A/E	attaching and effacing
AGR2	anterior gradient 2
AIM	absence in melanoma
AJs	adherens junctions
ALRs	absence in melanoma-like receptors
AMP	adenosinmonophosphate
AMPK	AMP-activated protein kinase
AMPs	antimicrobial peptides
APCs	antigen-presenting cells
CaMKK2	calcium/calmodulin-dependent kinase 2
CAZymes	carbohydrate-active enzymes
CD	Crohn’s disease
ClCa1	calcium-activated chloride channel 1
CLR	C-type lectin receptors
Convr	conventionally raised
CR2	cryptdin-2
CRS	cryptdin related sequence
DAMPs	damage-associated molecular patterns
DCs	dendritic cells
Dll	Delta-like
DSCs	desmocollin types
DSGs	desmoglein types
DSS	dextran-sulfate sodium
EGF	epidermal growth factor
EHEC	enterohaemorrhagic Escherichia coli
Emc3	endoplasmic reticulum membrane complex subunit 3
EPEC	enteropathogenic Escherichia coli
ER	endoplasmic reticulum
ERK	extracellular signal-regulated kinase
FAE	follicle-associated epithelium
Fc	crystallizable fragment
FCGBP	Fc-globulin binding protein
GALT	gut-associated lymphoid tissue
GAPs	goblet cells-associated antigen passages
GCs	goblet cells
GF	germ-free
GI	gastrointestinal
GP2	Glycoprotein 2
GVHD	graft-versus-host disease
HD5	human α-defensin5
IBD	inflammatory bowel diseases
IBDU	inflammatory bowel diseases-unclassified
icGCs	intercrypt goblet cells
IECs	intestinal epithelial cells
ISCs	intestinal stem cells
JAMs	junctional adhesion molecules
JNK	c-Jun N-terminal kinase
Lgr5+	leucine-rich repeat containing G protein-coupled receptor 5
LPS	lipopolysaccharide
Lypd8	Ly6/Plaur domain-containing 8
M	microfold
MAMPs	microbial-associated molecular patterns
MAPK	mitogen-activated protein kinase
MMP	metalloproteinase
MUC	mucin
MyD88	myeloid differentiation primary response gene-88
NEC	necrotizing enterocolitis
NLRs	nucleotide-binding oligomerization domain-like receptors
NOD	nucleotide-binding oligomerization domain
pIgR	polymeric immunoglobulin receptor
PKC	protein kinase C
PRRs	pattern recognition receptors
RegIII	regenerating islet-derived protein 3
RELMβ	resistin-like molecule β
RIG-I	retinoic acid-inducible gene I
RLRs	retinoic acid-inducible gene I-receptors
SCFAs	short-chain fatty acids
SED	subepithelial dome
senGCs	sentinel goblet cells
sIgA	secretory immunoglobulin A
sPLA2	secretory phospholipase A2
T3SS	type III secretion system
Tff3	trefoil factor family peptide 3
Tir	translocated intimin receptor
TIR	Toll/interleukin-1 receptor
TJs	tight junctions
TLRs	Toll-like receptors
TRIF	Toll/interleukin-1 receptor-domain–containing adapter-inducing interferon beta
UC	ulcerative colitis
ZG16	zymogen granule membrane protein 16
ZO	zonula occludens