Heatmap of nasal swab samples grouped by animal age.

<p>Bacterial OTUs were included where they had an abundance of ≥5% in at least one sample. DNA extraction kit reagent controls are labelled as Extraction control <i>n</i>.</p

Richness and diversity of bacterial communities in different sample types.

<p>Richness and diversity of bacterial communities in different sample types.</p

Heatmap of buccal swab samples grouped by animal age.

<p>Bacterial OTUs were included where they had an abundance of ≥5% in at least one sample. DNA extraction kit reagent controls are labelled as Extraction control <i>n</i>.</p

Bacterial genera in respiratory samples from chickens.

<p>The most abundant bacterial genera (A) and orders (B) on average in respiratory samples from chickens of different ages and in PBS and DNA extraction reagent controls.</p

Heatmap of BAL fluid samples grouped by animal age.

<p>Bacterial OTUs were included where they had an abundance of ≥7% in at least one sample. OTUs labelled <i>Pseudomonas</i> have been removed as their presence was likely due to reagent contamination. DNA extraction kit reagent controls are labelled as Extraction control <i>n</i>. PBS controls are labelled as <i>n</i> control PBS, where <i>n</i> is the chicken sampled immediately after the control sample was taken.</p

Clustering of chicken buccal swab samples according to age.

<p>PCOA graph showing the significantly separate clustering by community composition of the bacterial communities in buccal swabs from chickens of different ages (AMOVA: P<0.001).Each axis label shows the total percentage of variability between samples which is represented by that axis.</p

MOESM1 of Host-specific differences in the response of cultured macrophages to Campylobacter jejuni capsule and O-methyl phosphoramidate mutants

Additional file 1. Campylobacter jejuni capsule and MeOPN mutants elicit an enhanced cytokine responses in mBMDCs. The mBMDCs were differentiated from vials of frozen C57BL/6 mouse bone marrow following the protocol of Rose et al. [31] in the presence of GM-CSF (final concentration of 20 ng/mL; Peptro Tech) for 7 days. Live or fixed C. jejuni 11168H (WT), Δcj1417 (MeOPN) and Δcj1439 (capsule) mutants were incubated with mBMDCs at MOI 50 for 3 h. Salmonella LPS was used as a positive control, while PBS in the medium was used as a negative control. Graphs show representative results of two independent experiments. Error bars are the standard deviation of two independent experiments. Asterisks indicate a statistically significant difference of mRNA levels of inflammatory-related cytokines compared to C. jejuni WT (*P < 0.05; **P < 0.01)

Epitope prediction for MHC B4, B15, B19 and B21 based on anchor residues.

<p>Predicted epitopes and their localization based on anchor residues that have been described for B4, B15, B19 and B21 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031953#pone.0031953-Kaufman1" target="_blank">[32]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031953#pone.0031953-Koch1" target="_blank">[34]</a>. X represents any amino acid. Anchor residues specific for the different MHC types are indicated in bold. A variable number of amino acids between the anchor residues is indicted with (X).</p

Identification of MHC B4-, B15-, B19- and B21-restricted CD8+ T-cell epitopes using peptide pools.

<p>Lung cells isolated at 10 dpi were stimulated with B4 restricted peptide pools (A) or, B15 (B), B21 (C) and B19-restricted peptide pools (D–F) and IFNγ producing cells were determined by IFNγ Elispot analysis. Mean plus SEM is shown, n = 3 per group. Positive responses (*) and “significant” peptides inducing a positive response in 2 out of 3 chickens (↓) are indicated.</p

Identification of MHC B12-restricted CD8+ T-cell epitopes using peptide pools.

<p>Lung cells were stimulated with B12-restricted peptide pools and IFNγ-producing cells were determined by IFNγ ELIspot analysis. Results for three individuals birds are shown at 5 dpi (A–C), 7 dpi (D–F), 10 dpi (G–I) and 14 dpi (J–L). Mean plus SEM is shown, n = 3 per group. Positive responses (*) and “significant” peptides inducing a positive response in 2 out of 3 chickens (↓) are indicated.</p