Klebsiella Dysbiosis and Ankylosing Spondylitis: A Naturopathic Case Study

Exploring the gut–joint connection in a patient with ankylosing spondylitis, highlighting the role of Klebsiella overgrowth, naturopathic interventions, and sustained clinical remission.

Jennifer Cornell, ND

Abstract

Ankylosing spondylitis (AS) is a chronic inflammatory spondyloarthropathy strongly associated with HLA-B27 and commonly managed with biologic therapies targeting the IL-23/IL-17 axis^1,2. Increasing evidence implicates gut dysbiosis, particularly Klebsiella pneumoniae, in AS pathogenesis through mechanisms of molecular mimicry and immune activation.^3,4 This case report describes the clinical course of a middle-aged male who reported having been diagnosed with ankylosing spondylitis by his rheumatologist and was receiving ongoing biologic therapy at presentation. Comprehensive stool testing revealed overgrowth of the Klebsiella species. A targeted naturopathic treatment plan was implemented, including antimicrobial botanicals, dietary modifications, and microbiome support. Within weeks, the patient experienced marked improvement in joint stiffness and pain. Over subsequent months, he discontinued biologic medication under medical supervision and has remained symptom-free for several months at follow-up. This case highlights the potential role of identifying and treating Klebsiella dysbiosis in inflammatory conditions such as AS and suggests further research is warranted.

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Introduction

Ankylosing spondylitis (AS) is a progressive inflammatory disease of the axial skeleton characterized by chronic back pain, stiffness, and potential spinal fusion. The condition is often managed with nonsteroidal anti-inflammatory drugs (NSAIDs) and biologics targeting tumor necrosis factor (TNF) or interleukin (IL)-17.^1,2 While these therapies improve symptoms, they do not address underlying causes and may carry long-term risks.

Mounting evidence suggests that intestinal dysbiosis contributes to systemic inflammation. Klebsiella pneumoniae has been implicated in AS pathogenesis through molecular mimicry with HLA-B27 and cross-reactive antibodies.^3,4 Although this association has been debated, systematic reviews confirm increased prevalence of Klebsiella in AS patients’ stool and higher circulating anti-Klebsiella antibodies.^5,6 Diet interventions and microbiome modulation have been proposed as therapeutic strategies, but clinical case reports are rare.

This report adds to the literature by describing a patient who reported an AS diagnosis, was treated for stool-identified Klebsiella dysbiosis, and subsequently experienced sustained remission of symptoms.

Case Presentation

The patient was a middle-aged male who reported being diagnosed with ankylosing spondylitis by his rheumatologist in his mid-30s. He described chronic low back pain beginning in his 20s, waking daily with pain rated 4/10, and experiencing episodes of his back “going out” one to two times per year. Exercise often worsened stiffness, leading to cycles of activity and rest.

Over the years, he tried several medications, eventually starting biologic therapy. He took one biologic (adalimumab, Humira) for about a year with limited improvement. He then switched to another biologic (secukinumab, Cosentyx) about 7 years ago. At presentation, he was taking the biologic, in addition to intermittent use of celecoxib, mesalamine, and antihistamines, as well as a proton pump inhibitor he had been taking for two decades for chronic reflux. He also reported daily abdominal discomfort, longstanding reflux, and 2–3 bowel movements daily, without blood or mucus.

Initial visit: At his first naturopathic visit, the patient described feeling somewhat stronger than in previous years, but still struggled with back and joint pain, poor exercise recovery, and chronic gastrointestinal symptoms, including chronic reflux and stomach pain. He had completed a full workup with another provider and his rheumatologist. A comprehensive stool test and additional blood work were ordered.

6 weeks later: Stool analysis revealed significant overgrowth of Klebsiella pneumoniae. At this visit, the patient had not yet implemented recommendations and was waiting for lab results. A pre-gut protocol was initiated, beginning with two weeks of gut lining and immune support, along with foundational supplementation (vitamin D3/K2, B12, fish oil, alpha lipoic acid, chromium). After two weeks, this was transitioned to targeted antimicrobials plus a binder, while continuing nutritional support.

10 weeks later: The patient reported resolution of abdominal pain and improvement in reflux. Bowel habits remained stable at 2–3 movements daily. Back pain was reduced, though fatigue persisted. He completed the gut protocol phases, including antimicrobials, and reduced his pantoprazole dose by half.

5 weeks later: Pain was minimal, though fatigue remained. He had completed antimicrobials and introduced the next phase of the protocol, which included a daily probiotic, magnesium glycinate, adrenal support and a return to the previous gut supportive botanicals.

5 weeks later: The patient reported feeling “great,” with significant improvement in energy and no pain with exercise. He began training for an athletic event and addressed sleep apnea through another provider.

4 months later: The patient reported feeling “amazing,” with the best energy and health of his life. He completed the athletic event without consequence and recovered well. Bowel movements were well-formed and regular. He noted that he had discontinued his biologic medication two months prior, as well as all other medications, and remained symptom-free. Repeat stool testing was planned at this time.

Differential Diagnosis
Given the absence of rheumatology records, alternative explanations were considered:
– Mechanical low back pain or degenerative disc disease (addressed with personal trainer and movement coach/ruled out by orthopedist)
– Other inflammatory arthritides, such as reactive arthritis, psoriatic arthritis (ruled out by rheumatologist)
– Functional or microbiome-related gut–immune inflammation contributing to musculoskeletal symptoms.

The patient’s reported rheumatologist diagnosis and use of biologics support the likelihood of AS, though definitive confirmation was unavailable from the patient.

Interventions
A staged treatment plan was implemented to reduce Klebsiella burden, restore gut integrity, and support systemic health.

Phase 1: Gut-lining & immune support (2 weeks)
– Powdered blend (2 tsp daily):
  • Zinc carnosine 11 mg
  • L-glutamine 4 g
  • N-acetyl D-glucosamine 1 g
  • Glycyrrhiza glabra (root, deglycyrrhizinated) 400 mg
  • Abelmoschus esculentus (fruit) 300 mg
  • Aloe barbadensis (aerial part extract, 200:1) 50 mg
  • MSM (methylsulfonylmethane) 500 mg
– Foundational support: vitamin D3/K2, vitamin B12, fish oil, alpha-lipoic acid, chromium

Phase 2: Antimicrobial protocol (4 weeks)
– Herbal tincture (15 drops BID) with extracts of:
  • Vaccinium myrtillus (fruit), Vitis vinifera (seed), Lentinula edodes (fruiting body), Hydrastis canadensis (root), Morinda citrifolia (fruit), Allium sativum (bulb), Salix alba (bark), Silybum marianum (seed), Echinacea purpurea (herb), Echinacea angustifolia (root), Rubus idaeus (fruit), Juglans spp. (hull and leaf), Lavandula spp. (oil), Origanum vulgare (oil), Melaleuca alternifolia (oil), Fumaria officinalis (aerial parts), and Gentiana lutea (root).
– Binder (1 cap daily, away from food/supplements) containing: zeolite clay, activated charcoal, Aloe barbadensis (leaf extract), apple pectin, silica, humic substances.

Phase 3: Microbiome restoration & ongoing support
– Probiotic (multi-strain Lactobacillus and Bifidobacterium species)
– Prebiotic fibers: inulin, arabinogalactan
– Magnesium, adrenal support, and reintroduction of gut-supportive botanicals
– Lifestyle: stress management, graded exercise, sleep optimization

Outcomes

Over the course of treatment spanning approximately 10 months, the patient experienced progressive improvement in gastrointestinal and musculoskeletal symptoms, resolution of reflux and abdominal pain, restoration of energy, and discontinuation of biologic and other medications under supervision. At the most recent follow-up, he remained in remission with no back pain or stiffness, improved exercise tolerance, and enhanced quality of life. Although follow-up stool testing has not been performed to date to confirm eradication, this same protocol has previously demonstrated effectiveness in eliminating Klebsiella overgrowth in stool analysis testing.

Discussion

Research suggests a connection between Klebsiella pneumoniae and ankylosing spondylitis, most notably through mechanisms such as molecular mimicry with HLA-B27 and dysbiosis of the gut microbiota.¹⁻⁴ Meta-analyses show increased fecal Klebsiella and elevated anti-Klebsiella antibodies in affected patients, and older studies noted parallels between stool carriage and disease activity.⁵⁻⁶ Current dietary trials, such as low-starch interventions, are exploring whether reducing Klebsiella substrates influences outcomes.¹² However, clinical evidence directly linking symptom resolution with targeted treatment of Klebsiella remains limited. This case provides a clinical example of symptom resolution following targeted treatment of Klebsiella dysbiosis, supporting the relevance of this proposed mechanism.

Several in vitro studies show direct inhibition of Klebsiella pneumoniae by botanical agents, particularly essential oils.⁷⁻¹¹ Oregano and thyme oils have shown low minimum inhibitory concentrations against even multidrug-resistant strains of Klebsiella, while tea tree and lavender oils also exhibit measurable antimicrobial effects.⁷⁻⁹ These findings lend mechanistic support for the clinical improvements observed in this case, where a multi-agent antimicrobial herbal protocol contributed to sustained resolution of symptoms. No human clinical trials have tested these botanicals against Klebsiella, but evidence exists for other Gram-negative enteric pathogens. Garlic supplementation, for example, has demonstrated antimicrobial benefit against Helicobacter pylori, a Gram-negative bacterium associated with gastric disease.¹³ Berberine has been shown in randomized controlled trials to reduce stool volume and shorten the duration of diarrhea caused by enterotoxigenic Escherichia coli and Vibrio cholerae—both Gram-negative organisms.¹⁴⁻¹⁵ These findings suggest herbs effective against one group of Gram-negative pathogens may exert similar benefits when Klebsiella is present, as suggested by this case.

Previous NDNR publications have highlighted these concepts, including Molecular Mimicry in Pediatric Diseases, which referenced Klebsiella as a stealth pathogen in ankylosing spondylitis, and Chronic Pain & Gut-Joint Axis, which described microbial contributions to joint disease.¹⁶⁻¹⁷ Other NDNR articles, such as Micropathology of SIBO and Functional Medicine, Allopathic Medicine, and Naturopathic Medicine, have also touched on the role of gut bacteria like Klebsiella in systemic conditions.¹⁸⁻¹⁹ This case adds to that discussion by providing a clinical example of sustained symptom resolution following targeted treatment of Klebsiella dysbiosis.

Limitations

The primary limitation is the absence of rheumatology records or imaging to independently verify the AS diagnosis. The case relies on the patient’s self-report of diagnosis, HLA B27 gene, and biologic prescription. Spontaneous remission, while rare, cannot be excluded. Generalizability is limited, as this is a single case. Controlled studies are needed to establish causality between Klebsiella reduction and AS remission.

Conclusion

This case highlights the potential role of Klebsiella dysbiosis in inflammatory presentations resembling ankylosing spondylitis and the potential for clinical remission through microbiome-directed interventions. While caution is warranted in interpreting outcomes without confirmed diagnostics, the sustained resolution of symptoms after microbiome-directed treatment underscores the importance of gut assessment in autoimmune conditions. Further research, including case series and clinical trials, is warranted.

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