Table 1. Gene ontology (GO) analysis of differentially expressed genes (biological process).

GO ID	Description	#Genes	Enrichment	p-value	Genes
GO:0098542	Defense response to other organism	3	12.44	0.001	BPI, RSAD2, SLPI
GO:0001817	Regulation of cytokine production	3	11.54	0.002	LUM, BPI, RSAD2
GO:0001816	Cytokine production	3	10.57	0.002	LUM, BPI, RSAD2
GO:0051707	Response to other organism	3	7.90	0.005	BPI, RSAD2, SLPI
GO:0043207	Response to external biotic stimulus	3	7.87	0.005	BPI, RSAD2, SLPI
GO:0009607	Response to biotic stimulus	3	7.37	0.006	BPI, RSAD2, SLPI
GO:0042742	Defense response to bacterium	2	15.81	0.007	BPI, SLPI
GO:0010959	Regulation of metal ion transport	2	14.81	0.008	ATP2C2, KCNE3
GO:0010466	Negative regulation of peptidase activity	2	14.09	0.008	SLPI, SPAI-2
GO:0000730	DNA recombinase assembly	1	116.98	0.009	DMC1

BPI: Bactericidal/permeability-increasing protein, RSAD2: Radical SAM domain-containing 2, SLPI: Secretory leukocyte protease inhibitor, LUM: Lumican, ATP2C2: ATPase secretory pathway Ca2+ transporting 2, KCNE3: Potassium voltage-gated channel, Isk-related family, member 3, SPAI-2: Sodium/potassium ATPase inhibitor-2, DMC1: Disrupted meiotic cDNA 1. WebGestalt was used to perform analysis of DEGs co-occurrence in the ileum of piglets by comparison of the control and probiotics groups, and identified 10 gene ontologies in the biological process range. Seven out of 10 gene ontologies were significantly associated with immune response.