Background: Crohn's disease (CD) and ulcerative colitis (UC) diagnosis requires comprehensive examination of the patient. Faecalibacterium prausnitzii and Escherichia coli have been reported as representatives of Inflammatory Bowel Disease (IBD) dysbiosis. The aim was to determine whether or not quantification of these species can be used as a complementary tool either for diagnostic or prognostic purposes. Methods: Mucosa-associated F. prausnitzii and E. coli abundance was determined in 28 controls (H), 45 CD, 28 UC patients and 10 irritable bowel syndrome (IBS) subjects by quantitative polymerase chain reaction (qPCR) and the F. prausnitzii E. coli index (F-E index) was calculated. Species abundances were normalized to total bacteria and human cells. Data was analyzed taking into account patients' phenotype and most relevant clinical characteristics. Results: IBD patients had lower F. prausnitzii abundance than H and IBS (P. <. 0.001). CD patients showed higher E. coli counts than H and UC patients (P. <. 0.001). The F-E index discriminated between H, CD and UC patients, and even between disease phenotypes that are usually difficult to distinguish as ileal-CD (I-CD) from ileocolonic-CD and colonic-CD from extensive colitis. E. coli increased in active CD patients, and remission in I-CD patients was compromised by high abundance of this species. Treatment with anti-tumor necrosis factor (TNF) α diminished E. coli abundance in I-CD whereas none of the treatments counterbalanced F. prausnitzii depletion. Conclusion: F. prausnitzii and E. coli are useful indicators to assist in IBD phenotype classification. The abundance of these species could also be used as a supporting prognostic tool in I-CD patients. Our data indicates that current medication does not restore the levels of these two species to those found in a healthy gu

This work was partially funded by the Spanish Ministry of Education and Science through project SAF2010-15896. Mireia Lopez-Siles was recipient of an Fl grant from the Generalitat de Catalunya (2010FLB2 00135), which receives support from the European Union Commissionate. Prof. Harry J. Flint and Dr. Sylvia H. Duncan acknowledge support from the Scottish Government Food, Land and People programme. We thank Ms. Natalia Adell from the Serveis Tecnics de Recerca for statistical assistance. We are grateful to Dr. Laia Calvo (Research Unit, Institut d'Assistencia Sanitaria, Salt, Spain) for her assistance in qPCR design and to Dr. Rosalia Trias (Universitat de Girona, Spain), who critically revised the manuscript. We appreciate the generosity of the patients who freely gave their time and samples to make this study possible, and the theatre staff of all centers for their dedication and careful sample collection