# Inflammatory bowel disease through the lens of microbe-host interactions: immunomodulation, metabolic effects, and genetic susceptibility in microbiota dysbiosis

**Authors:** Qinghua Zou, Wumiao Zhang, Hua Xie, Shuyan Ying, Xueliang Zeng, Yihang Yao, Dingcheng Zeng, Jiulong Wang, Cheng Zhang, Fan Meng

PMC · DOI: 10.3389/fcimb.2026.1745929 · Frontiers in Cellular and Infection Microbiology · 2026-02-16

## TL;DR

This review explores how gut microbiome imbalances contribute to inflammatory bowel disease by affecting immunity, metabolism, and genetics.

## Contribution

The paper provides a systematic analysis of microbe-host interactions in IBD, integrating immune, metabolic, and genetic factors.

## Key findings

- Microbiota dysbiosis is linked to immune system dysfunction in IBD.
- Bacterial metabolites influence the progression of inflammatory bowel disease.
- Genetic susceptibility interacts with microbiota to affect IBD risk.

## Abstract

Inflammatory bowel disease (IBD), including ulcerative colitis, Crohn’s disease, and inflammatory bowel disease-unclassified, is a complex intestinal disease influenced by microbial factors, genetic and environmental. IBD has become a global disease with an increasing prevalence, endangering human health worldwide. Through its interactions with host immunity, bacterial metabolites, and genetic components, the intestinal microbiome plays a crucial role in initiating and advancing IBD. Treatment for IBD includes not only corticosteroids, aminosalicylates, antibiotics, TNF-α, α4β7 integrins, IL-12/23 antibodies, and small molecule antibodies, but also complementary and alternative medical therapies such as probiotics and prebiotics. This review primarily explores the relationship between dysbiosis of the microbiota and IBD, including the immune system, metabolites, and genetics related to microorganisms, to provide a deeper and more systematic understanding of the mechanisms linking microbial imbalance to IBD.

## Linked entities

- **Diseases:** inflammatory bowel disease (MONDO:0005265), ulcerative colitis (MONDO:0005101), Crohn’s disease (MONDO:0005011)

## Full-text entities

- **Genes:** IL10 (interleukin 10) [NCBI Gene 3586] {aka CSIF, GVHDS, IL-10, IL10A, TGIF}, NLRP3 (NLR family pyrin domain containing 3) [NCBI Gene 114548] {aka AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1}, Il1b (interleukin 1 beta) [NCBI Gene 16176] {aka IL-1beta, Il-1b}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, IL23R (interleukin 23 receptor) [NCBI Gene 149233] {aka PSORS7}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, NLRP10 (NLR family pyrin domain containing 10) [NCBI Gene 338322] {aka CLR11.1, NALP10, NOD8, PAN5, PYNOD}, CLDN4 (claudin 4) [NCBI Gene 1364] {aka CPE-R, CPER, CPETR, CPETR1, WBSCR8, hCPE-R}, CARD9 (caspase recruitment domain family member 9) [NCBI Gene 64170] {aka CANDF2, IMD103, hCARD9}, F11R (F11 receptor) [NCBI Gene 50848] {aka CD321, JAM, JAM1, JAMA, JCAM, KAT}, NOD1 (nucleotide binding oligomerization domain containing 1) [NCBI Gene 10392] {aka CARD4, CLR7.1, NLRC1, hNod1}, IL22 (interleukin 22) [NCBI Gene 50616] {aka IL-21, IL-22, IL-D110, IL-TIF, ILTIF, TIFIL-23}, NR1H4 (nuclear receptor subfamily 1 group H member 4) [NCBI Gene 9971] {aka BAR, FXR, HRR-1, HRR1, PFIC5, RIP14}, Nfkb1 (nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105) [NCBI Gene 18033] {aka NF-KB1, NF-kappaB, NF-kappaB1, p105, p50, p50/p105}, IL17A (interleukin 17A) [NCBI Gene 3605] {aka CTLA-8, CTLA8, IL-17, IL-17A, IL17, ILA17}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, TLR2 (toll like receptor 2) [NCBI Gene 7097] {aka CD282, TIL4}, Tnf (tumor necrosis factor) [NCBI Gene 21926] {aka DIF, TNF-a, TNF-alpha, TNFSF2, TNFalpha, Tnfa}, LAMB1 (laminin subunit beta 1) [NCBI Gene 3912] {aka CLM, LIS5, LKBMH, LUCAO}, Atg5 (autophagy related 5) [NCBI Gene 11793] {aka 2010107M05Rik, 3110067M24Rik, Apg5l, Atg5l, Paddy}, IL23A (interleukin 23 subunit alpha) [NCBI Gene 51561] {aka IL-23, IL-23A, IL23P19, P19, SGRF}, CSF2 (colony stimulating factor 2) [NCBI Gene 1437] {aka CSF, GMCSF}, Atg16l1 (autophagy related 16 like 1) [NCBI Gene 77040] {aka 1500009K01Rik, Apg16l, Atg16l, WDR30}, CLDN3 (claudin 3) [NCBI Gene 1365] {aka C7orf1, CPE-R2, CPETR2, HRVP1, RVP1}, Tab3 (TGF-beta activated kinase 1/MAP3K7 binding protein 3) [NCBI Gene 66724] {aka 4921526G09Rik, Map3k7ip3, mKIAA4135}, PYCARD (PYD and CARD domain containing) [NCBI Gene 29108] {aka ASC, CARD5, TMS, TMS-1, TMS1}, CD79A (CD79a molecule) [NCBI Gene 973] {aka IGA, IGAlpha, MB-1, MB1}, Nlrp3 (NLR family, pyrin domain containing 3) [NCBI Gene 216799] {aka AGTAVPRL, AII/AVP, Cias1, FCAS, FCU, MWS}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, NUP62 (nucleoporin 62) [NCBI Gene 23636] {aka IBSN, SNDI, p62}, CASP1 (caspase 1) [NCBI Gene 834] {aka ICE, IL1BC, P45}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, Tlr4 (toll-like receptor 4) [NCBI Gene 21898] {aka Lps, Ly87, Ran/M1, Rasl2-8}, GPBAR1 (G protein-coupled bile acid receptor 1) [NCBI Gene 151306] {aka BG37, GPCR19, GPR131, M-BAR, TGR5}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, Il22 (interleukin 22) [NCBI Gene 50929] {aka IL-22, IL-22a, ILTIFa, If2b1, Iltif}, Atg12 (autophagy related 12) [NCBI Gene 67526] {aka 4931423H11Rik, A330058M13Rik, Apg12l, Atg12l}, GNA12 (G protein subunit alpha 12) [NCBI Gene 2768] {aka HG1M1, NNX3, RMP, gep}, Tlr3 (toll-like receptor 3) [NCBI Gene 142980], Tab1 (TGF-beta activated kinase 1/MAP3K7 binding protein 1) [NCBI Gene 66513] {aka 2310012M03Rik, Map3k7ip1, b2b449Clo}, IL2 (interleukin 2) [NCBI Gene 3558] {aka IL-2, TCGF, lymphokine}, Nod2 (nucleotide-binding oligomerization domain containing 2) [NCBI Gene 257632] {aka ACUG, BLAU, CD, Card15, F830032C23Rik, IBD1}, PRKAA2 (protein kinase AMP-activated catalytic subunit alpha 2) [NCBI Gene 5563] {aka AMPK, AMPK2, AMPKa2, PRKAA}, Ifng (interferon gamma) [NCBI Gene 15978] {aka IFN-g, If2f, Ifg}, IL12B (interleukin 12B) [NCBI Gene 3593] {aka CLMF, CLMF2, IL-12B, IMD28, IMD29, NKSF}, FOXP3 (forkhead box P3) [NCBI Gene 50943] {aka AIID, DIETER, IPEX, JM2, PIDX, XPID}, TNFRSF1B (TNF receptor superfamily member 1B) [NCBI Gene 7133] {aka CD120b, TBPII, TNF-R-II, TNF-R75, TNFBR, TNFR1B}, RELA (RELA proto-oncogene, NF-kB subunit) [NCBI Gene 5970] {aka AIF3BL3, CMCU, NFKB3, p65}, Igha (immunoglobulin heavy constant alpha) [NCBI Gene 238447] {aka IgA, Igh-2}, Xbp1 (X-box binding protein 1) [NCBI Gene 22433] {aka D11Ertd39e, TREB-5, TREB5, XBP-1}, Il6 (interleukin 6) [NCBI Gene 16193] {aka Il-6}, Fut2 (fucosyltransferase 2) [NCBI Gene 14344] {aka MFUT-II}, Card9 (caspase recruitment domain family, member 9) [NCBI Gene 332579] {aka Gm782}, IL21 (interleukin 21) [NCBI Gene 59067] {aka CVID11, IL-21, Za11}, Dock2 (dedicator of cyto-kinesis 2) [NCBI Gene 94176] {aka CED-5, Hch, MBC}, CDH1 (cadherin 1) [NCBI Gene 999] {aka Arc-1, BCDS1, CD324, CDHE, ECAD, LCAM}, Il18 (interleukin 18) [NCBI Gene 16173] {aka Igif, Il-18}, Map3k7 (mitogen-activated protein kinase kinase kinase 7) [NCBI Gene 26409] {aka B430101B05, Tak1}, HCAR2 (hydroxycarboxylic acid receptor 2) [NCBI Gene 338442] {aka GPR109A, HCA2, HM74a, HM74b, NIACR1, PUMAG}
- **Diseases:** colorectal cancer (MESH:D015179), PP (MESH:D010300), pancreatic duct adenocarcinoma (MESH:D010190), folate deficiency (MESH:C562799), immunodeficiency (MESH:D007153), diarrheal (MESH:D004403), hyperlipidemia (MESH:D006949), rheumatoid arthritis (MESH:D001172), metastasis (MESH:D009362), Clostridioides difficile infection (MESH:D003015), inflammation (MESH:D007249), ulcer (MESH:D014456), Microbial dysbiosis (MESH:D064806), diabetes (MESH:D003920), gastrointestinal (MESH:D005767), cancer (MESH:D009369), colitis (MESH:D003092), CD (MESH:D003424), Alzheimer's disease (MESH:D000544), cardiovascular disease (MESH:D002318), perianal lesions (MESH:D000694), infections (MESH:D007239), diarrhea (MESH:D003967), carcinogenesis (MESH:D063646), immune-mediated diseases (MESH:C567355), hyperhomocysteinemia (MESH:D020138), autoimmunity (MESH:D001327), IBD (MESH:D015212), type 2 diabetes (MESH:D003924), inflammatory cytokines (MESH:D000080424), enteric bacterial infections (MESH:D004751), chronic (MESH:D002908), post-COVID-19 syndrome (MESH:D000094024), UC (MESH:D003093), intestinal disease (MESH:D007410), immune dysregulation (OMIM:614878), metabolic (MESH:D008659)
- **Chemicals:** oxygen (MESH:D010100), ustekinumab (MESH:D000069549), sugar (MESH:D000073893), AMP (MESH:D000089882), TMAO (MESH:C005855), linoleic acid (MESH:D019787), histamine (MESH:D006632), L-ornithine (MESH:D009952), Bile acids (MESH:D001647), phosphatidylethanolamine (MESH:C483858), DCA (MESH:D003840), Hydrogen sulfide (MESH:D006862), 5-aminosalicylic acid (MESH:D019804), ABO antigens (-), aminosalicylates (MESH:D010131), carbon (MESH:D002244), emodin (MESH:D004642), LCA (MESH:D008095), monosaccharides (MESH:D009005), propionate (MESH:D011422), Lactic acid (MESH:D019344), imidazole propionate (MESH:C018976), Polysaccharides (MESH:D011134), Butyrate (MESH:D002087), niacin (MESH:D009525), S-adenosylmethionine (MESH:D012436), spermine (MESH:D013096), LPS (MESH:D008070), vitamin B3 (MESH:D009536), luminal (MESH:D010634), Prebiotics (MESH:D056692), UDCA (MESH:D014580), taurine (MESH:D013654), Polyphenols (MESH:D059808), SCFA (MESH:D005232), trimethylamine (MESH:C023336), Folate (MESH:D005492), AMPs (MESH:C014308), Anthraquinone (MESH:D000880), indole (MESH:C030374), Tryptophan (MESH:D014364), kynurenine (MESH:D007737), indole-3-acetic acid (MESH:C030737), indole-3-aldehyde (MESH:C012381), branched-chain amino acids (MESH:D000597), tryptamine (MESH:C030820), acetate (MESH:D000085)
- **Species:** Candida albicans (species) [taxon 5476], Porphyromonas gingivalis (species) [taxon 837], Bifidobacterium (genus) [taxon 1678], Lactobacillus (genus) [taxon 1578], Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090], Pseudomonas aeruginosa (species) [taxon 287], Helicobacter pylori (species) [taxon 210], Campylobacter jejuni (species) [taxon 197], Pseudomonadota (proteobacteria, phylum) [taxon 1224], Bacillota (clostridial firmicutes, phylum) [taxon 1239], Bacteroidia (class) [taxon 200643], Actinomycetota (actinobacteria, phylum) [taxon 201174], Shigella flexneri (species) [taxon 623]
- **Mutations:** rs41313262, rs2066844, rs2066847, rs11209026, p.Gly908Arg, rs76418789

## Full text

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## Figures

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## References

155 references — full list in the complete paper: https://tomesphere.com/paper/PMC12950560/full.md

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Source: https://tomesphere.com/paper/PMC12950560