Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome
Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome
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DOI：
10.3109/00365521.2015.1027261
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发表时间：
2015-01-01
影响因子：
1.9
通讯作者：
Pimentel, Mark
中科院分区：
文献类型：
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作者：
Giamarellos-Bourboulis, Evangelos;Tang, Jie;Pimentel, Mark
目标。呼气测试和十二指肠培养研究表明，相当大比例的肠易激综合征(IBS)患者存在小肠细菌过度生长。在这项研究中，我们通过对一大群IBS、非IBS和对照组的十二指肠抽吸物的16S rDNA扩增序列和定量聚合酶链式反应(QPCR)分析来扩展这些数据。材料和方法。连续的只接受食管胃十二指肠镜检查的受试者和健康对照被招募。排除标准包括最近使用抗生素或益生菌。在广泛的医疗检查之后，对患者的IBS症状进行了评估。从内窥镜检查中获得的十二指肠抽吸物中提取DNA。通过16S图谱比较了IBS受试者和对照组中的微生物种群。然后通过定量聚合酶链式反应对整个队列中的十二指肠微生物进行定量，并将结果与定量的活培养数据进行比较。结果。共招募了258名受试者(21名健康受试者、163名非健康非IBS受试者和74名IBS受试者)。5个IBS和5个对照组的16S图谱显示IBS患者十二指肠微生物多样性显著降低，有12个属的微生物发生显著变化(错误发现率为0.15)，包括大肠杆菌/志贺氏菌(p=0.005)和气单胞菌(p=0.051)的高表达，不动杆菌(p=0.024)、柠檬酸杆菌(p=0.031)和微病毒(p=0.036)的低表达。在所有258名受试者中，定量聚合酶链式反应证实了IBS中更高水平的大肠杆菌，也显示了克雷伯氏菌的增加，这与定量培养数据密切相关。结论。16S rDNA测序证实IBS患者的小肠中微生物过度生长，并伴随着多样性的减少。定量聚合酶链式反应支持IBS特定微生物种群的改变。
Objective. Breath testing and duodenal culture studies suggest that a significant proportion of irritable bowel syndrome (IBS) patients have small intestinal bacterial overgrowth. In this study, we extended these data through 16S rDNA amplicon sequencing and quantitative PCR (qPCR) analyses of duodenal aspirates from a large cohort of IBS, non-IBS and control subjects. Materials and methods. Consecutive subjects presenting for esophagogastroduodenoscopy only and healthy controls were recruited. Exclusion criteria included recent antibiotic or probiotic use. Following extensive medical work-up, patients were evaluated for symptoms of IBS. DNAs were isolated from duodenal aspirates obtained during endoscopy. Microbial populations in a subset of IBS subjects and controls were compared by 16S profiling. Duodenal microbes were then quantitated in the entire cohort by qPCR and the results compared with quantitative live culture data. Results. A total of 258 subjects were recruited (21 healthy, 163 non-healthy non-IBS, and 74 IBS). 16S profiling in five IBS and five control subjects revealed significantly lower microbial diversity in the duodenum in IBS, with significant alterations in 12 genera (false discovery rate < 0.15), including overrepresentation of Escherichia/Shigella (p = 0.005) and Aeromonas (p = 0.051) and underrepresentation of Acinetobacter (p = 0.024), Citrobacter (p = 0.031) and Microvirgula (p = 0.036). qPCR in all 258 subjects confirmed greater levels of Escherichia coli in IBS and also revealed increases in Klebsiella spp, which correlated strongly with quantitative culture data. Conclusions. 16S rDNA sequencing confirms microbial overgrowth in the small bowel in IBS, with a concomitant reduction in diversity. qPCR supports alterations in specific microbial populations in IBS.