Additional file 2: Table S2. of Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract

Genes encoding virulence factors in the E. coli BG1 genome (XLSX 31 kb

Additional file 4: Figure S1. of Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract

Hierarchical clustering of E. coli strains according to adherence systems encoding genes. The dendrogram and associated heatmap are generated on the basis of gene presence/absence considering 78 genes involved in adherence, using binary distance and complete clustering method, R version 3.3.1. [43]. Blue color indicates gene presence, red gene absence. The origin of each strain is identified with B (Bovine) or H (Human). The color of the strain name corresponds to its phylogroup as in Fig. 2. (DOCX 67 kb

Additional file 6: Figure S2. of Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract

Nucleotide sequence alignment of the eutT gene. The sequences of the eutT gene and the translated EutT polypeptide were aligned respectively from E. coli strains BG1 and EDL933 using Seaview version 4.6.1 [56]. (DOCX 15 kb

Additional file 1 of Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

Supplementary Material

Additional file 2 of Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

Supplementary Material

Additional file 4 of Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

Supplementary Material

Additional file 3 of Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

Supplementary Material

Growth competition assays between EHEC EDL933 and its mutant EDL933 Δ<i>ppsA</i>Δ<i>pckA</i>.

<p>The BSIC samples were inoculated with a 1:1 mixture of the two strains. Bars represent the SEM of three independent experiments. ***, denotes statistical significance, P <0.01 as determined by the Student <i>t</i> test for paired samples.</p

Metabolic pathways involved in the utilization of carbon nutriments by EHEC EDL933 incubated in BSIC.

<p>Genes with transcription up-regulated (red) and not altered (black) in EHEC EDL933 incubated in BSIC compared with M9-Glc. Genes encoding enzymes involved in irreversible GNG reactions are shown in blue. G3P: glycerol-3-phosphate; G3P-ROH: glycerophosphodiester; DHAP: dihydroxyacetone phosphate; PEP: phosphoenopyruvate; Pi: inorganic phosphate; UQ: ubiquinone; UQH₂: ubiquinol.</p

Genes involved in central metabolism and catabolism of gluconeogenic substrates up-regulated in EHEC EDL933 incubated in BSIC compared to M9-Glc.

<p>Genes involved in central metabolism and catabolism of gluconeogenic substrates up-regulated in EHEC EDL933 incubated in BSIC compared to M9-Glc.</p