Table 1.

Invasive and noninvasive enteric bacteria that have been studied using human organoids and enteroids and the respective research focus. *Enteroid – no mesenchyme; from duodenum, jejunum, or ileum. **Colonoid – no mesenchyme; from colon or cecum. ***HIO: human induced pluripotent stem cell derived-intestinal organoid (epithelium and mesenchyme).

Bacteria	Origin	Intestinal section	Type	Research focus	Refs
Invasive pathogens
Shigella flexneri	Human Biopsy	Duodenum, Ileum, Colon	2D Enteroid*, 2D Colonoid**	Invasion, intracellular replication, host gene expression	21
	Human Biopsy	Duodenum, Jejunum, Ileum, Colon	2D Enteroid, 2D Colonoid	Invasion, M cells, intracellular replication, mucus changes, cytokine secretion	22
	Human Biopsy	Cecum	2D Colonoid	Testing bacteriophage therapy	23
	Human Biopsy	Colon	2D Colonoid	Adherence factor expression	24
Listeria monocytogenes	Human Biopsy	Ileum	3D Enteroid	Reversing enteroid polarity to facilitate apical infection	25
Salmonella enterica serovar Typhimurium	iPSC (dermal fibroblasts)	n/a	3D HIO***	Invasion, infection-associated transcriptional changes	26
	iPSC	n/a	3D HIO	Organoids derived from healthy iPSC and infant IBD patient; role of IL-22 in controlling infection	27
	Human Biopsy	Ileum	3D Enteroid	Reversing enteroid polarity to facilitate apical infection	25
Salmonella enterica serovar Typhi	Human Biopsy	Ileum	2D Enteroid	Cytoskeletal changes during infection	28
Noninvasive pathogens
Enterotoxigenic E. coli	Human biopsy	Duodenum, jejunum	3D Enteroid	Toxin-mediated inhibition of ion transporter NHE3	29
	Human biopsy	Jejunum	2D Enteroid	Toxin-induced polarized cyclic nucleotide secretion	30
	Human biopsy	Jejunum	2D Enteroid	ST-induced pathology in Intestine Chip model	31
	Human biopsy	Jejunum, ileum	2D Enteroid	Minor adhesin-mediated adherence & cyclic nucleotide production	32
	Human biopsy	Duodenum, jejunum, colon	2D Enteroid, 2D Colonoid	Effect of macrophage co-culture on infection and epithelial cell differentiation	33
Enterohemorrhagic E. coli	Human biopsy	Colon	2D Colonoid	Role of mucus and SPATE EspP in infection	34
	Human biopsy	Colon	2D Colonoid	SPATE EspP-induced ion transport	35
	iPSC	n/a	3D HIO	Pathogen vs. commensal effect on epithelium; co-culture with neutrophils	36
	iPSC	n/a	3D HIO	Shiga toxin effects and mesenchymal-epithelial cross talk	37
Enteroaggregative E. coli	Human biopsy	Duodenum, ileum, colon	2D Enteroid, 2D Colonoid	Adherence patterns by donor and intestinal segment type	38
	Human biopsy	Colon	2D Colonoid	SPATE SepA-induced ion transport	35
Enteropathogenic E. coli	Human biopsy	Duodenum, jejunum, colon	2D Enteroid, 2D Colonoid	Effect of macrophage co-culture on infection and epithelial cell differentiation	33
Clostridium difficile	iPSC	n/a	3D HIO	Viable bacterial infection, toxin-induced pathology	39
	Human biopsy	Colon	3D Colonoid	Toxin receptor expression	40
	Human biopsy	Jejunum	2D Enteroid	Toxin-induced pathology, toxin receptor expression	41
	Human biopsy	Colon	3D Colonoid	Toxin binding to intestinal receptors	42
	iPSC	n/a	3D HIO	Role of mucus in infection	43
	iPSC	n/a	3D HIO	Dysregulation of ion transporter NHE3 and microbiota	44
	iPSC	n/a	3D HIO	Human alpha-defensin-1 and toxin neutralization	45
	iPSC	n/a	3D HIO	Bacitracin as defense against toxins	46
Vibrio cholerae	Human biopsy	Duodenum, jejunum	3D Enteroid	Toxin-mediated inhibition of ion transporter NHE3	29
	Human biopsy	Ileum, colon	2D Enteroid, 2D Colonoid	Toxin-induced cyclic nucleotide production	47
	Human biopsy	Rectum	3D Enteroid	Toxin inhibitors to reduce pathology	48
	Human biopsy	Rectum	3D Enteroid	Toxin inhibitors to reduce pathology	49
	Human biopsy	Jejunum	2D Enteroid	Toxin inhibitors targeting a non-canonical binding site	50
Extraintestinal pathogenic E. coli (ExPEC)	Human biopsy	Jejunum	2D Enteroid	Pilus-mediated adherence & invasion	51
Bacteria causing necrotizing enterocolitis (NEC)	Human biopsy, fetal	Duodenum	2D & 3D Enteroid	Immune response, maturation, & barrier function in fetal vs. adult intestine	52
	Human biopsy, fetal	Ileum	3D Enteroid	Anti-inflammatory metabolite as probiotic	53
	Human biopsy, fetal	Ileum	3D Enteroid	Human milk oligosaccharides as probiotic	54
	Human biopsy, fetal	Not specified	3D Enteroid	Cell stress and apoptosis of intestinal stem cells	55
	Human biopsy, fetal	Ileum	3D Enteroid	Impaired signaling and its role in dysfunction of intestinal regeneration	56