第三代测序分析检测出功能性消化不良患者和对照组之间十二指肠微生物组组成的显著差异。

IF 3.5 3区 医学 Q1 CLINICAL NEUROLOGY Neurogastroenterology and Motility Pub Date : 2024-11-03 DOI:10.1111/nmo.14955
Georgios Tziatzios, Emmanouil Stylianakis, Georgia Damoraki, Paraskevas Gkolfakis, Gabriela Leite, Ruchi Mathur, Mark Pimentel, Evangelos J Giamarellos-Bourboulis, Konstantinos Triantafyllou
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引用次数: 0

摘要

背景:功能性消化不良(FD)是一种多因素疾病,其发病可能基于几种不同的病理生理机制。肠道微生物组与宿主的相互作用被认为是该疾病发病机制中的一个潜在机制:我们旨在分析 FD 患者十二指肠管腔内容物(DLC)的微生物组特征,并将其与对照组(CG)和肠易激综合征(IBS)患者进行比较。符合罗马IV标准的FD、肠易激综合征和对照组(CG)门诊患者接受上消化道内窥镜检查,并在无菌收集器中吸取2毫升十二指肠吸出物(第3-4部分)。在牛津纳米孔 MinION 上进行 DNA 提取和 16S 基因测序,然后进行 EPI2ME 分析(ONT/Metrich-ore Ltd)后,对十二指肠微生物组进行评估。微生物组的生物分析(α-、β-多样性、所有分类等级的相对丰度比较)由 Python 实现。多组均值比较采用单因子方差分析(ANOVA)和 Kruskal-Wallis 检验,并分别采用 Tuckey's 和 Dunn's post hoc 检验进行显著性检验(P-value 结果:对 20 名 FD 受试者(8 名女性;年龄 49.9 ± 13.5 岁)、20 名 IBS 受试者(14 名女性;年龄 57.6 ± 14.8 岁)和 10 名 CG 受试者(6 名女性;年龄 49.2 ± 13.8 岁)的 DLC 进行了分析。与对照组相比,FD 受试者的 α 多样性指数明显较低(香农指数,p = 0.0218),与肠易激综合征患者相似。根据物种相对丰度(β-多样性)生成的主坐标分析(PCoA)显示,与对照组相比,FD 和 IBS 患者的 DLC 特征没有差异(p = 0.513)。与对照组相比,FD(p = 0.017)和 IBS(p = 0.026)受试者绿藻门的相对丰度(RA)分别较低。此外,与对照组相比,FD(分别为 p = 0.017 和 p = 0.018)和 IBS(分别为 p = 0.15 和 p = 0.06)患者的红热菌门(Rhodothermota)和热菌门(Thermotogota)的丰度较低。有趣的是,在随后所有主要分类级别的分析中,与对照组相比,FD 受试者的绿藻门(Chloroflexota)、红藻门(Rhodothermota)和热藻门(Thermotogota)特定类群的RA值一直较低,但与 IBS 相似。在类别水平上,FD 组和 CG 组之间在合成细菌、酸性硫杆菌、嗜胞杆菌和黄杆菌方面存在显著差异(p 结论与推论:FD患者十二指肠腔内容物的微生物组图谱与对照组有显著差异,包括微生物区系多样性较低、微生物区系结构/组成和特定分类群不同。胃食管反流患者和肠易激综合征患者的 DLC 没有明显的类似差异。
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Third generation sequencing analysis detects significant differences in duodenal microbiome composition between functional dyspepsia patients and control subjects.

Background: Functional dyspepsia (FD) is a multifactorial disorder as its development may be based on several different pathophysiological mechanisms. Interaction of gut microbiome with the host has been proposed as a potential mechanism involved in the disease's pathogenesis.

Aim/methods: We aimed to characterize microbiome profiling on duodenal luminal content (DLC) of FD patients and compare it to that of controls (CG) and patients with irritable bowel syndrome (IBS). Outpatients fulfilling Rome IV criteria for FD, IBS, and control group (CG) underwent upper gastrointestinal endoscopy and 2 cc of duodenal aspirate (3rd - 4th part) was aspirated in sterile traps. Duodenal microbiome was assessed after DNA extraction and 16S gene-based sequencing on Oxford Nanopore MinION followed by EPI2ME analysis (ONT/Metrich-ore Ltd). Bioanalysis of the microbiome (alpha-, beta-diversity, comparisons of relative abundances for all taxonomic ranks) was implemented in Python. Multiple group means comparisons were performed with one-way Analysis of Variance (ANOVA) and Kruskal-Wallis test with Tuckey's and Dunn's post hoc tests respectively, in case of significance (P-value <0.05).

Results: 20 subjects with FD (8 females; age 49.9 ± 13.5 yrs.), 20 with IBS (14 females; age 57.6 ± 14.8 yrs.) and 10 CG (6 females; age 49.2 ± 13.8 yrs.) had their DLC analyzed. The α-diversity index of subjects with FD was significantly lower compared to controls (Shannon's index, p = 0.0218) and similar to that of patients with IBS. Principal Coordinate Analysis (PCoA) generated from species relative abundances (beta-diversity) showed no difference in the DLC profile of subjects with FD and IBS when compared to controls (p = 0.513). Compared to controls, the relative abundance (RA) of Chloroflexota phylum was lower in subjects with FD (p = 0.017) and IBS (p = 0.026), respectively. Additionally, the RA of the Rhodothermota and Thermotogota phyla was lower in FD (p = 0.017 and p = 0.018, respectively) but not in IBS patients (p = 0.15 and p = 0.06, respectively) compared to controls. Interestingly, the RA of specific taxa from Chloroflexota, Rhodothermota and Thermotogota phyla were consistently lower in subjects with FD when compared to CG but similar to IBS, during analysis of all the subsequent major ranks of taxonomy. At the class level, there were significant differences in Syntrophobacteria, Acidithiobacillia, Cytophagia and Flavobacteriia between the FD and CG groups (p < 0.05), but no such difference between FD and IBS was found. Finally, multiple significant differences at the order, family, genus and species level between the FD and CG groups were also detected. A positive relationship between the RA of Streptococcus and those from genus Granulicatella was observed both in FD (p = 0.014) and IBS (p = 0.014) patients.

Conclusion & inferences: The microbiome profiling from duodenal luminal content of FD patients is significantly different to that of controls, including lower microflora diversity, different microflora structure/composition and specific taxa. Similar differences in the DLC between FD and IBS patients were not evident.

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来源期刊
Neurogastroenterology and Motility
Neurogastroenterology and Motility 医学-临床神经学
CiteScore
7.80
自引率
8.60%
发文量
178
审稿时长
3-6 weeks
期刊介绍: Neurogastroenterology & Motility (NMO) is the official Journal of the European Society of Neurogastroenterology & Motility (ESNM) and the American Neurogastroenterology and Motility Society (ANMS). It is edited by James Galligan, Albert Bredenoord, and Stephen Vanner. The editorial and peer review process is independent of the societies affiliated to the journal and publisher: Neither the ANMS, the ESNM or the Publisher have editorial decision-making power. Whenever these are relevant to the content being considered or published, the editors, journal management committee and editorial board declare their interests and affiliations.
期刊最新文献
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