evaluate broader metabolomic profiles in dogs with acute diarrhea are indicated.