ADDITIONAL FILE 1. The gating strategies used to analyze numbers and
function of NK cells, γδ T cells and cytotoxic CD8+ T cells in the ileum.
Gating included consecutive selection for lymphocytes (FSC-A vs SSC-A),
viable cells (Live/Dead marker-negative) followed by selection of the specific
cellular subsets and the expression of activation markers by NK and T
cells according to the staining panels (Table 1). NK cell subsets were gated
on CD3−
cells expressing either IL-2Rα or 20E5 and NK cell activation
was gated on CD3−
CD41/61− cells expressing CD107 or on CD3−
cells
expressing IFNγ. T cell subsets were gated on CD3+
CD4− cells positive
for TCRγδ (γδ) or negative (
CD8+ αβ) with both γδ and cytotoxic αβ T
cells expressing either CD8αα or CD8αβ. T cell activation was gated on
CD3+
CD41/61−CD8α+ cells expressing CD107 or on CD3+
TCRγδ+CD8α+
and CD3+
TCRγδ−CD8α+ cells expressing IFNγ, and only in spleen also
CD3+
TCRγδ−CD8α− (
CD4+) cells expressing IFNγ. The marker CD41/61 is
included in the CD107 assay to exclude thrombocytes from analysis, since
activated thrombocytes have been reported to express CD107 [69]. In the
CD107 assay NK cells are gated by excluding T cells and thrombocytes
since a pan NK marker is missing while for phenotyping the NK cells are
gated based on expression of the NK markers IL-2Rα and 20E5, which are
known to be expressed on cells with NK function [48].
ADDITIONAL FILE 2. Effect of GM on numbers of intraepithelial and
splenic γδ T cells and cytotoxic T cells expressing either CD8αα+ and
CD8αβ+ before and during SE infection in broiler chickens. A Numbers
(cells/mg) of intraepithelial CD8αα+ γδ T cells, B CD8αβ+ γδ T cells,
C cytotoxic CD8αα+ T cells and D CD8αβ+ T cells in chickens either fed
standard (control) or long-chain glucomannan supplemented (GM) diet
in course of time before and during SE infection. E Numbers (cells/mg) of
splenic CD8αα+ γδ T cells, F CD8αβ+ γδ T cells, G cytotoxic CD8αα+ T cells
and H CD8αβ+ T cells in chickens either fed standard or GM diet before
and during SE infection. Mean + SEM per diet group and time point are
shown (n = 6), if n = 5; one chicken was excluded due to numbers of
events acquired in the gate of interest were < 100. Statistical significance
between diet groups is indicated as ***(p < 0.001).
ADDITIONAL FILE 3. Effect of GM on T cell activation in IELs and spleen
before and during SE infection in broiler chickens. A Percentages of
intraepithelial CD8+
T cells expressing CD107 (including both γδ and αβ T
cells), B CD8+
γδ T cells expressing IFNγ and C CD8+
αβ T cells expressing
IFNγ in chickens either fed standard (control) or long-chain glucomannan
supplemented (GM) diet in course of time before and during SE infection.
D Percentages of splenic CD8+
T cells expressing CD107 (including both
γδ and αβ T cells), E CD8+
γδ T cells expressing IFNγ, F CD4+
αβ T cells
expressing IFNγ and G CD8+
αβ T cells expressing IFNγ in chickens either
fed standard or GM diet before and during SE infection. Mean + SEM per
diet group and time point are shown (n = 6), for IFNγ expression of CD8+
γδ T cells in the IEL population at 0 dpi percentages were not determined (nd) due to numbers of events acquired in the gate of interest were
< 100.
ADDITIONAL FILE 4. Correlation between serum antibody titers and
SE-CFUs in broiler chickens. Correlation between SE-specific antibody
titers and splenic SE-CFUs of chickens either fed standard (control) or
long-chain glucomannan (GM) diet using the Spearman rank correlation
test. Statistical significance is indicated as p = 0.01.
ADDITIONAL FILE 5. Intestinal microbial taxa significantly increased
with diet at 0, 3 and 7 dpi of SE in broiler chickens. Standardized
relative fluorescence intensities of the microbial taxa as measured by
the microarray in the ileum and caeca (Table 3) that were significantly
increased either with standard (control) or long-chain glucomannan
supplemented (GM) diet at 0, 3 and 7 dpi of SE in broiler chickens. LS
mean per microbial taxa and diet group are shown (n = 6) with statistical
significance of FDR adjusted p values set at < 0.05.
ADDITIONAL FILE 6. Correlation between microbial taxa and intraepithelial
and splenic immune parameters at 0, 3 and 7 dpi of SE in
broiler chickens. A Correlation values between intestinal microbial taxa
in the ileum or B caeca significantly increased with diet and percentages
of NK cell activation (CD107 or IFNγ expression) or numbers of NK and
T cell subsets of the ileum (IEL) and spleen (Spln) per diet (control, GM)
at 0, 3 and 7 dpi of SE in broiler chickens. Pearson’s correlation (r) values
are depicted in a heatmap as positive (yellow) or negative (dark blue)
correlations.