Additional file 5: of Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

Distribution of genes in selected categories among representatives of major gut colonisers belonging to phyla Bacteroidetes and Firmicutes. X axes indicate the numbers of genes in a given category per genome. (PDF 23 kb

Additional file 2: of Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

Phylogenetic tree of 133 sequenced isolates obtained from chicken caecum based on the Clustal alignment of the full-length sequence of RpoB proteins. Families within the phylum Firmicutes are shown in light blue, green and yellow. Families within the phylum Bacteroidetes are shown in shades of purple. The whole genome size and genomic GC content of each isolate is shown external to the dendrogram. (PDF 576 kb

Prevalence of antibiotic resistance genes in ornamental fish carriage water.

<p>Antibiotic resistance gene prevalence is presented with the median, 25% and 75% percentiles (box) and the whiskers indicating the minimum and maximum values recorded.</p

Heat map showing the correlation coefficients of the presence of individual families and particular antibiotic resistance genes.

<p>Three main clusters according to their positive and negative correlation with the prevalence of antibiotic resistance genes tested in this study are indicated by red, blue and green color.</p

Distribution of selected genes in integron structures determined by pyrosequencing and real-time PCR.

<p>Average values calculated from data available for 48 samples were used for both real-time PCR based pie charts. Quantification of genes in integrons by pyrosequencing and real-time PCR resulted in similar results whereas the comparison of these results with the results from carriage water DNA indicated that <i>dfrA</i> was associated with integrons as its representation decreased when total carriage water was used as a template in real-time PCR. On the other hand, <i>aacA</i> and <i>ereA</i> must have been common in genetic elements different from integrons.</p

Genes detected in class I integrons in carriage water microbiota of ornamental fish. Numbers show percentages out of a total of 18,806 reads.

<p>*QAC-quaternary ammonium compounds, Tp-trimethoprim, Str-streptomycin, AG-aminoglycosides, Cm-chloramphenicol, Ery-erythromycin, Kan–kanamycin, Rif–rifampicin, Enr–enrofloxacin.</p

Additional file 3: of Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

Aerobic survival of chicken gut anaerobes. (XLS 43 kb

List of primers used in this study.

<p>List of primers used in this study.</p

Additional file 1: of Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

List of 133 different isolates characterised in this study. The file contains taxonomical classification using NCBI and RDP databases based on whole sequence of 16S rRNA, similarity to the closest relative in the NCBI database, genome size, number of contigs into which the genome was assembled, genomic and 16S rRNA GC content, consensus 16S rRNA sequences with SNP positions indicated with lower case letters, 16S rRNA copy number estimated based on sequencing coverage and 16S rRNA copy number determined by RT PCR (only for the isolates in which sequencing coverage predicted more 10 copies of 16S rRNA genes). (XLSX 338 kb

Additional file 4: of Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

List of proteins encoded by individual anaerobes. (XLSX 7930 kb