Two phylogenetic trees were created for bacteria and viruses with different colors distinguishing the phylum. For sequence homology analysis, a pair-wise BLAST analysis was carried out on the antigen protein sequences of validated antibodies for CDvshealthy control analysis. We also identified antibodies against the antigen ofStreptococcus pyogenes(SPy_2009) showing higher prevalence in healthy controls relative to UC patients. Using these novel antibodies, we built biomarker panels with area under the curve (AUC) of 0.81, 0.87, and 0.82 distinguishing CDvscontrol, UCvscontrol, and CDvsUC, respectively. Subgroup analysis revealed that penetrating CD behavior, colonic CD location, CD patients with a PTTG2 history of surgery, and extensive UC exhibited highest antibody prevalence among all patients. We demonstrated that autoantibodies and anti-microbial antibodies in CD patients had minimal correlation. == CONCLUSION == We have identified antibody signatures for CD and UC using a comprehensive analysis of anti-microbial antibody response in IBD. These antibodies and the source microorganisms of their target antigens improve our understanding of the role of specific microorganisms in IBD pathogenesis and, after future validation, should aid early and accurate diagnosis of IBD. Keywords:Inflammatory bowel disease, Anti-microbial antibody, Protein microarray, Crohns disease, Ulcerative colitis, Gut microbiome Core Tip:We performed the largest serological profiling of anti-microbial antibodies to date in using 100 Crohns disease (CD) and 100 ulcerative colitis (UC) patients. We identified novel anti-microbial antibodies with differential prevalence in inflammatory bowel disease (IBD) patients compared with healthy controls. There was minimal correlation between anti-microbial antibodies and our previously reported autoantibodies in CD patients. We combined novel anti-microbial antibodies to build biomarker panels distinguishing CDvscontrol, UCvscontrol and CDvsUC with an area under the curve of 0.81, 0.87, and 0.82, respectively. Subgroup analysis revealed that IBD patients with severe disease had the highest antibody prevalence. == INTRODUCTION == Inflammatory bowel disease (IBD) represents a group of intestinal disorders that causes chronic inflammation in the digestive tract. The two Amyloid b-peptide (1-42) (rat) main clinical phenotypes are ulcerative colitis (UC) and Crohns disease (CD). The Amyloid b-peptide (1-42) (rat) public health burden of IBD is rising globally[1]. Early and accurate diagnosis is key to reducing this burden. Gastroenterologists often use a combination of relatively invasive procedures, like ileocolonoscopy with biopsy for diagnosis, and to determine the disease extent and activity. There is a need for serological biomarkers that can reveal the disease state non-invasively. Herein, our objectives were to discover anti-microbial antibody signatures in IBD patients and understand the association of microbial infection with IBD pathogenesis. IBD is caused by a combination of genetic predisposition, faulty immune responses, and environmental factors[2]. The interaction of microbes with the gut mucosa in a genetically susceptible individual and the corresponding immune response play a pivotal role Amyloid b-peptide (1-42) (rat) in the initiation and progression of IBD[3]. After birth, a limited diversity microbial community develops into a complex community due to the influence of diet and environmental factors[4]. During the second or third decade of life, a dysbiosis is observed in IBD patients which leads to an imbalance between commensal and potentially pathogenic microorganisms[5]. The healthy gut microbiota predominately comprises Firmicutes and Bacteroidetes, and to a lesser extent, Actinobacteria and Proteobacteria[6,7]. In IBD, dysbiosis is observed with reduced abundance of Firmicutes and either higher or similar abundance of Proteobacteria. Besides compositional changes, genetic alterations also contribute to gut dysbiosis that leads to disease initiation and progression. For example, NOD2 variants were found in 20%-40% of European and American CD patients[8,9]. NOD2 encodes an intracellular receptor for the bacterial peptidoglycan muramyl dipeptide, which helps maintain the balance of commensal bacterial flora[10]. Immune response to microbes results in the production of antibodies to microbial antigens[11]. Anti-Saccharomyces cerevisiaeantibodies (ASCA) are associated with CD patients, with sensitivities and specificities ranging between 55% to 65% and 80% to 95%, respectively[12]. Perinuclear antineutrophil cytoplasmic antibodies (pANCA) are associated with UC patients, with sensitivities and specificities ranging between 50% to 71% and 75% to 98%, respectively[13]. Outer membrane protein ofEscherichia coli(OmpC) and flagellin (CBir1) antibodies are prevalent in CD patients, with prevalence ranging between 24%-55% and 50%-56%[13]. The number and response magnitude of anti-microbial antibodies have previously been shown to indicate the presence of IBD, its severity and its clinical course; however, the clinical utility of available antibodies in diagnosis and clinical management of IBD patients has been limited. The techniques used to discover the known anti-microbial antibodies associated with IBD are of low throughput, and have only been applied to test on small number.