Gut Microbiome Dysbiosis in Crohn's Disease: 16S rRNA Amplicon Sequencing Reveals Reduced Faecalibacterium prausnitzii Abundance and Increased Adherent-Invasive E. coli in 284-Patient Cohort

This study investigates gut microbiome composition in Crohn's disease versus healthy controls using 16S rRNA amplicon sequencing, identifying keystone taxa associated with disease activity and mucosal inflammation within the context of gastroenterology and microbiome research, an area of growing scientific importance given its implications for F. prausnitzii-based probiotic design for Crohn's remission maintenance, microbiome biomarker panel for disease activity monitoring, and AIEC as therapeutic target for anti-adhesion therapy. Using V4 16S rRNA amplicon sequencing (Illumina MiSeq, 250 bp paired-end), QIIME2 DADA2 ASV calling, alpha diversity (Shannon, Faith PD), beta diversity (UniFrac), and LEfSe differential abundance with validation by quantitative PCR, we examine Faecalibacterium prausnitzii producing butyrate that nourishes colonocytes and suppresses NF-kB inflammatory signaling; its depletion in Crohn's disease correlated with mucosal cytokine elevation; AIEC adherent-invasive E. coli invading epithelium and persisting in macrophages amplifying IL-12 and IL-18 cytokine response driving granuloma formation in 284 participants: 124 active Crohn's (HBI >=5), 84 Crohn's remission (HBI <5), 76 healthy controls; mucosal biopsy and stool collected at colonoscopy; 24,000 reads/sample after quality filter drawn from Lakeside Medical Center IBD Center with IRB-approved colonoscopy tissue banking; Illumina MiSeq at GLNI Genomics Core; QIIME2 v2023.2 pipeline on university HPC cluster. Results indicate that active Crohn's has Shannon diversity 2.84 vs. 4.48 healthy (p<0.001); F. prausnitzii depleted 8.4x in active vs. healthy (p<0.001); AIEC E. coli enriched 12.4x; F. prausnitzii abundance inversely correlated with fecal calprotectin (r=-0.72, p<0.001) (p < 0.001), with Shannon 2.84 vs. 4.48; F. prausnitzii 8.4x depleted; AIEC 12.4x enriched; r=-0.72 calprotectin as the primary quantitative benchmark. Concordance between primary and confirmatory measurement approaches exceeded 93%, validating the analytical framework. These findings contribute empirically to gastroenterology and microbiome research and carry actionable implications for the design of programs and policies targeting F. prausnitzii-based probiotic design for Crohn's remission maintenance, microbiome biomarker panel for disease activity monitoring, and AIEC as therapeutic target for anti-adhesion therapy.