# Gut–Brain Axis in Inflammatory Bowel Disease: Pathogenesis and Therapeutics

**Authors:** Samantha Perry, Lekha Pillarisetti, Tamara Gelfman, Devendra K. Agrawal

PMC · DOI: 10.26502/aimr.0227 · Archives of internal medicine research · 2026-01-21

## TL;DR

This paper explores how gut health and brain function are connected in inflammatory bowel disease, and how this connection can guide new treatments.

## Contribution

The paper introduces a holistic model linking gut dysbiosis, immune activation, and neuroinflammation to improve IBD treatment.

## Key findings

- Gut microbiome disruption promotes inflammation and affects mental health through the gut-brain axis.
- Microbial metabolites, vagal tone, and the HPA axis form a feedback loop that perpetuates IBD symptoms.
- Therapies like fecal microbiota transplantation and phage therapy show promise in addressing gut-brain interactions.

## Abstract

Inflammatory Bowel Disease (IBD), encompassing Crohn’s disease and ulcerative colitis, is a chronic inflammatory disorder of the gastrointestinal tract driven by complex interactions between genetic susceptibility, environmental triggers, microbial dysbiosis, and immune dysregulation. The gut microbiome, composed primarily of Firmicutes and Bacteroidetes, plays a crucial role in maintaining intestinal barrier integrity, immune balance, and neuroimmune signaling. Disruption of this microbial ecosystem is characterized by loss of beneficial short chain fatty acid producing bacteria and expansion of pathogenic species which promotes mucosal inflammation, cytokine release, and neuroimmune signaling that can disrupt mental health through the gut-brain axis. Emerging evidence links microbial metabolites, vagal tone, and the hypothalamic-pituitary-adrenal axis in a feedback loop that perpetuates inflammation and alters mood regulation. Current therapeutic approaches include diet modification, osteopathic manipulative treatments, fecal microbiota transplantation and phage therapy. This article focuses on understanding mechanisms linking dysbiosis, immune activation, and neuroinflammation to guide future interventions. A holistic model addressing the gut-brain axis holds the greatest promise for improving outcomes and personalizing care for IBD.

## Linked entities

- **Diseases:** Inflammatory Bowel Disease (MONDO:0005265), Crohn’s disease (MONDO:0005011), ulcerative colitis (MONDO:0005101)

## Full-text entities

- **Genes:** CDC42 (cell division cycle 42) [NCBI Gene 998] {aka CDC42Hs, G25K, TKS}, REN (renin) [NCBI Gene 5972] {aka ADTKD4, HNFJ2, RTD}, ATG16L1 (autophagy related 16 like 1) [NCBI Gene 55054] {aka APG16L, ATG16A, ATG16L, IBD10, WDR30}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, NR1H4 (nuclear receptor subfamily 1 group H member 4) [NCBI Gene 9971] {aka BAR, FXR, HRR-1, HRR1, PFIC5, RIP14}, TLR4 (toll like receptor 4) [NCBI Gene 7099] {aka ARMD10, CD284, TLR-4, TOLL}, ACE2 (angiotensin converting enzyme 2) [NCBI Gene 59272] {aka ACEH}, ORMDL3 (ORMDL sphingolipid biosynthesis regulator 3) [NCBI Gene 94103], IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, NOD2 (nucleotide binding oligomerization domain containing 2) [NCBI Gene 64127] {aka ACUG, BLAU, BLAUS, CARD15, CD, CLR16.3}, NLRP3 (NLR family pyrin domain containing 3) [NCBI Gene 114548] {aka AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1}, GPBAR1 (G protein-coupled bile acid receptor 1) [NCBI Gene 151306] {aka BG37, GPCR19, GPR131, M-BAR, TGR5}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}
- **Diseases:** Dysbiosis (MESH:D064806), cognitive deficits (MESH:D003072), IBS (MESH:D007410), COVID-19 (MESH:D000086382), depression (MESH:D003866), neurological dysfunction (MESH:D009461), diabetes (MESH:D003920), mood and cognitive disorders (MESH:D019964), Inflammation (MESH:D007249), Barrier dysfunction (MESH:C536830), long COVID (MESH:D000094024), anxiety (MESH:D001007), neuropsychiatric symptoms (MESH:D001523), immune dysregulation (OMIM:614878), Mental Health (OMIM:603663), mucosal dysfunction (MESH:D052016), colitis (MESH:D003092), neuroinflammation (MESH:D000090862), gut disorders (MESH:C536735), infections (MESH:D007239), Crohn's disease (MESH:D003424), Clostridium difficile infections (MESH:D003015), IBD (MESH:D015212), chronic low back pain (MESH:D017116), toxicity (MESH:D064420), ulcerative colitis (MESH:D003093), neurotoxic (MESH:D020258)
- **Chemicals:** carbohydrates (MESH:D002241), acetate (MESH:D000085), Prebiotics (MESH:D056692), quinolinic acid (MESH:D017378), lactulose (MESH:D007792), lactosucrose (MESH:C081752), serotonin (MESH:D012701), bile acid (MESH:D001647), tryptophan (MESH:D014364), cortisol (MESH:D006854), propionate (MESH:D011422), kynurenine (MESH:D007737), inulin (MESH:D007444), butyrate (MESH:D002087), oligofructose (MESH:C120489), SCFA (MESH:D005232), SCFAa (-)
- **Species:** Pseudomonadota (proteobacteria, phylum) [taxon 1224], Mus musculus (house mouse, species) [taxon 10090], Severe acute respiratory syndrome coronavirus 2 (no rank) [taxon 2697049], Escherichia coli (E. coli, species) [taxon 562], Listeria monocytogenes (species) [taxon 1639], Bacteroidia (class) [taxon 200643], gut metagenome (species) [taxon 749906], Bacillota (clostridial firmicutes, phylum) [taxon 1239], Faecalibacterium prausnitzii (species) [taxon 853], Homo sapiens (human, species) [taxon 9606], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Roseburia hominis (species) [taxon 301301]

## Full text

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## References

45 references — full list in the complete paper: https://tomesphere.com/paper/PMC12818948/full.md

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Source: https://tomesphere.com/paper/PMC12818948