The collection of whole microbial communities (bacteria, archaea, fungi, and viruses) together constitutes the gut microbiome. Diet, age, stress, host genetics, and diseases cause increases or decreases in the relative abundance and diversity of bacterial species (dysbiosis). We aimed to investigate the gut microbial composition at different taxonomic levels of healthy controls (HCs) with active Crohn’s disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) using culture- and non-culture-based approaches and identify biomarkers to discriminate CD, UC, or IC. We determined the specific changes in the gut microbial profile using culture-independent (16S rRNA gene amplicon sequencing) as well as culture-based (culturomic) approaches. Biomarkers were validated using quantitative Real-Time PCR (qPCR). In both methods, bacterial diversity and species richness decreased in disease-associated conditions compared with that in HCs. Highly reduced abundance ofFaecalibacterium prausnitziiandPrevotellasp. and an increased abundance of potentially pathogenic bacteria such asEnterococcus faecium,Enterococcus faecalis, andEscherichia coliin all CD, UC, or IC conditions were observed. We noted a high abundance ofLatilactobacillus sakeiin CD patients;Ligilactobacillus ruminisin UC patients; andEnterococcus faecium,Escherichia coli, andEnterococcus faecalisin IC patients. Highly reduced abundance ofFaecalibacterium prausnitziiin all cases, and increased abundance ofLatilactobacillus sakeiandEnterococcus faeciumin CD,Ligilactobacillus ruminisandEnterococcus faeciumin UC, andEnterococcus faecium,Escherichia coli, andEnterococcus faecalisin IC could be biomarkers for CD, UC, and IC, respectively. These biomarkers may help in IBD (CD or UC) and IC diagnosis.