Table 2.

List of 25 of the most induced or suppressed proteins in the chicken caecum following colonisation with microbiota of different composition in comparison to protein abundance in the caecum of germ-free chickens (only the significant fold changes to the expression in germ free chickens are shown)

Microbiota INDUCED caecal proteins										Microbiota SUPPRESSED caecal proteins
Protocol	Label-free								Label		Label-free								Label
Microbiota	E. coli			Enterococcus			Tetra	Conv	Conv		E. coli			Enterococcus			Tetra	Conv	Conv
Age (days)	14	28	56	14	28	56	56	56	56		14	28	56	14	28	56	56	56	56
Ig λ		6.61	8.77		2.67		7.30	8.00	20.00	PCNA	1.79								20.00
GRPEL1						1.41			20.00	GSTK1							2.44		3.93
PRSS2					1.72			2.92	17.59	IVD					1.82				3.62
CLIC5				1.76		1.81			15.53	COL6A3		2.72	3.39			6.21			2.50
RPL14					1.44				9.59	UCHL1					1.38				2.44
TXN							1.79		8.40	COL6A2						4.81			2.34
HDGF						1.52			7.83	BAG2					1.61				2.29
CATHL2		2.50							4.12	BASP1								3.99	2.25
PLS1								2.63	3.49	COL6A1		2.02	1.91			4.28			2.20
PACSIN1		1.61							3.21	MYH10			2.07			3.29			2.19
SULT1C3	1.23							1.85	2.95	ACTA1			1.49						2.06
SYNJ2BP		2.04			1.73				2.57	SYNM		1.71							2.03
PAPSS2	1.70								2.49	PYGB		1.74	2.21			4.34			2.01
B2 M			1.58						2.47	PLEKHC1			2.21			5.95			1.95
ASS1								3.57	2.28	POSTN		1.59			1.79				1.78
CALB1								3.04	2.26	SARNP				1.35				1.65	1.75
PSAP	1.95					3.17			2.18	YWHAQ		1.30							1.74
TXNL1							1.44		2.08	EIF4A2		1.61	3.55			6.45			1.71
ISG12-2		1.42							2.00	VAT1					1.41				1.70
PON2					2.64				1.85	MYH11			1.79			2.71			1.67
CDH17		1.19				1.79			1.81	TPPP3			1.24			1.22			1.67
MPP1		1.61	2.26	2.23	2.00	2.66	2.08		1.81	TLN1						3.37			1.66
HSD17B4							2.02		1.78	DPYSL2			1.24						1.61
TST		1.33			1.40	1.20			1.77	COL5A1							2.49	3.69	1.61
CNN3			1.44			1.55			1.75	ATP1A1						3.33			1.60