I’d like to offer a contemporary perspective on recent patient reports from the cluster headache (CH) community alongside my own experience regarding the treatment of CH with nutritional interventions. This draws on a range of emerging research to explore how modulation of the gut microbiota more so than any one diet may present as a novel future therapeutic target in CH. As best I can as a CH patient, I will attempt to integrate the converging lines of evidence that support this hypothesis including a case report, drawn from the grey literature, illustrating the clinical application of such a targeted microbiome-based approach and conclude with some final thoughts on what really is a fascinating subject.
More bacteria than we are human…
The human genome encodes for between 20,000 and 25,000 genes. In remarkable comparison our collective microbial genome, comprised of trillions of microbes that inhabit our bodies, contains an estimated 3,000,000 to 4,000,000 million genes. The gut microbiota is a vast community of bacteria, fungi, viruses and archaea that inhabit the gastrointestinal tract, with the highest density of microbes anywhere in the body found in the colon. The diversity of this community is influenced by a number of factors including diet, environment, motility, autonomic tone, antibiotic exposure, previous infection, vitamin D3 and psychedelics (more on the vitamin D3 and psychedelics later). Their primary energy source is dietary fibre and other non-digestible carbohydrates of which they ferment into short-chain fatty acids (SCFA’s) such as acetate, propionate and butyrate. They also synthesize vitamins such as vitamin K and several B-group vitamins, amino acid derivatives like indole and GABA and secondary bile acids that in turn regulate metabolism and immune function. Together these microbes and their metabolites play an existential role in maintaining gut integrity, modulating inflammation and supporting our overall health.
Balance is the key to life… that sentiment resonates with me…
When this community of microbes is balanced, or in eubiosis, the relationship is mutually beneficial. We nourish the microbes and they nourish us. When the balance of this community is disrupted, disease may follow through a process referred to as dysbiosis. Imbalance of the microbiota may degrade the mucin layer, a protective layer of mucous that protects the epithelial lining of the gut. When the mucosal layer is degraded, disruption may occur at the level of the epithelium where the tight junctions that maintain integrity of permeable membranes are compromised, increasing the translocation of toxins from the gut into blood and lymph where they invoke an immune response. An example of this is lipopolysaccharide (LPS), a structural component of the outer membrane of gram-negative bacteria. LPS engages the toll like receptor 4 (TLR4) complex on innate immune cells, activating the transcription factor nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), which translocates to the nucleus and upregulates the expression of pro-inflammatory cytokines such as interleukin-1β (IL-1β) and tumor necrosis factor-alpha (TNF-α). This cascade contributes to a process commonly referred to as “leaky gut” syndrome.
Emerging Migraine Research…
Whilst CH and migraine are clinically distinct disorders they do share several overlapping mechanisms including activation of the trigeminovascular system and neurogenic inflammation, as well as responsiveness to medications such as triptans and anti-CGRP monoclonal antibodies such as Emgality. Both conditions also exhibit cyclical patterns and hypersensitivity within pain processing networks. Given the larger body of research on migraine, it is useful to cautiously draw insights from migraine studies given they may reveal potential pathophysiological processes and therapeutic targets relevant to CH.
In my view recent literature seems to have shifted the understanding of migraine from a neurovascular disorder toward a systemic inflammatory condition modulated by the gut-brain-immune axis. Multiple independent studies now converge on the idea that gut dysbiosis and intestinal permeability are central to migraine pathophysiology.
A study by He et al. (2023) confirmed a causal relationship between gut microbial composition and migraine risk, identifying protective taxa such as Bifidobacteriales and pathogenic associations with Anaerotruncus and Clostridium genera, providing what I believe was the first robust evidence that microbiota composition can directly influence migraine susceptibility. In a 2024 study, Vuralli et al. found elevated serum LPS, VE-cadherin, HMGB1 and IL-6 in chronic migraine patients with medication overuse, supporting a “leaky-gut” inflammatory phenotype linked to trigeminal sensitization.
Recent reviews and meta-analyses converge on much the same theme; migraineurs show lower microbial diversity, depletion of SCFA producing species such as Faecalibacterium and Roseburia and a relative overgrowth of pro-inflammatory species. Emerging clinical research supports therapeutic modulation of the microbiota. Grodzka and Domitrz (2025) conducted a meta-analysis that showed probiotic supplementation reduced migraine frequency with mixed effects on severity whilst Kappéter et al. (2023) proposed fecal microbiota transplantation (FMT) as a means of microbial restoration and normalizing the inflammatory mediators implicated in migraine chronification.
What does the CH literature say?
Comparable findings in CH are absent however new evidence does show an emerging persistent inflammatory signature. In peripheral blood, Lund et al. (2025) found distinct cytokine profiles across all CH types with oncostatin M (OSM), an IL-6 family cytokine, elevated in cCH, eCH in-cycle and eCH in remission groups. In cerebrospinal fluid, Ran et al. (2024) demonstrated higher chemokine concentrations with a serum-to-CSF gradient, concentrating inflammation within the central nervous system (CNS) and present both during active cycle and remission periods. More recently, PACAP-38 has also been found to be elevated in CH compared with controls, further supporting the presence of sustained neuroimmune activation involving vasoactive peptides even during remission periods.
And whilst an underlying inflammatory signature has now been identified, the upstream driver of these elevated markers remains unlinked to dysbiosis. Taken together however these new findings point to CH as a condition underpinned by ongoing inflammation within the CNS rather than a series of isolated pain events attributed to dysfunction of the hypothalamus.
So, what was this about a diet? Sign me up!
What has recently been referenced by myself and others in the CH community is a 2018 case-control study by Di Lorenzo et al. that examined the effects of a ketogenic diet in a small cohort of 18 chronic CH patients refractory to standard preventive treatments. The authors reported that 15 participants responded favorably, with 11 achieving sustained pain-free remission and 12 choosing to remain on the intervention even after the study concluded. Although the mechanism of action was not explored, it is my view that the therapeutic benefit of the ketogenic diet likely extends beyond the metabolic effects of ketone production to include modulation of the gut microbiota and its associated inflammatory milieu. To my knowledge, this remains the only dietary intervention in CH and while the sample size was small the findings were nonetheless remarkable.
Here warrior – I recommend giving this a try…
Consider this a brief pause, a half-time reflection, before moving into the following sections. Few examples illustrate the power of patient-led initiatives better than what the CH community has been able to achieve. Out of necessity and sheer persistence, patients have effectively conducted some of the most successful citizen science projects in existence. From the early work exploring psychedelic therapy to the development of the vitamin D3 anti-inflammatory regimen, each step has been driven by individuals determined to find solutions where few existed. These remarkable efforts have produced measurable results and practical treatment tools that continue to change the lives of CH patients, indeed not all heroes wear capes.
Where vitamin D3 & psilocybin converge…
What I find particularly intriguing is that both of these therapies, psychedelic compounds and the Vitamin D regimen, according to emerging research, may exert part of their therapeutic effect through interactions with the gut microbiota. At the same time, their variable efficacy from one CH patient to another may be influenced by the baseline state and diversity of that patient’s microbiome. This bidirectional relationship, in which treatment both shapes and is shaped by its interaction with the microbiota, may help explain why some experience complete remission while others achieve only partial or temporary relief, or require higher or repeated doses. In the following sections, I will examine the literature that highlights the potential points of convergence between Vitamin D and psilocybin, focusing on microbiome mediated interactions.
Oh vitamin D3, you have been kind to me…
For almost a decade now, the Vitamin D3 anti-inflammatory regimen has kept me mostly pain-free from CH. Beyond its role in calcium homeostasis Vitamin D3 plays a key role in maintaining gastrointestinal homeostasis. The active form, 1,25-dihydroxyvitamin D3, binds to the Vitamin D receptor (VDR), which is expressed throughout the intestinal epithelium and immune cells. Through this signaling pathway Vitamin D3 influences epithelial integrity, microbial diversity and modulates the immune response (Vemulapalli et al., 2025).
In refining the original regimen, Pete Batcheller included a B-complex, taking inspiration from Gominak’s work linking Vitamin D restoration to improved sleep and gut function through the microbiota’s production of B vitamins (Gominak, 2016). Gominak proposes that both Vitamin D and the microbiota exist in a symbiotic relationship, where Vitamin D supports the host environment necessary for microbial balance while a healthy microbiota contributes to the production of essential cofactors necessary for neuronal and immune health.
Charoennngam et al. (2020) demonstrated that Vitamin D3 supplementation shifts the microbiota toward a less inflammatory profile, increasing beneficial commensal species such as Bacteroides while reducing pathogenic species like Porphyromonas. In regards to maintenance of the epithelial membranes, Vitamin D3 upregulates tight-junction proteins such as claudins and occludins while lowering zonulin expression, a key marker for intestinal permeability. By strengthening tight junctions Vitamin D3 may limit translocation of bacterial endotoxins such as LPS into systemic circulation (Fedele et al., 2018; Stio et al., 2016).
In addition to maintaining gut barrier integrity, Vitamin D3 modulates the immune response by inhibiting NF-κB activation and reducing the production of pro-inflammatory cytokines while supporting T regulatory cell function and the production of antimicrobial peptides such as cathelicidins and beta defensins (Vemulapalli et al., 2025).
Taken together these findings place Vitamin D3 as a key mediator in gut-immune homeostasis, acting at the bleeding edge between the microbial landscape and host defense. Importantly, as demonstrated by Holick and colleagues in Scientific Reports (2019), the genomic actions of Vitamin D3 are dose and blood-level responsive with higher 25-hydroxy vitamin D levels resulting in broader transcriptional changes across hundreds of genes involved in immune regulation. The fact that Pete Batcheller’s regimen has been assembled into a simple and accessible protocol with consistently impressive response rates is in itself a remarkable achievement given the devastating nature of CH. Whilst Vitamin D3 almost certainly acts on receptors within the trigeminal ganglion and hypothalamus, these recent findings suggest its actions in the periphery, particularly within the gut, may play an important role in the therapeutic efficacy of the anti-inflammatory regimen.
What can mushrooms possibly have to do with any of this?
Intriguing new research suggests that the therapeutic effects of psychedelics, particularly psilocybin, may in part be mediated through interactions with the gut microbiota. While its best described actions involve modulation via the serotonergic receptor, new findings reveal that psilocybin also exerts systemic effects on inflammation, immune signaling, intestinal barrier integrity as well as shaping the microbial landscape itself.
Wang et al. (2025) provide an elegant synthesis of this evolving concept in a recent ACS Chemical Neuroscience viewpoint, suggesting that the therapeutic effects of psychedelics including psilocybin extend beyond cortical serotonergic circuits to modulate the gut-brain axis via interactions with the microbiome. Building on emerging evidence they position these compounds as both neuroactive and immunomodulatory agents, potentially influencing inflammation along the microbiota-gut-brain pathway via NF-κB mediated cytokine modulation as shown in complementary models like Zanikov et al., 2024.
Zanikov et al. (2024) were able to show in a mouse model of colitis that psilocybin reduced gut driven neuroinflammation and lowered the expression of inflammatory cytokines IL-1β, IL-6 and COX-2 in brain parenchyma. These findings link intestinal inflammation directly to a central inflammatory response and confirm that psilocybin’s anti-inflammatory effects occur along the gut-brain axis rather than within the brain alone. Complementary in vitro work in human macrophages shows dose dependent suppression of LPS induced cytokines via modulation of NF-κB signaling, highlighting its broad immunoregulatory potential.
Kelly et al. (2023) introduced the term “psilocybiome” as a framework to describe the bidirectional relationship between psychedelics and the microbiota-gut-brain axis, they propose that microbial diversity and metabolism influence every phase of psychedelic therapy from preparation and acute experience to integration. Caspani et al. (2024) build on this by exploring psychedelics potential antimicrobial effects and how they may reshape gut ecology, suggesting that microbial composition modulates psychedelic pharmacokinetics while remarkably, psychedelics, in turn, remodel the microbiota.
This research suggests that psilocybin’s therapeutic benefit may indeed depend on the baseline composition and inflammatory state of the gut microbiome. This perspective offers a fresh view for the variability in dose response observed within the CH community’s collective busting experiences. It appears reasonable to suspect that interventions which restore microbial balance and support gut integrity may enhance the therapeutic window for psychedelic therapy. Although the degree to which these microbial mediated mechanisms contribute to the therapeutic benefit we see in busting for CH remains speculative, these new findings make clear that psilocybin’s actions reach beyond the mind, extending into the intricate microbial terrain in a complex dance that is beginning to be revealed.
So what about that case report?
Recent clinical evidence provides an example of how restoring microbial homeostasis may be achieved through an integrative approach. A 2023 case report by Beltran and Guimarães described the successful treatment of a patient with psoriasis vulgaris refractory to conventional therapies using a combined anti-inflammatory diet, high-dose vitamin D3 therapy and targeted herbal antimicrobials.
The case report used a diagnostic workup that included the Gastrointestinal Microbial Assay Plus (GI-MAP), a DNA-based stool test that identifies bacterial, fungal and parasitic taxa as well as markers of gut inflammation and intestinal permeability by Quantitative PCR (qPCR). This diagnostic framework provided a precision-based view of the patient’s baseline microbial state and guided subsequent therapeutic choices. Such testing reveals that, just as no two microbiomes are identical, one size may not fit all in nutritional or supplement interventions. Importantly, dysbiosis patterns and their immunological signatures vary between individuals which necessitates personalized modulation of the microbiota rather than blanket probiotic or dietary advice.
In the specific case testing revealed small intestinal fungal overgrowth (SIFO) driven by Candida albicans. These results informed a selection of herbal antimicrobials, notably oregano oil for its antifungal and biofilm-disruptive properties. Oregano oil’s mechanisms include membrane disruption and inhibition of fungal enzyme activity which reduce microbial burden and help restore mucosal homeostasis. To complement this, Curcumin longa (turmeric) was used for its capacity to inhibit NF-κB-mediated inflammation and upregulate VDR expression in epithelial and immune cells.
Following five months of intervention immunofluorescence analysis of VDR expression in skin biopsies revealed upregulation of receptor density compared with baseline, correlating in full clinical remission. This finding parallels the discussion advanced in Beltran’s companion paper, Vitamin D Receptor Renewal Through Anti-Inflammatory Diet, which identifies the suppression of VDR by LPS, mycotoxins and inflammatory cytokines as key drivers of vitamin D resistance in chronic inflammatory and autoimmune diseases. By resolving dysbiosis and improving epithelial integrity through diet, the intervention removed the upstream inflammatory blockade to VDR transcription and restored immune tolerance.
Where and how to even conclude this…?
Cluster headache, long regarded as the most devastating disorder, may find part of its explanation not in the brain alone but in the microbial world that indeed sustains it. As our understanding of the gut-brain-immune axis deepens, the concept that dysbiosis and intestinal permeability may act as upstream drivers of neuroinflammation becomes increasingly difficult to ignore.
While the literature in CH remains in its infancy, speculative bridges are clearly already being built with patents having been filed for microbial modulating technologies aimed at treating headache disorders, such as US9987224B2, which describes methods for altering gut microbiota composition to influence neurological outcomes including migraine and CH. Such developments are another signal of the growing recognition that modulating our microbial landscape presents as an attractive therapeutic target for disorders once considered purely neurogenic in origin.
All being said, it’s early days – what I think we have is an interesting hypothesis more so than settled science for CH specifically. The ketogenic results are impressive but need larger, controlled trials; vitamin D3 works for many but the anti-inflammatory regimen remains without clinical validation in CH and psilocybin’s ties to the microbiome are certainly intriguing but mostly preclinical. All three treatment options are available for patients to pursue at their own discretion.
I hope I have been able to articulate my take on the current literature and of course welcome your thoughts, comments and ideas. Many questions remain covering other important topics in CH such as genetics, periodicity and the role of personality; still – I feel like it is an exciting and hopeful time and look forward to seeing what future research may show in regards CH and the microbiome.
References
Migraine
Vuralli, D., Akgör, M.C., Gök Dağıdır, H. et al. (2024) ‘Lipopolysaccharide, VE-cadherin, HMGB1 and HIF-1α are elevated in chronic migraine with MOH: evidence of leaky gut/inflammation’, J Headache Pain.
Link: https://pmc.ncbi.nlm.nih.gov/articles/PMC10875763/
He, Q., Zhang, Y. and Li, R. (2023) ‘A causal effects of gut microbiota in the development of migraine’, J Headache Pain.
Link: https://thejournalofheadacheandpain.biomedcentral.com/articles/10.1186/s10194-023-01609-x
Grodzka, O. and Domitrz, I. (2025) ‘Gut microbiota, probiotics, and migraine: a clinical review and meta-analysis’, Journal of Oral & Facial Pain and Headache.
Link (journal): https://www.jofph.com/articles/10.22514/jofph.2025.043
Kappéter, Á., Zając, A., Domitrz, I. (2023) ‘Migraine as a disease associated with dysbiosis and possible therapy with fecal microbiota transplantation’, Biomedicines.
Link: https://pmc.ncbi.nlm.nih.gov/articles/PMC10458656/
Cluster Headache
Lund, N.L.T., Pedersen, S.H., Ashina, M. et al. (2025) ‘Distinct alterations of inflammatory biomarkers in cluster headache: a case–control study’, Annals of Neurology.
Link (journal): https://onlinelibrary.wiley.com/doi/10.1002/ana.27205
Ran, C., Yang, Y., Guo, S. et al. (2024) ‘Elevated cytokine levels in the central nervous system of patients with cluster headache’, J Headache Pain.
Link: https://thejournalofheadacheandpain.biomedcentral.com/articles/10.1186/s10194-024-01829-9
Søborg, M.L.K., Amin, F.M., Ashina, M. et al. (2025) ‘PACAP-38 in cluster headache: a prospective, case-control study of a potential treatment target’, Eur J Neurol.
Link (PubMed): https://pubmed.ncbi.nlm.nih.gov/41002104/
Ketogenic Diet
Di Lorenzo, C., Coppola, G., Sirianni, G. et al. (2018) ‘Efficacy of Modified Atkins Ketogenic Diet in Chronic Cluster Headache: An Open-Label, Single-Arm Clinical Trial’, Frontiers in Neurology.
Link: https://www.frontiersin.org/journals/neurology/articles/10.3389/fneur.2018.00064/full
Vitamin D3
Vemulapalli, R., Thomas, A. (2025) ‘The Role of Vitamin D in Gastrointestinal Homeostasis and Gut Inflammation.’, Int. J. Molecular Sciences
Link: https://pubmed.ncbi.nlm.nih.gov/40243631/
Gominak, S.C. (2016) ‘Vitamin D deficiency changes the intestinal microbiome reducing B-vitamin production in the host: a hypothesis explaining chronic sleep disorder’, Medical Hypotheses.
Link (PubMed): https://pubmed.ncbi.nlm.nih.gov/27515213/
Charoenngam, N., Shirvani, A., Holick, M.F. (2020) ‘The Effect of Various Doses of Oral Vitamin D3 Supplementation on Gut Microbiota in Healthy Adults: A Randomized, Double-blinded, Dose-response Study’, Anticancer Research.
Link: https://pubmed.ncbi.nlm.nih.gov/31892611/
Stio, M. et al. (2016) ‘Vitamin D regulates the tight-junction protein expression in active ulcerative colitis’, Scand J Gastroenterol.
Link (PubMed): https://pubmed.ncbi.nlm.nih.gov/27207502/
Scricciolo A, Roncoroni L, Lombardo V,Ferretti F, Doneda L,Elli L (2018) ‘Vitamin D3 Versus Gliadin: A Battle to the Last Tight Junction’, Digestive Diseases and Sciences. Link: https://pubmed.ncbi.nlm.nih.gov/29159680/
Shirvani A, Kalajian TA, Song A, Holick MF. (2019) ‘Disassociation of vitamin D’s calcemic and non-calcemic genomic activity & individual responsiveness: RCT’, Scientific Reports.
Link: https://www.nature.com/articles/s41598-019-53864-1
Psychedelics
Wang, X., Li, H. and Zhou, Z. (2025) ‘Psychedelics and the Gut Microbiome: Unraveling the Interplay and Therapeutic Implication’ (Viewpoint), ACS Chemical Neuroscience.
Link (journal page): https://pubs.acs.org/doi/abs/10.1021/acschemneuro.5c00418
Zanikov, T., Gerasymchuk, M. and Robinson, G.I. (2024) ‘Psilocybin and eugenol prevent DSS-induced neuroinflammation in mice’, Biocatalysis and Agricultural Biotechnology.
Link: https://www.sciencedirect.com/science/article/pii/S1878818124000161
Caspani et al. (2024) ‘Mind over matter: the microbial mindscapes of psychedelics and the gut-brain axis’, Progress in Neuro-Psychopharmacology & Biological Psychiatry.
Link: https://www.sciencedirect.com/science/article/pii/S1043661824002834
Kelly, J.R., and Clarke, G. (2023) ‘Seeking the Psilocybiome: Psychedelics meet the microbiota-gut-brain axis’, International Journal of Psychopharmacology
Link: https://pmc.ncbi.nlm.nih.gov/articles/PMC9791138/
Case Report & Other
Beltran, E.P. and Guimarães, G. (2023) ‘High-dose vitamin D3, anti-inflammatory diet and targeted antimicrobials in psoriasis vulgaris: clinical case with VDR immunofluorescence’, Zenodo case report (grey literature).
Link: https://zenodo.org/record/7799594
Beltran, E.P. (2023) ‘Vitamin D Receptor Renewal Through Anti-inflammatory Diet’, ResearchGate/Institutional page (grey literature).
US 9,987,224 B2 (2018) ‘Method and system for preventing migraine headaches, cluster headaches and dizziness.’
Link (Google Patents): https://patents.google.com/patent/US9987224B2/en
