TNFα protein secreted by MDM cells exposed to over time was measured by ELISA

<p><b>Copyright information:</b></p><p>Taken from "Cytokine responses of bovine macrophages to diverse clinical subspecies strains"</p><p>BMC Microbiology 2006;6():10-10.</p><p>Published online 14 Feb 2006</p><p>PMCID:PMC1382238.</p><p>Copyright © 2006 Janagama et al; licensee BioMed Central Ltd.</p> Total amount of protein (pg/ml) is plotted on Y-axis (note that the Y1-axis scales have been optimized for magnitude of TNFα expression for each strain). Intracellular bacterial numbers were calculated based on the genome size of and represented as genome equivalents (GE) on second Y-axis. MDMs stimulated with B1018 secreted low amounts of TNFα protein relative to other cell stimulations

TNFα mRNA expressed by MDM cells exposed to over time was measured by Real time RT PCR and fold change in gene expression relative to β actin was calculated by 2method

<p><b>Copyright information:</b></p><p>Taken from "Cytokine responses of bovine macrophages to diverse clinical subspecies strains"</p><p>BMC Microbiology 2006;6():10-10.</p><p>Published online 14 Feb 2006</p><p>PMCID:PMC1382238.</p><p>Copyright © 2006 Janagama et al; licensee BioMed Central Ltd.</p> Mean fold change in gene expression is plotted on Y-axis (note that the Y1-axis scales have been optimized for magnitude of IL-10 expression for each strain). Intracellular bacterial numbers based on the amplification of were calculated based on the genome size of and represented as genome equivalents (GE) on second Y-axis. MDMs stimulated with B1018 expressed lower levels of TNFα mRNA relative to other cell stimulations

Comparative genomics of two super-shedder isolates of <i>Escherichia coli</i> O157:H7

<div><p>Shiga toxin-producing <i>Escherichia coli</i> O157:H7 (O157) are zoonotic foodborne pathogens and of major public health concern that cause considerable intestinal and extra-intestinal illnesses in humans. O157 colonize the recto-anal junction (RAJ) of asymptomatic cattle who shed the bacterium into the environment through fecal matter. A small subset of cattle, termed super-shedders (SS), excrete O157 at a rate (≥ 10⁴ CFU/g of feces) that is several orders of magnitude greater than other colonized cattle and play a major role in the prevalence and transmission of O157. To better understand microbial factors contributing to super-shedding we have recently sequenced two SS isolates, SS17 (GenBank accession no. CP008805) and SS52 (GenBank accession no. CP010304) and shown that SS isolates display a distinctive strongly adherent phenotype on bovine rectal squamous epithelial cells. Here we present a detailed comparative genomics analysis of SS17 and SS52 with other previously characterized O157 strains (EC4115, EDL933, Sakai, TW14359). The results highlight specific polymorphisms and genomic features shared amongst SS strains, and reveal several SNPs that are shared amongst SS isolates, including in genes involved in motility, adherence, and metabolism. Finally, our analyses reveal distinctive patterns of distribution of phage-associated genes amongst the two SS and other isolates. Together, the results of our comparative genomics studies suggest that while SS17 and SS52 share genomic features with other lineage I/II isolates, they likely have distinct recent evolutionary histories. Future comparative and functional genomic studies are needed to decipher the precise molecular basis for super shedding in O157.</p></div

Additional file 4: of High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite

Tables showing significantly different bacteria at genus level between different types of wastes solid. (DOCX 55 kb

Comparative analysis of SS strains and reference O157 genomes.

<p>(A) Dendrogram representing cluster analysis of SS isolates based on PFGE patterns as previously described [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182940#pone.0182940.ref012" target="_blank">12</a>] highlighting the two representative isolates, SS17 and SS52, that have been completely sequenced; (B) Circular genome representations of SS17 and SS52. Larger circles depict chromosomal DNA with smaller circles representing plasmids. The blue circles represent the ORFs and the outer circle (purple) represents the phages in each genome; (C) Cladogram based on whole genome alignment reveals that SS17 and SS52 clusters closely with lineage I/II “spinach” outbreak isolates (EC4115 and TW14359) as compared with lineage I outbreak isolates (Sakai and EDL933) or the bovine lineage II isolates; (D) Whole genome alignments of SS strains with reference O157 strains using progressiveMauve depicting 8 homology blocks of similarity and patterns of divergence among the strains.</p

Characteristics of <i>E</i>. <i>coli</i> O157:H7 isolates.

<p>Characteristics of <i>E</i>. <i>coli</i> O157:H7 isolates.</p

Phage diversity in SS and reference O157 strains.

<p>(A) MAUVE alignment of SS17 and SS52 showing the ~37 Kb insertion of CP-933O phage in the SS17 genome; (B) BLAST analysis of the region reveals that SS17, TW14359, and EC4115 all contain the same phage, whereas EDL933, Sakai, and SS52 do not; (C) Dot matrix representation of the results of megaBLAST analysis of the 37.5kb CP-933O region reveals its presence in SS17 (left panel) but not SS52 (right panel).</p

Solid black lines represent homology (approximately 99% identity) with the MAA TMC724 (ATCC 25291) glycopeptidolipid biosynthesis cluster (accession number ), while dashed green lines represent sequences absent in isolate 397

Solid or dashed red and blue lines represent regions of homology with MAH 104 and MAP K-10, respectively. Vertical lines are spaced at 1600 base intervals for reference and represent the number of nucleotides from the start of the Genbank entry.<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic analysis of subspecies obtained from multiple host species"</p><p>http://www.biomedcentral.com/1471-2164/9/135</p><p>BMC Genomics 2008;9():135-135.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2323391.</p><p></p

474 ORFs with 3-fold or greater differences in hybridization between at least two isolates and MAP K-10 are displayed in rows

Columns represent individual mycobacterial isolates that were grouped by hierarchical clustering (Pearson correlation, average linkage). Grey colored data points represent no data. Isolate designations are listed in the right margin next to a colored bar indicating the location of the isolates on the graph. Selected gene clusters are labeled by the first and last ORFs. A complete listing of the ORFs and log ratios has also been provided [see Additional file ].<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic analysis of subspecies obtained from multiple host species"</p><p>http://www.biomedcentral.com/1471-2164/9/135</p><p>BMC Genomics 2008;9():135-135.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2323391.</p><p></p

Phages in SS17, SS52, and reference O157 strains.

<p>The location and identities of phages were determined in each strain using the Phast server [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182940#pone.0182940.ref025" target="_blank">25</a>]. The color-coded blocks represent phage identity with similar colors showing the same phage on the circular genome. The highlighted area around 1.7MB depicts the insertion of a phage within another phage in SS17 but not SS52. From inner ring: TW14359, EC4115, Sakai, EDL933, SS52, and SS17.</p