The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease.

Recent molecular studies have revealed a highly complex bacterial assembly in the canine intestinal tract. There is mounting evidence that microbes play an important role in the pathogenesis of acute and chronic enteropathies of dogs, including idiopathic inflammatory bowel disease (IBD). The aim of this study was to characterize the bacterial microbiota in dogs with various gastrointestinal disorders. Fecal samples from healthy dogs (n = 32), dogs with acute non-hemorrhagic diarrhea (NHD; n = 12), dogs with acute hemorrhagic diarrhea (AHD; n = 13), and dogs with active (n = 9) and therapeutically controlled idiopathic IBD (n = 10) were analyzed by 454-pyrosequencing of the 16S rRNA gene and qPCR assays. Dogs with acute diarrhea, especially those with AHD, had the most profound alterations in their microbiome, as significant separations were observed on PCoA plots of unweighted Unifrac distances. Dogs with AHD had significant decreases in Blautia, Ruminococcaceae including Faecalibacterium, and Turicibacter spp., and significant increases in genus Sutterella and Clostridium perfringens when compared to healthy dogs. No significant separation on PCoA plots was observed for the dogs with IBD. Faecalibacterium spp. and Fusobacteria were, however, decreased in the dogs with clinically active IBD, but increased during time periods of clinically insignificant IBD, as defined by a clinical IBD activity index (CIBDAI). Results of this study revealed a bacterial dysbiosis in fecal samples of dogs with various GI disorders. The observed changes in the microbiome differed between acute and chronic disease states. The bacterial groups that were commonly decreased during diarrhea are considered to be important short-chain fatty acid producers and may be important for canine intestinal health. Future studies should correlate these observed phylogenetic differences with functional changes in the intestinal microbiome of dogs with defined disease phenotypes

Effects of Administration of Live or Inactivated Virulent Rhodococccus equi and Age on the Fecal Microbiome of Neonatal Foals

BACKGROUND: Rhodococcus equi is an important pathogen of foals. Enteral administration of live, virulent R. equi during early life has been documented to protect against subsequent intrabronchial challenge with R. equi, indicating that enteral mucosal immunization may be protective. Evidence exists that mucosal immune responses develop against both live and inactivated micro-organisms. The extent to which live or inactivated R. equi might alter the intestinal microbiome of foals is unknown. This is an important question because the intestinal microbiome of neonates of other species is known to change over time and to influence host development. To our knowledge, changes in the intestinal microbiome of foals during early life have not been reported. Thus, the purpose of this study was to determine whether age (during the first month of life) or administration of either live virulent R. equi (at a dose reported to protect foals against subsequent intrabronchial challenge, viz., 1×10(10) colony forming units [CFU]) or inactivated virulent R. equi (at higher doses, viz., 2×10(10) and 1×10(11) [CFU]) altered the fecal microbiome of foals. METHODOLOGY/PRINCIPAL FINDINGS: Fecal swab samples from 42 healthy foals after vaccination with low-dose inactivated R. equi (n = 9), high-dose inactivated R. equi (n = 10), live R. equi (n = 6), control with cholera toxin B (CTB, n = 9), and control without CTB (n = 8) were evaluated by 454-pyrosequencing of the 16S rRNA gene and by qPCR. No impact of treatment was observed among vaccinated foals; however, marked and significant differences in microbial communities and diversity were observed between foals at 30 days of age relative to 2 days of age. CONCLUSIONS: The results suggest age-related changes in the fecal microbial population of healthy foals do occur, however, mucosal vaccination does not result in major changes of the fecal microbiome in foals

Public Response to Community Mitigation Measures for Pandemic Influenza

Results from a national survey indicated that most persons would follow public health officials’ guidelines

Median and range percentages of sequences represented in the fecal DNA of rectal swab samples from foals (Phylum, class, order, and family).

<p>Fecal swab samples were collected from 37 Quarter Horse foals on days 2 and 30 of life. *P values represent the results of Wilcoxon sign-rank tests for paired differences, adjusted by the method of Hochberg. NP  =  Not Performed.</p

Median and range proportion of foals with sequences detected in the fecal DNA of rectal swab samples (Phylum, class, order, and family).

<p>Fecal swab samples collected from 37 Quarter Horse foals on days 2 and 30 of life. *P values represent the results of McNemar’s test for paired dichotomous data, adjusted by the method of Hochberg. NP  =  Not Performed.</p

Summary of alpha diversity measures.

<p>Summary of alpha diversity measures.</p

Principal coordinates analysis (PCoA) of unweighted UniFrac distances of 16 S rRNA genes.

<p>Analysis for 42 foals in groups control with CTB (red square), control without CTB (yellow triangle), low-dose inactivated <i>R. equi</i> (dark blue triangle), high-dose inactivated <i>R. equi</i> 2 (green dot), and live <i>R. equi</i> (light blue triangle) at 30 days of age only. Differences among groups were not significant (ANOSIM, P = 0.449). The 3 panels represent the comparison of the first 2 principal components (A), the second and third principal components (B), and the first and third principal components (C).</p

Rarefaction analysis of 16 S rRNA gene sequences obtained from fecal swabs from foals.

<p>Lines represent the average of each vaccination group at all ages (panel A) or at 30 days only (panel B), while the error bars represent the standard deviations. The analysis was performed on a randomly selected subset of 1,300 sequences per sample and included samples from 42 foals. Note that both the greatest and least number of species observed occurred among foals that received no enteral bacteria (live or inactivated), indicating an absence of evidence of treatment effect. Control  =  control plus CTB group; Control_no_CTO  =  control without CTB group; High  =  high-dose inactivated <i>R. equi</i> group; Live  =  live <i>R. equi</i> group; Low  =  low-dose inactivated <i>R. equi</i> group.</p

Results of qPCR analysis.

<p>Median (range) of log DNA. *P value for Wilcoxon rank-sum test comparing differences between ages day 30 and day 2, adjusted by the method of Hochberg.</p

Principal coordinates analysis (PCoA) of unweighted UniFrac distances of 16 S rRNA genes.

<p>Analysis for 42 foals in groups control with CTB (red square), control without CTB (yellow triangle), low-dose inactivated <i>R. equi</i> (dark blue triangle), high-dose inactivated <i>R. equi</i> 2 (green dot), and live <i>R. equi</i> (light blue triangle) at 2 and 30 days of age (ANOSIM, P = 0.236). The 3 panels represent the comparison of the first 2 principal components (A), the second and third principal components (B), and the first and third principal components (C). The pattern in the panel A is attributable to effects of age (please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066640#pone-0066640-g004" target="_blank">Figures 4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066640#pone-0066640-g005" target="_blank">5</a>).</p