# Exploring microorganism–host interactions: Emerging organoid models and analytical approaches

**Authors:** Yue Shi, Min Xu, Yanhong Huang, Jing Qu, Shumin Liao, Yingzi Liu, Liang Li

PMC · DOI: 10.1002/mlf2.70053 · mLife · 2026-02-24

## TL;DR

This review explores new organoid models and techniques for studying how microorganisms interact with the human body.

## Contribution

The paper highlights the use of newly developed organoid models for studying host-microbe interactions.

## Key findings

- Organoid models derived from human tissues offer advantages over traditional systems.
- Advanced analytical techniques combined with organoids provide deeper insights into host-microbe interactions.
- The paper discusses limitations and effective uses of these models in interaction studies.

## Abstract

Microorganisms play a vital role in human health through their interactions with the body. Studies of host–microbe mechanisms and interactions are crucial for advancing health management. Recently, the organoid‐based models have provided new platforms in this field. Derived from human tissues, these models offer several advantages over traditional systems and, when combined with advanced analytical techniques, they enable deeper insights into host–microbe interactions. In this review, we summarize the different models and techniques used, with a particular focus on the newly developed organoid models. We discuss how these models can be effectively utilized in microorganism–host interaction studies and address their associated limitations.

## Full-text entities

- **Genes:** NFE2L2 (NFE2 like bZIP transcription factor 2) [NCBI Gene 4780] {aka IMDDHH, NRF2, Nrf-2}, ATOH1 (atonal bHLH transcription factor 1) [NCBI Gene 474] {aka ATH1, DFNA89, HATH1, MATH-1, bHLHa14}, IL1RN (interleukin 1 receptor antagonist) [NCBI Gene 3557] {aka CRMO2, DIRA, ICIL-1RA, IL-1RN, IL-1ra, IL-1ra3}, ATG16L1 (autophagy related 16 like 1) [NCBI Gene 55054] {aka APG16L, ATG16A, ATG16L, IBD10, WDR30}, IL17A (interleukin 17A) [NCBI Gene 3605] {aka CTLA-8, CTLA8, IL-17, IL-17A, IL17, ILA17}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, CAMP (cathelicidin antimicrobial peptide) [NCBI Gene 820] {aka CAP-18, CAP18, CRAMP, FALL-39, FALL39, HSD26}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, LIF (LIF interleukin 6 family cytokine) [NCBI Gene 3976] {aka CDF, DIA, HILDA, MLPLI}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, KRT20 (keratin 20) [NCBI Gene 54474] {aka CD20, CK-20, CK20, K20, KRT21}, NQO1 (NAD(P)H quinone dehydrogenase 1) [NCBI Gene 1728] {aka DHQU, DIA4, DTD, NMOR1, NMORI, QR1}, IL22 (interleukin 22) [NCBI Gene 50616] {aka IL-21, IL-22, IL-D110, IL-TIF, ILTIF, TIFIL-23}, RASAL2 (RAS protein activator like 2) [NCBI Gene 9462] {aka NGAP}, AGFG1 (ArfGAP with FG repeats 1) [NCBI Gene 3267] {aka HRB, RAB, RIP}, MYC (MYC proto-oncogene, bHLH transcription factor) [NCBI Gene 4609] {aka MRTL, MYCC, bHLHe39, c-Myc}, MAP1LC3A (microtubule associated protein 1 light chain 3 alpha) [NCBI Gene 84557] {aka ATG8E, LC3, LC3A, MAP1ALC3, MAP1BLC3}, STAT1 (signal transducer and activator of transcription 1) [NCBI Gene 6772] {aka CANDF7, IMD31A, IMD31B, IMD31C, ISGF-3, STAT91}, IL10RB (interleukin 10 receptor subunit beta) [NCBI Gene 3588] {aka CDW210B, CRF2-4, CRFB4, D21S58, D21S66, IBD25}, CFTR (CF transmembrane conductance regulator) [NCBI Gene 1080] {aka ABC35, ABCC7, CF, CFTR/MRP, MRP7, TNR-CFTR}, IL12B (interleukin 12B) [NCBI Gene 3593] {aka CLMF, CLMF2, IL-12B, IMD28, IMD29, NKSF}, CYP24A1 (cytochrome P450 family 24 subfamily A member 1) [NCBI Gene 1591] {aka CP24, CYP24, HCAI, HCINF1, P450-CC24}
- **Diseases:** UPEC infections (MESH:D004927), UTIs (MESH:D014552), weight loss (MESH:D015431), immune deficiencies (MESH:D007154), pulmonary tuberculosis (MESH:D014397), infected (MESH:D007239), bacterial colonization (MESH:D015179), Bacterial-viral co-infections (MESH:D014777), PA (MESH:D011552), gut (MESH:C536735), Chronic infections (MESH:D000088562), chronic (MESH:D002908), primary sclerosing cholangitis (MESH:D015209), infectious diseases (MESH:D003141), Ctr infection (MESH:D002690), ulcerative colitis (MESH:D003093), tissue damage (MESH:D017695), intestinal infections (MESH:D007410), atopic dermatitis (MESH:D003876), necrosis (MESH:D009336), gastritis (MESH:D005756), Mtb infection (MESH:D014376), OOC (MESH:D000092124), invasive aspergillosis (MESH:D055744), inflammatory bowel disease (MESH:D015212), PCD (MESH:D002925), bacterial infection (MESH:D001424), Gastric (MESH:D013272), CF (MESH:D003550), inflammatory lung diseases (MESH:D008171), cancer (MESH:D009369), H. pylori infection (MESH:D016481), surfactant deficiency (MESH:C580477), respiratory diseases (MESH:D012140), fibrosis (MESH:D005355), gut inflammation (MESH:D007249), hypoxia (MESH:D000860), bladder infection (MESH:D001745), lyme neuroborreliosis (MESH:D020852), genetic disorders (MESH:D030342), Salmonella enterica infection (MESH:D012480), Haemophilus influenzae infections (MESH:D006192), tinea pedis (MESH:D014008), gastric tumorigenesis (MESH:D063646), pneumonia (MESH:D011014), COPD (MESH:D029424), gastric cancer (MESH:D013274), lesions (MESH:D009059), microbial infections (MESH:D015163), hypoxic (MESH:D002534), neurological diseases (MESH:D020271)
- **Chemicals:** cyclic di-GMP (MESH:C062025), macrolide (MESH:D018942), H&amp;E (MESH:D006371), BAA-835 (-), glucose (MESH:D005947), LPS (MESH:D008070), lipids (MESH:D008055), colibactin (MESH:C569566), oxygen (MESH:D010100), indoleacrylic acid (MESH:C001446), vitamin D (MESH:D014807), pyruvate (MESH:D019289), methicillin (MESH:D008712), NO (MESH:D009569), vancomycin (MESH:D014640), iron (MESH:D007501), phospholipids (MESH:D010743)
- **Species:** Clostridioides difficile (species) [taxon 1496], Homo sapiens (human, species) [taxon 9606], Proteus mirabilis (species) [taxon 584], Mycobacterium tuberculosis (species) [taxon 1773], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Helicobacter pylori (species) [taxon 210], Staphylococcus aureus (species) [taxon 1280], Vibrio cholerae (species) [taxon 666], Viruses (acellular root) [taxon 10239], Listeria monocytogenes (species) [taxon 1639], Mycobacteroides abscessus (species) [taxon 36809], Streptococcus sp. 'group B' (species) [taxon 1319], Akkermansia muciniphila (species) [taxon 239935], Moraxella catarrhalis (species) [taxon 480], Fusobacterium nucleatum (species) [taxon 851], Peptostreptococcus (genus) [taxon 1257], Salmonella enterica subsp. enterica serovar Typhi (no rank) [taxon 90370], Klebsiella pneumoniae (species) [taxon 573], Mus musculus (house mouse, species) [taxon 10090], Human rhinovirus sp. (species) [taxon 169066], Borreliella burgdorferi (Lyme disease spirochete, species) [taxon 139], Escherichia coli (E. coli, species) [taxon 562], Cutibacterium acnes (species) [taxon 1747], Aspergillus fumigatus (species) [taxon 746128], Salmonella enterica subsp. enterica serovar Typhimurium (no rank) [taxon 90371], Shigella flexneri (species) [taxon 623], Streptococcus pneumoniae (species) [taxon 1313], Trichophyton rubrum (species) [taxon 5551], Campylobacter jejuni (species) [taxon 197], Mycoplasma (genus) [taxon 2093], Salmonella enterica (species) [taxon 28901], Bifidobacterium adolescentis (species) [taxon 1680], Enterococcus faecalis (species) [taxon 1351]
- **Mutations:** rs2241880
- **Cell lines:** HBE — Homo sapiens (Human), Transformed cell line (CVCL_0287), Caco-2 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0025), NHBE — Homo sapiens (Human), Transformed cell line (CVCL_S124), HBMEC — Homo sapiens (Human), Transformed cell line (CVCL_0307), HUVEC — Homo sapiens (Human), Finite cell line (CVCL_2959), SAEC — Sparus aurata (Gilthead sea bream), Embryonic stem cell (CVCL_A7MV), HAEC — Homo sapiens (Human), Transformed cell line (CVCL_C0EQ), PHK — Homo sapiens (Human), Transformed cell line (CVCL_XX44), MEF — Mus musculus (Mouse), Finite cell line (CVCL_9115), AECII — Homo sapiens (Human), Telomerase immortalized cell line (CVCL_VR37), HUC — Homo sapiens (Human), Transformed cell line (CVCL_3798)

## Full text

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## Figures

3 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12948489/full.md

## References

211 references — full list in the complete paper: https://tomesphere.com/paper/PMC12948489/full.md

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Source: https://tomesphere.com/paper/PMC12948489