Dysbiosis of fecal microbiota in Crohnʼs disease patients as revealed by a custom phylogenetic microarray

TLDR

The study developed and evaluated a custom phylogenetic microarray targeting ~500 gut bacterial species to analyze fecal microbial diversity in healthy individuals and Crohn’s disease patients. Fecal 16S rDNA from six healthy and six Crohn’s disease subjects was amplified into fluorescent cRNA and hybridized to the array. The array identified significant shifts, with commensal species such as *Eubacterium rectale* and *Faecalibacterium prausnitzii* 5–10× more abundant in healthy controls, while opportunistic pathogens like *Enterococcus*, *Clostridium difficile*, and *Escherichia coli* were enriched in Crohn’s disease patients, confirming prior clone‑library results and demonstrating the array’s utility for microbiota profiling.

Abstract

A custom phylogenetic microarray composed of small subunit ribosomal RNA probes, representing ≈500 bacterial species from the human and animal gut, was developed and evaluated for analysis of gut microbial diversity using fecal samples from healthy subjects and Crohn's disease (CD) patients.Oligonucleotide probes (≈40 mer) used on the microarray were selected from published articles or designed with the "GoArray" microarray probe design program using selected bacterial 16S rRNA sequences. Fecal 16S rDNA from individual samples of six healthy subjects and six CD patients were used as template to generate fluorescently labeled cRNA that was hybridized to the microarray. Differences revealed by the microarray in relative abundance of microbial populations between healthy and diseased patients were verified using quantitative real-time polymerase chain reaction (PCR) with species-specific primer sets.The microarray analyses showed that Eubacterium rectale, Bacteroides fragilis group, B. vulgatus, Ruminococcus albus, R. callidus, R. bromii, and Faecalibacterium prausnitzii were 5-10-fold more abundant in the healthy subjects than in the CD patients, while Enterococcus sp., Clostridium difficile, Escherichia coli, Shigella flexneri, and Listeria sp. were more abundant in the CD group.The microarray detected differences in abundance of bacterial populations within the phylum Firmicutes that had been reported previously for the same samples based on phylogenetic analysis of metagenomic clone libraries. In addition, the microarray showed that Enterococcus sp. was in higher abundance in the CD patients. This microarray should be another useful tool to examine the diversity and abundance of human intestinal microbiota.