Study of the gut microbiome in Egyptian patients with active ulcerative colitis

INTRODUCTION AND AIM

Ulcerative colitis (UC) is characterized by chronic, uncontrolled inflammation of the intestinal mucosa. Gut microbiota dysbiosis was reported to be a factor in intestinal inflammation. The aim of the present study was to study changes in the gut microbiome in Egyptian patients with active UC.

MATERIALS AND METHODS

In this cross-sectional study, the gut bacterial microbiome of 21 UC patients and 20 control subjects was analyzed using the quantitative SYBR Green real-time PCR technique, targeting the 16S rRNA gene of selected bacterial phyla/genera and/or species.

RESULTS

UC patients showed marked dysbiosis evidenced by a significant decrease in the Firmicutes and F. prausnitzii anti-inflammatory bacteria. The Firmicutes/Bacteroidetes ratio was also lower in the UC cases (1.65), compared with the healthy controls (2.93). In addition, the UC cases showed a statistically significant decrease in Ruminococcus, compared with the control group. However, there were no statistically significant differences between UC patients and the controls, regarding A. muciniphila, Bifidobacterium, Lactobacillus, Bacteroides, and Prevotella. One UC case was positive for the pathogenic bacterium, Clostridioides difficile, with low relative abundance.

CONCLUSION

The current study showed differences in the gut microbiome of UC patients, compared with healthy controls. This may help in identifying the gut microbiome and specific bacterial changes that can be targeted for treatment of UC.

Rapid detection of porcine DNA in processed food samples using a streamlined DNA extraction method combined with the SYBR Green real-time PCR assay

A specialized DNA extraction method and a SYBR Green quantitative polymerase chain reaction (SyG-qPCR) assay were combined to generate a ready-to-use kit for rapid detection of porcine admixtures in processed meat products. Our qPCR assay utilized repetitive LINE-1 elements specific to the genome of Sus scrofa domesticus (pig) as a target and incorporated internal controls. We improved the genomic DNA extraction method, and reduced extraction times to the minimum. The method was validated for specificity, sensitivity (0.001% w/w) and robustness, and values were compared with those of a commercially available kit. We also tested our method using 121 processed food products and consistently detected amplification only in samples containing pork. Due to its efficiency and cost-effectiveness, our method represents a valuable new method for detecting food adulteration with pork that is superior to existing quality control approaches.