The present invention relates to the use of components of the IL23 pathway as biomarkers, e.g., IL22, LCN2 and combinations thereof, to stratify or identify populations of patients suffering from IL23-mediated diseases (e.g., Crohn's disease) responsive to treatment with an anti-IL23 antagonist (including, e.g., anti-IL23 antibodies or antigen-binding fragments thereof). Levels of IL23 pathway biomarkers above or below a predetermined threshold can be used, for example, (i) to determine whether a patient with an IL23-mediated disease or disorder such a Crohn's disease is eligible or non-eligible for treatment with a therapeutic agent (e.g., an anti-IL23 antibody), (ii) to determine whether treatment with a certain agent should be commenced, suspended, or modified, (iii) to diagnose whether the IL23-mediated disease is treatable or not treatable with a specific therapeutic agent, or (iv) to predict the outcome of treating the IL23-mediated disease with a specific therapeutic agent.

The present invention relates to detecting serum anti-FadA antibodies in test samples from a patient. Additionally, aspects of the present invention provide the basis for detection of serum anti-FadA antibody levels from test samples and correlation with various conditions of clinical relevance.

In general the present invention concerns a method for predicting the therapeutic outcome of a treatment of in inflammatory bowel disease for anti-TNF agents, anti-α.sub.4β.sub.7-integrin agents and/or anti-IL-12/23 agents. The method defines which the agents are likely to provide the best healing effect for a particular patients affected by an inflammatory bowel disease. In particular the method predicts the therapeutic outcome of a treatment of anti-TNF agents in inflammatory bowel disease.

Methods of assessing or monitoring the effect, efficacy, responsiveness to treatment, and/or determining a dose or dosing regimen of therapeutic agents, such as integrin beta7 antagonists, for the treatment of gastrointestinal inflammatory disorders are provided. In certain aspects, methods of using integrin beta7 subunit-containing receptor occupancy by the integrin beta7 antagonist on colonic lymphocytes as an indicator (“biomarker”) of the effect, efficacy, or responsiveness to treatment, and/or as a means to determine dosing or dosing regimens of therapeutic agents such as beta7 integrin antagonists for the treatment of gastrointestinal inflammatory disorders are provided. In certain aspects, methods of assessing the effect, efficacy, or responsiveness to beta7 integrin antagonist treatment by measuring gene expression levels of one or more integrin receptor ligands, lymphocyte genes, cytokine genes, or the number of alphaE-positive cells in intestinal crypt epithelium are provided.

The present invention relates to a method of determining the probability that an individual has irritable bowel syndrome and whether the individual will respond to dietary intervention. The present invention also provides a method of determining the probability that an individual with irritable bowel syndrome will respond to dietary intervention. There is also provided the use of a compound as defined herein as a biomarker.

Disclosed are methods for conducting diagnostic tests for the detection of the inflammatory bowel diseases, such as Crohn’s disease and ulcerative colitis. Also described are methods for monitoring a patient by administering tests of the present invention. Also described are methods for monitoring patient’s treatment by administering tests of the present invention. Also described are methods for evaluating the effectiveness of a drug or a drug candidate by administering tests of the present invention to samples from patients, animal models, and cell cultures treated with a drug or a drug candidate. Also disclosed are methods for determining the usefulness of analytes, e.g. cytokines, for acting as diagnostic and monitoring markers for inflammatory bowel disease in the various methods of the invention.

This invention comprises compositions and methods to detect and treat gastrointestinal diseases.

Methods and compositions are provided herein for treating and/or diagnosing ulcerative colitis in a subject, using one or more bacterial strains such as Bacillus sp. BT1B_CT2, Bacteroides coprocola M16, Bacteroides eggerthii CCUG 9559, Bacteroides vulgatus 8482, Butyricimonas virosa MT12, Coprococcus eutactus ATCC 27759, Desulfovibrio piger DSM 749, Dolosigranulum pigrum IFO 15550, Eubacterium biforme DSM 3989, Eubacterium eligens DSM 3376, Fusobacterium prausnitzii ATCC 27768, Howardella ureilytica GPC 589, Megasphaera elsdenii LC1, Parabacteroides johnsonii M-165, Phascolarctobacterium sp. YIT 12067, Roseburia hominus A2-183, or Ruminococcus callidus VPI 57-31.

The present invention relates to a method for determining the distinctive nutritional requirements of a patient with specific nutritional needs and providing a composition meeting the distinctive nutritional requirements of said patient.

Methods of culturing and detecting a biomarker which may be associated with autoimmune diseases, in particular inflammatory bowel disease and Crohn's disease; also a screening method for substances suitable for the treatment of inflammatory bowel disease including Crohn's disease; the method including culturing a biomarker in a culture media which includes a culture broth, OADC, PANTA and Mycobactin J.