Schmidt Kenneth, Noel-MacDonnell Janelle, Vyhlidal Carrie, Heruth Daniel P, Singh Vivekanand, Ahmed Atif A, Hudson Taina, Williams Veronica, Shakhnovich Valentina
School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA.
Children's Mercy Kansas City, Kansas City, MO 64108, USA.
Pharmaceuticals (Basel). 2022 Jul 11;15(7):850. doi: 10.3390/ph15070850.
Manipulation of the microbiome is a rational treatment strategy for inflammatory bowel disease (IBD). Compared to the colon and terminal ileum (TI), understanding of the microbial composition in the duodenum is sparse. This gap in knowledge is especially significant for children with Crohn’s disease (CD) because the prevalence of duodenal CD is higher in children than in adults. Our aim was to characterize the bacterial composition of the mucosally-adherent duodenal microbiome in children with and without CD as a first step toward development of targeted IBD treatment strategies at this disease location. Fresh-frozen mucosal biopsies were obtained from the duodenum and TI of children with treatment-naïve CD and age- and sex-matched controls. Extracted DNA was analyzed for sequence variation in the 16S ribosomal RNA bacterial gene region V4 (Novogene; Beijing, China). Bacterial relative abundance, alpha and beta composition, and diversity, were compared across duodenal and TI samples from the controls and CD groups with and without chronic active inflammation (118 samples from 73 children total; approx. 50% CD), using UniFrac dissimilarity coefficients (α < 0.05), Linear Discriminant Analysis Effect Size (LEfSe) analysis (LDA score ≥ 2), and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) analysis. The relationships between bacterial abundance, sex, age, concomitant medication use, and villous length were assessed. The microbial composition in the duodenum was significantly different from the TI in the control population(R-value = 0.558, p = 0.001) and in children with active CD (R-value = 0.301, p = 0.001). Significant differences in bacterial abundance were noted between the control and CD duodena (LDA > 4). The duodenum of children without CD was characterized by increased abundance in Pseudomonodales, whereas the actively inflamed duodenum in CD was characterized by increased abundance of Bacteroidales, specifically the family Prevotellaceae. This trend is opposite of previously published observations of microbial composition in the TI, where active inflammation was associated with a relative decrease in the abundance of Bacteroidetes and an increase in Proteobacteria, including Pseudomonadales. No statistically significant correlations were noted between abundance and age, sex, concomitant medication use or villous length, except for Bacteroidetes, which significantly decreased in abundance in the TI with age (p = 0.048). The pediatric duodenal microbiome is distinct from the TI and characterized by an increased abundance of Pseudomonodales and Spirochetes in healthy children, and an increased abundance of Bacteroidales in active CD patients.
微生物群的调控是炎症性肠病（IBD）的一种合理治疗策略。与结肠和回肠末端（TI）相比，对十二指肠中微生物组成的了解较少。对于克罗恩病（CD）患儿而言，这一知识空白尤为显著，因为儿童十二指肠CD的患病率高于成人。我们的目的是描述患有和未患有CD的儿童十二指肠黏膜附着微生物群的细菌组成，作为在此疾病部位开发针对性IBD治疗策略的第一步。从初治CD患儿以及年龄和性别匹配的对照组患儿的十二指肠和TI获取新鲜冷冻的黏膜活检组织。对提取的DNA进行16S核糖体RNA细菌基因区域V4的序列变异分析（诺禾致源；中国北京）。使用UniFrac差异系数（α<0.05）、线性判别分析效应大小（LEfSe）分析（LDA分数≥2）和算术平均非加权配对组方法（UPGMA）分析，比较对照组和CD组十二指肠和TI样本中有无慢性活动性炎症的细菌相对丰度、α和β组成以及多样性（共73名儿童的118个样本；约50%为CD）。评估细菌丰度、性别、年龄、伴随用药情况和绒毛长度之间的关系。对照组人群中十二指肠的微生物组成与TI显著不同（R值=0.558，p=0.001），活动性CD患儿中也是如此（R值=0.301，p=0.001）。对照组和CD组十二指肠之间细菌丰度存在显著差异（LDA>4）。未患CD儿童的十二指肠特征是假单胞菌目丰度增加，而CD中活动性炎症的十二指肠特征是拟杆菌目丰度增加，特别是普雷沃氏菌科。这一趋势与先前发表的TI中微生物组成的观察结果相反，在TI中，活动性炎症与拟杆菌门丰度相对降低以及包括假单胞菌目在内的变形菌门丰度增加有关。除了拟杆菌门在TI中随着年龄增长丰度显著降低（p=0.048）外，丰度与年龄、性别、伴随用药情况或绒毛长度之间未发现统计学上的显著相关性。儿童十二指肠微生物群与TI不同，其特征是健康儿童中假单胞菌目和螺旋体丰度增加，活动性CD患者中拟杆菌目丰度增加。
