Irritable bowel syndrome, Microbiome profiling, Fecal microbiota transplantation, Low FODMAPs diet, Diet, Dysbiosis, PCR-based microbiome profiling

Irritable Bowel Syndrome: Microbiome Profiling and Fecal Microbiota Transplantation

David Quig, PhD

Vice President of Scientific Support

Doctor’s Data, Inc.

Irritable bowel syndrome (IBS) affects up to 20% of adults and is associated with life-disruptive symptomatology. The multifactorial pathogenesis of IBS includes gastrointestinal dysbiosis, altered microbial metabolism, intestinal barrier dysfunction, and dietary intolerance—especially to soluble fiber. Intervention with a traditional IBS diet or a low FODMAP diet may not be sufficient for amelioration of immoderately disrupted gut microbiota and metabolism, and recent efforts indicate that fecal microbial transplantation may provide an effective option.

Microbial-host crosstalk between key gut bacteria and the mucosa is essential for intestinal barrier functions, inclusive of surveillance, protection and selection of the microbial ecosystem. Disruption of a healthy microbiome, and/or insufficient consumption of soluble fiber (SF), blunts desirable production of short chain fatty acids (SCFA) and stymies communication with specialized cells in the mucosa.¹ Propionate contributes to immune defense via binding to the G protein coupled receptor GPR-43 that is expressed on lymphocytes.² Propionate and butyrate stimulate release of glucagon-like peptide-1 (GLP-1) by enteroendocrine L cells; GLP-1 facilitates regulation of mucosal barrier function and glucose metabolism.³ Butyrate and acetate stimulate colonic cells to “breath” via activation of peroxisome activated receptor- γ (PPAR- γ); PPAR- γ mediates increased fatty acid uptake, β-oxidation and oxygen consumption.⁴ Removal of oxygen from the microenvironment directly adjacent to the mucosa limits colonization of anaerobic pathogens such as Escherichia and Salmonella.⁵ Butyrate and acetate stimulate the release by goblet cells of vast quantities of mucins that constitute the essential, and too often underappreciated, mucus barrier.⁶ Diminished regulation of mucosal metabolism subsequently perpetuates dysbiosis, and causes low-grade mucosal inflammation and breaches of the barrier system. Low levels of fecal SCFA are common for IBS patients.

Extensive research has culminated in a novel PCR-based microbiome profiling approach that targets the most clinically relevant bacteria to differentiate normobiosis from dysbiosis in IBS patients (classified by Rome III criteria).

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From that model a dysbiosis index (DI) was algorithmically derived; DI>2 (maximum 5) indicates the extent to which a microbiota profile deviates from that of a healthy reference population (n=500). Dysbiosis was evident across subtypes in 73% of IBS patients (n=297) with a significant percentage of DI values >4 (severe dysbiosis). Predominant bacteria contributing to the IBS-associated dysbiosis were Proteobacteria (Shigella/ Escherichia), Bacilli, Acintobacteria and Ruminococcus gnarvus.

Formal studies indicate that the “traditional” and low FODMAPs diets variably alleviate symptoms for some IBS patients, but in many cases the gut dysbiosis appears to be irreparable with reasonable dietary intervention. Long-term adherence to a strict low FODMAPs diet has adverse effects on gut microbiota and intestinal barrier integrity; the clinical ramifications are under deliberation. A four-week study of IBS patients consuming a low FODMAP diet indicated higher than baseline DI despite some symptom improvement; many patients did not respond favorably at all.⁸

Fecal microbiota transplantation (FMT) may be an effective alternative option for long-standing immoderate dysbiosis. FMT is widely accepted as the treatment of choice for C. difficile enterocolitis. The efficacy and kinetics of FMT was studied in IBS patients and healthy donors (n=16).⁹ The aforementioned targeted PCR-based microbiota profiling method was used to follow both donor and FMT recipients before and at intervals up to 28 weeks after a single FMT. At baseline IBS patients had significantly higher DI than donors (4±0.5 and 2.6±0.2, respectively). Patient DI decreased steadily over 12 weeks (2.9±0.20, mild) but trended up after seven months. At that time the microbiota profiles for patients and donors were very similar (abundance and diversity). The most significant changes in bacteria were Bifiodobacteria (increase), and Proteobacteria and Shigella/Escherichia (decrease). Symptoms improved rapidly and markedly.

Application of the novel PCR-based targeted microbiota profiling method of analysis, along with symptom improvement, provides evidence that FMT may be an effective means to restore microbial balance for IBS patients with long-standing dysbiosis. Follow up studies should evaluate appropriate “feeding” in addition to microbiota “seeding” towards support of intestinal barrier functions and staying power of FMT.

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