Behavioral and locomotion tests.

<p>10A. The number of entries to the open arm for the three groups. There were no significant differences detected between NCS and OS-HA7 or HA7 and OS-HA7, but there were significant differences between NCS and HA7. Values represent the mean number of entries to open arm in each group ± SEM, n = 16/group. *<i>p</i><0.05. 10B. Time spent in the open arm for the three groups. There were no significant differences detected between NCS and OS-HA7, but there were significant differences between NCS and HA7 and OS-HA7 and HA7. Values represent the mean time spent in the open arm in each group ± SEM, n = 16/group. *<i>p</i><0.05. 10C. Time spent in the closed arm for the three groups. There were no significant differences detected between NCS and OS-HA7, but there were significant differences between NCS and HA7 and OS-HA7 and HA7. Values represent the mean time spent in the closed arm in each group ± SEM, n = 16/group. *<i>p</i><0.05. 10D. Overall locomotion of mice during the open field test (10D). Values represent the mean time spent in each quadrant in each group ± SEM, n = 16/group. *<i>p</i><0.05. 10E. Overall locomotion of mice during the open field test (10E). Values represent the mean distance travelled ± SEM, n = 16/group.</p

Taxonomic distribution of the bacterial genera.

<p>The average relative distribution of the most abundant genera is shown for mice fed control and RS diets are shown by each vertical bar. Bacterial genera are as indicated on the right.</p

Global effects of diet on mouse gut microbiota.

<p>Unweighted UniFrac distance PCoA plots comparing three principal components are shown. Samples representing each diet and time point of collection are indicated by distinct symbols.</p

Bacterial Community Profiling of Milk Samples as a Means to Understand Culture-Negative Bovine Clinical Mastitis

<div><p></p><p>Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1–V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease.</p> </div

<i>p</i>-values for phyla with significant changes (Kruskal-Wallis) in relative abundance within the feces for each diet over time.

<p>Phyla with <i>p</i>-values >0.05 are given for comparison. Arrows indicate if members of the phyla are more (↑) or less (↓) abundant over the time course.</p

<i>p</i>-values for the differences (Kruskal-Wallis and Wilcoxon Rank Sum tests) in relative abundance of class.

<p>Samples from feces (6A) and cecal contents (6B) were analyzed from weeks 1, 3, and 6 for each diet. Only those taxa with significant <i>p</i>-values are shown. Arrows indicate if members of the phyla are more (↑) or less (↓) abundant in pairwise comparisons.</p

<i>p</i>-values for the differences (Kruskal-Wallis and Wilcoxon Rank Sum tests) in relative abundance of phyla.

<p>Samples from feces (4A) and cecal contents (4B) were analyzed from weeks 1, 3, and 6 for each diet. Arrows indicate if members of the phyla are more (↑) or less (↓) abundant in pairwise comparisons.</p

Significant results for univariate analyses of genera classifications between sample pairs.

<p>Mean abundance calculations were performed for each sample using counts normalized by the total bacterial domain classified sequences for each sample.</p

<i>p</i>-values for the differences (Kruskal-Wallis and Wilcoxon Rank Sum tests) in relative abundance of genus (or family).

<p>Samples from feces (8A) and cecal contents (8B) were analyzed from weeks 1, 3, and 6 for each diet. Only those taxa with significant <i>p</i>-values are shown. Arrows indicate if members of the phyla are more (↑) or less (↓) abundant.</p

Taxonomic classifications for samples utilizing the RDP database.

<p>The normalized abundances of the top 10 most abundant bacterial genera determined using a RDP confidence threshold of 0.7 are shown. Sample pairs are labeled by animal (1–10) and clinical status as A (culture-negative clinical) or B (healthy), and the LSCC samples are labeled 1 and 2. Sample 1A (clinical) contained a known mastitis pathogen (<i>Mycoplasma</i> spp.) that was not detected in the healthy quarter sample 1B.</p