Microbiome–Lactate–Lactylation Axis in Gastrointestinal Cancers: From Warburg Effect to Epigenetic Reprogramming

English companion to 20260724_v2.md (51 references) | Gap list: evidence_gaps.md | Evidence summary: evidence_summary.md

1. Lactate as a Master Regulator in the TME

1.1 From Metabolic Waste to Signaling Hub

Cancer cells preferentially rely on aerobic glycolysis (Warburg effect), elevating TME lactate to 10–40 mM vs. 1.5–3 mM in normal tissue [Li et al., 2022]. The lactate shuttle hypothesis describes intercellular lactate trafficking via MCT1/MCT4 transporters. Tumor-associated fibroblasts (CAFs) engage in a “reverse Warburg effect,” producing lactate that feeds adjacent cancer cells.

1.2 Immunosuppressive Functions

Lactate coordinates immune suppression through three parallel mechanisms:

  • M2 macrophage polarization: Microbial D-lactate induces M2 polarization more potently than host L-lactate via distinct receptors (GPR132 vs. GPR81) and signaling cascades [Han SL et al., 2023]
  • CD8+ T cell inhibition: p38/JNK-mediated suppression of IFN-γ and TNF-α [Chen et al., 2025]
  • Treg metabolic advantage: Foxp3+ Tregs upregulate LDHB to oxidize lactate in low-glucose, high-lactate environments, gaining a metabolic edge over CD8+ effector T cells [Angelin et al., 2017]
  • Dendritic cell dysfunction: Acidic lactate environment impairs antigen presentation

1.3 Angiogenesis and Metastasis

Lactate induces VEGF via HIF-1α-independent NF-κB/PI3K pathways and promotes EMT through H3K18 lactylation of Snail/Twist transcription factors [Fang et al., 2026].

2. Lactylation: A Metabolic-Epigenetic Interface

2.1 Discovery and Biochemical Basis

Histone lysine lactylation (Kla) was discovered in 2019 as a novel PTM directly regulated by intracellular lactate concentration [Zhang et al., 2019]. The “lactate clock” hypothesis proposes that Kla’s delayed kinetics (peaking at 16–24 h vs. ~6 h for acetylation) couples sustained metabolic stress to persistent gene expression changes.

2.2 Writers and Erasers

  • Writers: p300/CBP (histone lactyltransferases), AARS1/AARS2 (non-canonical, tRNA synthetase-linked), HBO1/KAT7 (H3K9la-specific) [Niu et al., 2024]
  • Erasers: HDAC1–3 (strong delactylase activity), SIRT1–3 (weaker); SIRT3 specifically erases H3K9la and cyclin E2 Kla in HCC [Yang et al., 2026]
  • CRC-specific lactylome heterogeneity was recently reviewed [Wei et al., 2026]

2.3 Functional Landscape in Cancer

  • Histone Kla: H3K18la at oncogene promoters (MYC, RUNX2); H3K9la/H3K56la in HCC prognosis
  • Non-histone Kla: RIG-I K852la → immune evasion; HMGB1 Kla → inflammatory cascade; METTL16 Kla → cuproptosis resistance; MRE11 Kla → DNA repair; STAT3 K631la (D-lactate) → ferroptosis resistance; cyclin E2 Kla → HCC cell cycle
  • Therapy resistance: CNN1-mediated autophagy (docetaxel in CRPC) [Mao et al., 2026]; B7-H3 upregulation (immune evasion)

2.4 Lactylation and Ferroptosis

Histone Kla upregulates GPX4/FTH1, establishing a “glycolysis↑ → Kla↑ → ferroptosis resistance” axis. This creates a treatment vulnerability window: inhibiting Kla restores ferroptosis sensitivity [Yang et al., 2026].

3. Microbial Contributions to GI Cancers

3.1 Multimodal Carcinogenic Mechanisms

Gut microbiota drives carcinogenesis via three parallel pathways [Nobels et al., 2025]:

  • Genotoxicity: colibactin from pks+ E. coli → DNA crosslinking
  • Inflammation: LPS/peptidoglycan → TLR/NF-κB → ROS/RNS → indirect DNA damage
  • Epigenetics: SCFAs, folate, choline metabolites → host DNA methylation and histone modification

In gastric cancer, distinct oral and fecal microbiome signatures improve early diagnosis [Qin et al., 2026]; H. pylori infection drives metabolic reprogramming of host glycolysis and TCA cycle [Liu T et al., 2025]; statin chemoprevention is mediated by microbiota-derived tryptophan catabolites [Han JX et al., 2023].

3.2 Tumor-Resident Microbiota: From Passenger to Driver

Intratumoral bacteria are present in CRC, pancreatic, lung, and esophageal cancers. Their low diversity (1–3 dominant genera) belies disproportionate functional impact through three core modules:

  1. Metabolic reprogramming — enhancing host glycolysis
  2. Epigenetic remodeling — driving histone and non-histone Kla
  3. Immune modulation — subverting innate immunity and suppressing adaptive responses

Key discoveries:

  • E. coli in CRLM: lactate → RIG-I K852la → MAVS disruption → M2 polarization [Gu et al., 2024]
  • F. nucleatum in CRC: GLUT1↑ → glycolysis → histone Kla → proliferation [Zhou S et al., 2026]
  • Lactobacillus in ESCC: D-lactate → STAT3 K631la → GPX4/FTH1 → ferroptosis resistance [Wang D et al., 2026]
  • L. iners in cervical cancer: L-lactate → histone Kla → DNA repair → chemoradiation resistance [Colbert et al., 2023]
  • Radiotherapy-induced dysbiosis enriches lactate-producing bacteria (Lactobacillus, Enterococcus), potentially fueling Kla-driven radioresistance [Kong et al., 2019]

3.3 Microbiota-Directed Therapeutic Strategies

  • FMT: ~30–40% response in ICI-refractory melanoma [Hajjar et al., 2026]
  • Engineered probiotics: Quorum-sensing consortium syncing anti-tumor payload release [Guo et al., 2025]; synthetic E. coli Nissle 1917 [Chung et al., 2021]; Pediococcus pentosaceus SL4 drug delivery exploiting lactic acid secretion [An et al., 2019]
  • Smectite-probiotic biofilms: Enhancing colonization for durable immunotherapeutic effect [Han CW et al., 2021]
  • Phage therapy: Precise pks+ E. coli and F. nucleatum clearance
  • Nanoplatforms: Bacteria-membrane-coated particles for microbiota-targeted drug delivery [Li et al., 2026]
  • Dietary interventions: Resistant starch reduces glycolysis via HK2 inhibition → decreased lactate supply [Zhang Y et al., 2024]

4. The Microbiome–Lactate–Lactylation Bridge

4.1 Bidirectional Lactate Regulation

Gut microbiota contribute ~100–200 mmol lactate/day through dietary fiber fermentation. In homeostasis, lactate-utilizing bacteria (Veillonella, Megasphaera) rapidly convert lactate to SCFAs via cross-feeding [Nobels et al., 2025]. Microbiota-derived lactate drives colonic epithelial turnover via GPR81 [Okada et al., 2013].

Dysbiosis shifts the lactate-producer/utilizer ratio: lactate accumulation → pH drop → barrier disruption → selective enrichment of acid-tolerant pathogens → portal vein lactate → hepatic metastases.

4.2 The Enantiomeric Lactate Code

Host cells produce only L-lactate; bacteria produce both L- and D-lactate. D-lactate has negligible metabolism in mammalian cells (D-LDH activity extremely low), leading to intracellular accumulation and selective D-lactoylation of substrates like STAT3 K631 [Wang D et al., 2026]. This suggests an enantiospecific modification code: L-lactoylation and D-lactoylation may target different proteins and sites.

4.3 Three-Tier Intervention Framework

  • Tier 1 (microbial): FMT, phage therapy, selective antibiotics → reduce microbial lactate supply
  • Tier 2 (metabolic): LDHA/MCT1-4 inhibitors, lactate oxidase, LDH-silenced probiotics [Macharia et al., 2023], bacteria-vesicle lactate reprogramming delivery [Peng et al., 2026]
  • Tier 3 (epigenetic): p300/CBP inhibitors, SIRT3 activators, site-specific blocking peptides

4.4 ILA: A Parallel Microbial-Immune Axis

Beyond lactate, gut microbiota produce ILA from dietary tryptophan. ILA epigenetically enhances CD8+ T cell immunity via H3K27ac [Zhang Q et al., 2023], suppresses anti-PD-1 efficacy via PRDX1/c-Myc in ESCC [Zhou JF et al., 2026], and disrupts PRDX1/c-Myc in meningioma [Jiang et al., 2026]. Since ILA-producing Lactobacillus spp. also produce lactate, these metabolites may form a coordinated immunosuppressive network in the TME.

5. The Axis as a Closed-Loop Positive Feedback

  1. Dysbiosis → lactate-producer overgrowth + lactate-utilizer decline → luminal lactate accumulation
  2. Tumor cells + intratumoral bacteria → enhanced glycolysis → further lactate production
  3. Elevated lactate → p300/CBP/HBO1/AARS1/2-mediated lactylation → histone and non-histone protein reprogramming → proliferation, metastasis, immune evasion, drug resistance
  4. Kla-induced immunosuppression (M2 polarization, CD8+ T cell suppression, DC dysfunction) → selective advantage for tumor and pro-tumorigenic bacteria → feedback loop closure

6. Conclusions and Open Questions

The microbiome–lactate–lactylation axis provides a unified framework linking microbial ecology, tumor metabolism, and epigenetic gene regulation. The 14 remaining evidence gaps (see evidence_gaps.md) center on:

  • D- vs. L-lactylome systematic comparison
  • Lactate clock kinetics on non-histone substrates
  • Safety of lactylation inhibition in physiologically high-lactate tissues
  • Quantitative contribution of microbial vs. host-derived lactate
  • Clinical validation of multi-tier combination strategies

Expanded references and detailed discussion in 20260724_v2.md (Chinese, 51 refs).

References

Selected 51 references — all clickable hyperlinks are embedded in the text above. Comprehensive BibTeX list available in 20260724_v2.md.

Key Papers

  1. Zhang D et al. Nature (2019) — Discovery of histone Kla
  2. Gu J et al. Oncogene (2024) — E. coli → RIG-I K852la → immune evasion in CRLM
  3. Wang D et al. Gut Microbes (2026) — D-lactate → STAT3 K631la → ferroptosis resistance in ESCC
  4. Zhou S et al. J Transl Med (2026) — F. nucleatum → GLUT1 → histone Kla in CRC
  5. Colbert LE et al. Cancer Cell (2023) — L. iners → lactate → chemoradiation resistance
  6. Han SL et al. Sci Adv (2023) — D-lactate vs. L-lactate in M2 macrophage polarization
  7. Zhang Q et al. Cell Metab (2023) — ILA → H3K27ac → CD8+ T cell immunity
  8. Nobels A et al. Nat Metab (2025) — Gut microbiome and cancer comprehensive review
  9. Hajjar R et al. Nat Rev Microbiol (2026) — Harnessing microbiome for cancer therapy
  10. Fang C et al. Sig Transduct Target Ther (2026) — Lactate metabolism and lactylation in cancer
  11. Angelin A et al. Cell Metab (2017) — Foxp3 Treg metabolism in high-lactate
  12. Okada T et al. Nat Commun (2013) — Microbiota-derived lactate and colon turnover
  13. Peng F et al. Adv Sci (2026) — Bacteria-vesicle lactate reprogramming for radiosensitization
  14. Macharia JM et al. Biomed Pharmacother (2023) — LDH silencing in probiotic LAB
  15. Wei D et al. Int J Mol Sci (2026) — Lactylation in CRC regulatory networks