Table 1.
Studies reporting host-pathogenic bacteria interactions using organoids
| Bacteria | Source of organoid | Culture system | Key findings | References |
|---|---|---|---|---|
| Shigella flexneri | Human small intestine, colon | ODM | ↑IL-8 secretion | (24) |
| Human (unspecified) | ODM | ↑IL-8 secretion | (34) | |
| ↑Muc2 expression | ||||
| Human small intestine | ODM | Basolateral infection, | (35) | |
| ↑Pro-inflammatory signals | ||||
| Human small intestine, colon | ODM | Testing the therapeutic effect of bacteriophage | (36) | |
| Salmonella enterica | Human small intestine | 3D-microinjection | ↓Organoid growth | (38) |
| ↑NF-kB signaling | ||||
| ↑Pro-inflammatory cytokine, | ||||
| ↓LGR5 expression | ||||
| Human/mouse small intestine | 3D-microinjection | Recapitulation of early infection cycle, TTSS-1 is required for colonization | (39) | |
| Human iPSC | 3D-microinjection | ↑Proinflammatory cytokines, InvA-dependent invasion | (40) | |
| Human ESC | 3D-microinjection | T3SS-1-dependent invasion, | (41) | |
| ↑Inflammatory chemokine | ||||
| Human small intestine, colon | Apical-out | Cytoskeletal rearrangement | (30) | |
| Human small intestine | ODM | YrbE-dependent inflammatory response | (42) | |
| EHEC | Human colon | ODM | ↓Colonic mucus | (45) |
| Brush border damage | ||||
| Human colon | ODM | Change in active ion transport | (47) | |
| ETEC | Human small intestine | ODM | PDE5-mediated restriction of intracellular cGMP accumulation | (50) |
| Pig small intestine | ODM | F4-mediated adhesion | (51) | |
| pks+ E. coli | Human colon | ODM | Long-term exposure caused mutational signature | (54) |
| Human/mouse colon | ODM/Shredded 3D | ↑Proliferation Wnt-independent growth | (21) | |
| Clostridium difficile | Human iPSC, ESC | 3D-microinjection | ↓Epithelial barrier function | (11) |
| Human iPSC | 3D-microinjection | ↓NHE3 expression | (56) | |
| Human/mouse colon | 3D derived from infected mice/3D-toxin treatment | ↓Adherens junction, | (57) | |
| ↓Epithelial regeneration | ||||
| Human small intestine | ODM | Adherence mechanism in human ODM model | (58) | |
| Human iPSC | 3D-toxin treatment | ↓Transmembrane adhesion protein | (18) | |
| Human iPSC | 3D-toxin treatment | Protective effect of HSA | (59) | |
| Human (unspecified) | 3D-toxin treatment | Protective effect of antibiotic Bacitracin | (60) | |
| Human/mouse iPSC | 3D-microinjection | Protective effect of Paneth cells on C. difficile-infected IO | (19) | |
| Vibrio cholerae | Mouse small intestine | 3D-toxin treatment | ↑cAMP pathway | (62) |
| Human small intestine | 3D-toxin treatment | Testing CT inhibitor with swelling assay | (63) | |
| Human small intestine | 3D-toxin treatment | O-blood group exhibited different responses to CT | (64) | |
| Listeria monocytogenes | Mouse small intestine | Shredded 3D | ↑Organoid growth | (20) |
| ↓Lgr5+ ISCs | ||||
| ↑Paneth cells | ||||
| Mouse small intestine | Shredded 3D | ↑TNFa | (66) | |
| ↑Paneth cell, goblet cell | ||||
| ↓Notch signaling | ||||
| Mouse small intestine | Shredded 3D | ↑TLR 2/4 signaling | (67) | |
| Human small intestine, colon | Apical-out | Binding with basolateral receptor | (30) | |
| Mouse small intestine | 3D-microinjection | InlA-Ecad-dependent translocation through goblet cells | (68) | |
| Mouse (unspecified) | Shredded 3D | TMT-based quantitative proteomic analysis in different strains | (69) | |
| Campylobacter jejuni | Mouse small intestine | 3D-bacterial lysate | DNA damage | (72) |
| Fusobacterium nucleatum | Human (unspecified) | ODM-OMV treatment | ↑TNF, NF-κB, MAPK signaling | (74) |
| Porphyromonas gingivalis | Mouse small intestine | 3D | Regulation of cell composition | (75) |