Table 2.

List of downregulated posterior intestine proteins of rainbow trout in response to Yersinia ruckeri strains

Accession Refseq	Protein name	Number of quantified peptides	Biological process	Intestine in response to Y. ruckeri strain	3 dpe (fold change)	9 dpe (fold change)	28 dpe (fold change)
NP_001117719.1	Apolipoprotein A-I-1	6	Lipid metabolism	Biotype 1	−1.3	−1.1	−1.6
				Biotype 2	−2.2*	−1.2	−1.1
NP_001154920.1	Apolipoprotein A-II	4	Lipid metabolism	Biotype 1	−2.1*	−1.0	−1.7
				Biotype 2	−4.0*	1.1	−1.3
XP_021447265.1	Apolipoprotein C-I	2	Lipid metabolism	Biotype 1	−1.7	1.1	−3.1*
				Biotype 2	−4.6*	−1.3	−2.7
XP_021422847.1	Filamin-A	6	Actin filament binding	Biotype 1	−3.2*	−2.8	−1.5
				Biotype 2	−10.4*	−2.8	−1.4
XP_021438757.1	Alpha-actinin-1	6	Actin filament binding	Biotype 1	−2.4*	−1.7	−1.2
				Biotype 2	−6.3*	−1.9	1.3
XP_021474949.1	PDZ and LIM domain protein 3	2	Alpha-actinin binding	Biotype 1	−4.2*	−2.5*	−1.1
				Biotype 2	−22.6*	−1.7	1.1
XP_021479779.1	Dihydropyrimidinase-related protein 3	6	Actin filament bundle assembly	Biotype 1	−2.4*	−1.7	−1.3
				Biotype 2	−4.5*	−1.6	−1.1
XP_021449109.1	Tubulin alpha chain	3	Microtubule process	Biotype 1	−2.1*	1.2	−1.8
				Biotype 2	−4.9*	−1.2	−1.6
XP_021451765.1	Tubulin polymerization-promoting protein	6	Microtubule binding	Biotype 1	−3.6*	−1.7	−1.3
				Biotype 2	−7.0*	−1.5	−1.2
XP_021480500.1	DnaJ homolog subfamily C member 7	2	Chaperone binding	Biotype 1	−1.9	1.1	−1.2
				Biotype 2	−3.2*	−1.4	−1.0
XP_021478259.1	Lysosome membrane protein 2	2	Chaperone activity	Biotype 1	−2.6*	1.1	−1.3
				Biotype 2	−3.3*	−1.3	−1.3
NP_001117706.1	Heat shock 47 precursor	6	Stress response	Biotype 1	−3.7*	−1.4	−1.1
				Biotype 2	−9.6*	−1.2	1.0
XP_021438340.1	Heat shock cognate 70 kDa protein-like	6	Chaperone activity	Biotype 1	−1.9	−1.1	−1.3
				Biotype 2	−2.6*	−1.4	−1.1
XP_021441996.1	Programmed cell death protein 5	2	DNA binding	Biotype 1	−2.7*	1.2	−1.7
				Biotype 2	−4.4*	−1.4	−2.6*
XP_021418468.1	Annexin A13	6	Calcium ion binding	Biotype 1	−2.0*	−1.6	−1.8
				Biotype 2	−3.4*	−1.2	−1.1
XP_021416101.1	Protein S100 A13	2	Calcium binding	Biotype 1	−3.2*	−1.1	−1.5
				Biotype 2	−6.6*	−1.3	−1.1
NP_001117701.1	M-calpain	6	Calcium ion binding	Biotype 1	−2.0*	−1.2	−1.0
				Biotype 2	−4.0*	−1.4	1.0
NP_001117963.1	Calpain 2 catalytic subunit	5	Calcium ion binding	Biotype 1	−1.8	−1.1	−1.1
				Biotype 2	−2.6*	−1.0	−1.0
XP_021419099.1	l-Lactate dehydrogenase	2	Carboxylic acid metabolic process	Biotype 1	−3.4*	−1.5	−1.8
				Biotype 2	−7.4*	−1.7	1.3
XP_021452473.1	Glyceraldehyde-3-phosphate dehydrogenase	4	Glycolysis process	Biotype 1	−1.8	−1.2	−1.3
				Biotype 2	−2.9*	−1.1	−1.1
XP_021447060.1	Pyruvate dehydrogenase E1	4	Glucose metabolic process	Biotype 1	−2.1*	1.2	1.0
				Biotype 2	−1.7	1.1	−1.0
XP_021440913.1	Galectin-5-like isoform X2	2	Carbohydrate binding	Biotype 1	−2.3*	1.0	1.1
				Biotype 2	−3.9*	1.4	−1.2
XP_021476056.1	Eukaryotic translation initiation factor 5A	5	Translation	Biotype 1	−1.4	1.1	−1.4
				Biotype 2	−2.4*	−1.3	−1.6
XP_021467048.1	40S ribosomal protein S12	5	Translation	Biotype 1	−1.1	1.4	−1.2
				Biotype 2	−2.2*	1.2	1.3
XP_021456583.1	40S ribosomal protein S29	3	Translation	Biotype 1	−3.4*	1.0	−1.2
				Biotype 2	−2.9*	−1.0	−1.3

Fold change was statistically analyzed in the posterior intestine of rainbow trout exposed to Y. ruckeri biotype 1 (CSF007-82) and biotype 2 (A7959-11) versus control posterior intestine of rainbow trout samples (n = 3 per time point).

* Statistically significant difference according to both ANOVA and post hoc Tukey’s HSD with FDR-adjusted p-value < 0.05 and fold change < −2 or > +2. (Full table is presented in Additional file 4).