Metagenomic characterisation of gut microbiota in IBS patients

Introduction: Irritable Bowel Syndrome (IBS) is a gastrointestinal (GI) disorder that exhibits different GI and neurological symptoms such as abdominal pain, diarrhoea, constipation and mood disorders. The gut microbiota play an important role in modulating the communication between the Central Nervous System (CNS) and the GI tract, the so-called microbiota-gut-brain axis. In this context, IBS is a clear example of the alteration of the fine equilibrium between the gut microbiota and the CNS. Furthermore it has been observed that probiotic treatments of IBS results in the relief of GI and neurological symptoms, thus we could hypothesize the direct impact of the gut microbiota on IBS physiopathology. Since the IBS bacterial gut microbiota has been extensively studied we focused our attention also on the fungal counterpart of the gut microbiota, "the mycobiota". Methods and aims. The aim of the present work was to evaluate biodiversity in bacterial and fungal microbiota of a cohort of 20 IBS subject and 21 healthy subject (HS) through culture-based and metagenomics approaches. The bacterial diversity that relies on DNA polymorphism has been performed by means of cluster analysis of ARDRA profiles. Moreover the absolute abundances of bifidobacteria and enterobacteria has been evaluated by qPCR. For IBS gut mycobiota characterization, fungal strains from IBS stool samples were isolated and identified by mean of ITS1-4 sequencing. Furthermore, isolates were phenotypically characterized to evaluate their resistance to GI tract stresses (temperature, low pH and oxbile resistance), while Candida isolates were further clustered by means of their RAPD profiles. Results: The cluster analysis of ARDRA profiles showed that IBS bacterial microbiota clusters apart from HS microbiota. In addition we observed a 2.8-fold increase in the absolute abundance of enterobacteria in IBS subjects vs HS. The analysis of the gut mycobiota revealed significant differences in fungal isolates abundance in IBS subjects vs HS even if we did not find any significant difference in species richness. In particular, results showed an abundance of fungi (61.8% C. albicans), with a higher number of colony count 4.7 log10 CFU/g faeces in IBS subjects respect to HS faecal samples with 1.9 log10 CFU/g (48,75% C. albicans). RAPD prolfile analysis of C. albicans and C. parapsilosis showed that IBS isolates clustered apart from HS isolates, suggesting their different genotypical background. Finally, we observed that IBS fungal isolates showed different phenotypical features with an increased ability to growth to high temperatures and low pH respect to isolates from HS. Conclusions: Our results showed the presence of alterations in the microbial community structure of IBS subjects, both at bacterial and fungal level. The absolute abundance of enterobacteria in IBS subjects suggests their connection with putative inflammatory phenomena as previously observed in IBS and other pathologies (Lee and Park, 2014). The phenotypical characterization of IBS fungal isolates revealed that such isolates showed a different response in respect GI-like stresses. Moreover we observed that C. albicans and C. parapsilosis isolates from IBS are both phenotypically and genotypically different from HS Candida isolates suggesting their putative different ecological distribution. Finally we could hypotesize that dysbiosis of the gut microbiota in IBS could be one of the driving factor in IBS pathophysiology that could be responsible of intestinal fungal population overgrowth. Lee JY, Park KS. 2014. World J Gastroenterol 20:2456-2469