El Mouzan Mohammad, Savidge Tor C, Al Sarkhy Ahmed, Badu Shyam, Alsaleem Badr, Al Mofarreh Mohammad, Almasood Abdullah, Assiri Asaad
Department of Pediatrics (Gastroenterology Unit), College of Medicine, King Saud University, Riyadh, Saudi Arabia.
Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA.
Saudi J Gastroenterol. 2025 Jul 1;31(4):212-218. doi: 10.4103/sjg.sjg_24_25. Epub 2025 Apr 15.
Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.
Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-naïve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.
In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which ( Salmonella_phage_SEN4 , uncultured_crAssphage, Staphylococcus_phage_SPbeta-like , Streptococcus_phage_YMC-2011 and Siphoviridae_u_s ) were identified as candidate biomarker signatures.
We found a significantly altered bacteriophage signature in children with new onset, treatment naïve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.
在西方人群的溃疡性结肠炎（UC）中，肠道微生物群失衡已得到充分证实。关于肠道病毒组以及地理因素是否会影响与UC相关的微生物群，人们了解得要少得多。本研究的目的是描述肠道噬菌体的变化，并识别可作为UC潜在生物标志物的噬菌体-细菌关联。
本研究纳入了20名患有UC的儿童和20名健康对照。纳入标准包括新诊断的未经治疗的UC儿童，在样本采集前至少六个月未接触过抗生素。从粪便和直肠活检组织中提取脱氧核糖核酸（DNA），并进行鸟枪法宏基因组测序。进行了生物信息学和统计分析，以评估噬菌体多样性及其与肠道细菌的关联。使用随机森林分类器识别候选生物标志物。
在粪便样本中，噬菌体多样性没有显著改变，但在UC中有72个物种发生了显著改变，其中5个（沙门氏菌噬菌体SEN4、未培养的crAssphage、葡萄球菌噬菌体SPbeta样、链球菌噬菌体YMC - 2011和长尾噬菌体科u_s）被确定为候选生物标志物特征。
我们在中东人群沙特儿童新发病、未经治疗的UC患儿中发现了显著改变的噬菌体特征。这些变化与先前报道的西方UC病例不同，表明在为非西方人群开发基于微生物群的诊断和治疗应用时，需要考虑人口统计学偏差。
