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Ep 3130680 A1 (19) TZZ¥_¥ZZ_T (11) EP 3 130 680 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 15.02.2017 Bulletin 2017/07 C12Q 1/68 (2006.01) (21) Application number: 15382427.1 (22) Date of filing: 11.08.2015 (84) Designated Contracting States: (72) Inventors: AL AT BE BG CH CY CZ DE DK EE ES FI FR GB • LÓPEZ SILES, Mireia GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO 17403 Sant Hilari Sacalm (ES) PL PT RO RS SE SI SK SM TR • GARCÍA GIL, Librado Jesús Designated Extension States: 17833 Fontcuberta (ES) BA ME • ALDEGUER MANTÉ, Xavier Designated Validation States: 17003 Girona (ES) MA • MARTÍNEZ MEDINA, Margarita 17246 Santa Cristina d’Aro (ES) (71) Applicants: • Universitat de Girona (74) Representative: Hoffmann Eitle 17071 Girona (ES) Hoffmann Eitle S.L.U. • Institut d’Investigacio Biomedica de Girona Paseo de la Castellana 140, 3a planta Dr. Josep Trueta Edificio LIMA 17007 Girona (ES) 28046 Madrid (ES) • Goodgut S.L. 17003 Girona (ES) (54) METHOD FOR THE DETECTION, FOLLOW UP AND/OR CLASSIFICATION OF INTESTINAL DISEASES (57) The present invention relates to the field of di- sample from said subject. It further relates to a method agnosis and classification of intestinal diseases. It further for the differential diagnosis of inflammatory bowel dis- relates to the field of microbiology, more particularly it ease (IBD) phenotypes in a human subject comprising relates to the relationship between intestinal microbiota determining the abundance of a target microorganism in composition and inflammatory bowel disease (IBD). an intestinal sample from said subject, wherein said tar- Specifically it relates to a method for detecting intes- get microorganism is selected from the group consisting tinal diseases, in a human subject comprising determin- of Faecalibacterium prausnitzii members (total FP), Fae- ing the abundance of Faecalibacterium prausnitzii phy- calibacterium prausnitzii phylogroup I members (PHGI) logroup I members (PHGI) and/orFaecalibacterium and Faecalibacterium prausnitzii phylogroup II members prausnitziiphylogroup IImembers (PHGII) inan intestinal (PHGII). EP 3 130 680 A1 Printed by Jouve, 75001 PARIS (FR) EP 3 130 680 A1 Description FIELD OF INVENTION 5 [0001] The present invention relates to the field of diagnosis and classification of intestinal diseases. It further relates to the field of microbiology, more particularly it relates to the relationship between intestinal microbiota composition and inflammatory bowel disease (IBD). [0002] Specifically it relates to a method for detecting intestinal diseases, in a human subject comprising determining the abundance of Faecalibacterium prausnitzii phylogroup I members (PHGI) and/or Faecalibacterium prausnitzii phy- 10 logroup II members (PHGII) in an intestinal sample from said subject. It further relates to a method for the differential diagnosis of inflammatory bowel disease (IBD) phenotypes in a human subject comprising determining the abundance of a target microorganism in an intestinal sample from said subject, wherein said target microorganism is selected from the group consisting of Faecalibacterium prausnitzii members (total FP), Faecalibacterium prausnitzii phylogroup I mem- bers (PHGI) and Faecalibacterium prausnitzii phylogroup II members (PHGII). 15 BACKGROUND OF THE INVENTION [0003] Inflammatory bowel disease (IBD) represents a group of idiopathic chronic inflammatory intestinal conditions. The two main disease categories the term covers are Crohn’s disease (CD) and ulcerative colitis (UC), with both over- 20 lapping and distinct clinical and pathological features (World Gastroenterology Organisation Global Guidelines, Inflam- matory boweldisease: a global perspective,June 2009;and Silverberget al.,Can J Gastroenterol. 2005, 19 Suppl A:5-36). [0004] IBD affects as many as 1.6 million persons in the United States and 2.2 million in Europe. The incidence is increasing worldwide. In spite of advances in IBD-therapy, IBD hospitalizations and surgery rates in the United States have increased significantly since 1990. IBD is one of the five most prevalent gastrointestinal disease burdens in the 25 United States, with annual overall health care costs of more than $1.7 billion. One to two of every 1000 people in developed countries are affected with IBD, and global rates seem to be increasing, attributable to the rapid modernization and to the adoption of the Western world lifestyle. These chronic diseases result in significant morbidity and mortality, compromising quality of life and life expectancies. (M’Koma A. E., World J Gastrointest Surg 2014; 6(11), 208-219). [0005] An association between the increased incidence of IBD and environmental factors linked to socioeconomic 30 development has been persistently detected in different parts of the world, and it seems that the lifestyle in developed countries might impair the natural patterns of microbial colonization of the human gut. In IBD, mucosal lesions are generally associated to an excessive or dysregulated immune response against commensal microbes in the gut, and studies using molecular methods for intestinal microbiota analysis indicate that dysbiosis (that is, abnormal microbiota composition) and decreased complexity of the gut microbial ecosystem are common features in patients with CD or UC 35 (Manichanh et al., Nat. Rev. Gastroenterol. Hepatol. 2012; 9, 599-608). [0006] Faecalibacterium prausnitzii (Ruminococcaceae) is one of the three most abundant bacterial species found in the gut, representing between 2-20% of the fecal microbiota in healthy individuals, according to diversity studies of the human gut microbiome based on 16S rRNA gene analysis (Arumugam et al. Nature. 2011;473:174-180; Eckburg et al. Science. 2005;308:1635-1638; Hold et al. Appl Environ Microbiol. 2003;69:4320-4324; Schwiertz et al. J Pediatr. 40 2010;157:240-244; Suau et al. Systematic and Applied Microbiology. 2001;24:139-145; Walker et al. ISME J. 2011:220-230). On the other hand, it has been reported to represent 6% of bacteria in mucosa-associated microbial communities (Swidsinski et al. World J Gastroenterol. 2005;11:1131-1140), although some studies have indicated that these values can increase to around 20-50% in some individuals (Nava GM, Stappenbeck TS. Gut Microbes. 2011;2: 99-104; Baumgart et al. ISME J. 2007; 1:403-418). 45 [0007] In recent years, there has been increasing interest in F. prausnitziigiven its potentiallyimportant rolein promoting gut health (Louis et al. FEMS Microbiol Lett. 2009;294:1-8; Sokol et al. Proc Natl Acad Sci U S A. 2008;105:16731-16736) through the formation of anti-inflammatory compounds (Louis et al. FEMS Microbiol Lett. 2009;294:1-8; Sokol et al. Proc Natl Acad Sci USA. 2008;105:16731-16736; Barcenilla et al. Appl Environ Microbiol. 2000;66:1654-1661; Duncan et al. Int J Syst Evol Microbiol 2002;52:2141-2146; Lopez-Siles et al. Appl Environ Microbiol. 2012;78:420-428) and enhance- 50 ment of intestinal barrier function (Carlsson et al. Scand J Gastroenterol. 2013;48:1136-1144; Wrzosek et al. BMC Biol. 2013:11:61). [0008] Many studies have shown that F. prausnitzii prevalence and abundance is reduced in different intestinal dis- orders (Miquel et al. Curr Opin Microbiol. 2013;16:255-261), in particular the depletion inF. prausnitzii numbers has been most extensively reported in inflammatory bowel disease (IBD). Low counts of this species have been observed 55 in both fecal and mucosa-associated communities of adult CD patients (Sokol et al. Proc Natl Acad Sci USA. 2008;105:16731-16736;Lopez-Siles et al. International Journal of Medical Microbiology. 2014;304:464-475; Sokol et al. Inflamm Bowel Dis. 2009;15:1183-1189; Swidsinski et al. Inflamm Bowel Dis. 2008;14:147-161; Willing et al. Inflamm Bowel Dis. 2009;15:653-660). 2 EP 3 130 680 A1 [0009] Variable populations have been reported in UC patients (Swidsinski et al. World J Gastroenterol. 2005;11:1131-1140; Lopez-Siles et al. International Journal of Medical Microbiology. 2014;304:464-475; Sokol et al. Inflamm Bowel Dis. 2009;15:1183-1189; Hansen et al. Am J Gastroenterol. 2012;107:1913-1922; Jia et al. FEMS Micro- biol Lett. 2010;310:138-144; Kabeerdoss et al. BMC Gastroenterol. 2013;13:20; Machiels et al. Gut. 2013; McLaughlin 5 et al. Therap Adv Gastroenterol. 2010;3:335-348; Vermeiren et al. FEMS Microbiol Ecol. 2012;79:685-696), despite the reduction of Firmicutes having been repeatedly observed in this disorder (Machiels et al. Gut. 2013; Frank et al. Proc Natl Acad Sci USA. 2007;104:13780-13785; Nagalingam NA, Lynch SV. Inflamm Bowel Dis. 2012;18:968-984). A recent study conducted on 127 UC subjects points out that a reduction in F. prausnitzii is also involved in UC dysbiosis (Machiels et al. Gut. 2013). 10 [0010] Interestingly, lower counts of Faecalibacterium-related bacteria have also been observed in functional gut disorders such as irritable bowel syndrome (IBS) of alternating type (Rajilic-Stojanovic et al. Gastroenterology. 2011;141:1792-1801), that in turn shares some features with IBD patients (Ghoshal et al. Int J Inflam. 2012;2012:151085; Spiller RC. Best Practice & Research Clinical Gastroenterology. 2004;18:641-661), and in more severe intestinal disor- ders as colorectal cancer (CRC) (Balamurugan et al. J Gastroenterol Hepatol. 2008;23:1298-1303). Taken together 15 these findings suggest that shifts in F. prausnitzii numbers occur under several pathological disorders. [0011] Furthermore, relatively few studies have paid attention to the diversity within the genusFaecalibacterium. Recent phylogenetic analysis showed that mainly two differentF. prausnitzii phylogroups, which include the current cultured representatives, are found in fecal samples of healthy subjects (Lopez-Siles et al. Appl Environ Microbiol. 2012;78:420-428). 20 [0012] The diagnosis of IBD requires a comprehensive physical examination and a review of the patient’s history. Various tests, including blood tests, stool examination, endoscopy, biopsies, and imaging studies help exclude other causes and confirm the diagnosis (World Gastroenterology Organisation Global Guidelines, Inflammatory bowel disease: a global perspective, June 2009).
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