The microbiome of the esophagus, stomach and duodenum in patients with gastroesophageal reflux disease - pilot study

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F20%3A00073868" target="_blank" >RIV/65269705:_____/20:00073868 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14110/20:00120076

Výsledek na webu

<a href="https://onlinelibrary.wiley.com/doi/10.1177/2050640620927345" target="_blank" >https://onlinelibrary.wiley.com/doi/10.1177/2050640620927345</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1177/2050640620927345" target="_blank" >10.1177/2050640620927345</a>

Jazyk výsledku

angličtina

Název v původním jazyce

The microbiome of the esophagus, stomach and duodenum in patients with gastroesophageal reflux disease - pilot study

Popis výsledku v původním jazyce

Introduction: These days gastroesophageal reflux disease (GERD) represents one of the significant health problems of western countries as a result of several lifestyle factors. Prolonged GERD leads to esophageal inflammation and significantly increases the risk of Barrett&apos;s esophagus (BE) and the subsequent development of esophageal adenocarcinoma (EAC). There is an association between the esophageal microbiome and several esophageal diseases. However, it remains unclear whether the change in microflora leads to esophageal disease, or if this is a side effect of the highly acidic environment created by GERD. Our pilot study aimed to describe oral bacterial biota in patients with GERD and healthy controls from different parts of the esophagus, stomach and duodenum. Detailed microbiome analysis could contribute to early diagnosis and to the application of effective treatment in patients with GERD. Aims &amp; Methods: Tissue samples were taken from each patient with biopsy forceps from several sites in the esophagus, stomach and duodenum. From a total of 74 biopsy specimens obtained via endoscopic examination of 2 patients with GERD, 4 with BE, 4 with EAC and 6 healthy controls, nucleic acid was isolated using the All Prep DNA / RNA / miRNA Universal Kit (Qiagen). The composition of the bacterial community was analyzed by sequencing the 16S rDNA PCR products of the V3-V4 regions on the Illumina MiniSeq platform. Results: The sequence provided 8,335,646 pair-end reads passing quality filters. To describe the bacterial community richness in the collected samples, their alpha diversity was estimated, calculated using normalized rarefaction values. Specific pathological conditions did not significantly change alpha diversity measures (Shannon&apos;s diversity 2.52 Control; 2.48 RE; 2.51 BE; 2.32 EAC); however, there was a trend towards decreased diversity in EAC samples. The relative abundances of the five most abundant phyla in each sample collected were estimated to describe shifts in the bacterial community structure with different conditions. On average, the five most commonly represented bacterial genera were: Firmicutes (39%), Proteobacteria (45%), Bacteroidetes (9%), Actinobacteria (3%), and Fuso-bacteria (1%). Comparison of bacterial communities made using a non-metric multidimensional scaling (NMDS) plot (based on Jaccard similarity, with 97% identity) shows an apparent clustering of esophagus and stomach/duodenum samples. Distribution of taxonomic abundances showed that esophagus samples were dominated by Streptococcus and Prevotella with a lower representation of Veillonella, as reported previously. On the other hand, we did not observe significant clustering of samples from individual pathological conditions but only an increasing trend in gramnegative taxa (Fusobacterium, Campylobacter) was found in esophagus samples from RE and BE patients. Further, an increase in taxa Campylo-bacter and Lactobacillus taxa was observed in the group of EAC patients. Conclusion: In our pilot study, we demonstrated the feasibility of a testing procedure in clinical practice. Our findings are consistent with recent studies presenting the predominant colonization of the esophagus with the bacteria Streptococcus and Prevotella ans a lower proportion of Veillonella. Due to the small number of patients of the same age in the individual groups tested, we were not able to prove significant clustering in a metagenomic analysis. For this reason, we are currently conducting a more extensive study under physiological and pathological conditions in patients with GERD, whose results will be presented.

Název v anglickém jazyce

The microbiome of the esophagus, stomach and duodenum in patients with gastroesophageal reflux disease - pilot study

Popis výsledku anglicky

Introduction: These days gastroesophageal reflux disease (GERD) represents one of the significant health problems of western countries as a result of several lifestyle factors. Prolonged GERD leads to esophageal inflammation and significantly increases the risk of Barrett&apos;s esophagus (BE) and the subsequent development of esophageal adenocarcinoma (EAC). There is an association between the esophageal microbiome and several esophageal diseases. However, it remains unclear whether the change in microflora leads to esophageal disease, or if this is a side effect of the highly acidic environment created by GERD. Our pilot study aimed to describe oral bacterial biota in patients with GERD and healthy controls from different parts of the esophagus, stomach and duodenum. Detailed microbiome analysis could contribute to early diagnosis and to the application of effective treatment in patients with GERD. Aims &amp; Methods: Tissue samples were taken from each patient with biopsy forceps from several sites in the esophagus, stomach and duodenum. From a total of 74 biopsy specimens obtained via endoscopic examination of 2 patients with GERD, 4 with BE, 4 with EAC and 6 healthy controls, nucleic acid was isolated using the All Prep DNA / RNA / miRNA Universal Kit (Qiagen). The composition of the bacterial community was analyzed by sequencing the 16S rDNA PCR products of the V3-V4 regions on the Illumina MiniSeq platform. Results: The sequence provided 8,335,646 pair-end reads passing quality filters. To describe the bacterial community richness in the collected samples, their alpha diversity was estimated, calculated using normalized rarefaction values. Specific pathological conditions did not significantly change alpha diversity measures (Shannon&apos;s diversity 2.52 Control; 2.48 RE; 2.51 BE; 2.32 EAC); however, there was a trend towards decreased diversity in EAC samples. The relative abundances of the five most abundant phyla in each sample collected were estimated to describe shifts in the bacterial community structure with different conditions. On average, the five most commonly represented bacterial genera were: Firmicutes (39%), Proteobacteria (45%), Bacteroidetes (9%), Actinobacteria (3%), and Fuso-bacteria (1%). Comparison of bacterial communities made using a non-metric multidimensional scaling (NMDS) plot (based on Jaccard similarity, with 97% identity) shows an apparent clustering of esophagus and stomach/duodenum samples. Distribution of taxonomic abundances showed that esophagus samples were dominated by Streptococcus and Prevotella with a lower representation of Veillonella, as reported previously. On the other hand, we did not observe significant clustering of samples from individual pathological conditions but only an increasing trend in gramnegative taxa (Fusobacterium, Campylobacter) was found in esophagus samples from RE and BE patients. Further, an increase in taxa Campylo-bacter and Lactobacillus taxa was observed in the group of EAC patients. Conclusion: In our pilot study, we demonstrated the feasibility of a testing procedure in clinical practice. Our findings are consistent with recent studies presenting the predominant colonization of the esophagus with the bacteria Streptococcus and Prevotella ans a lower proportion of Veillonella. Due to the small number of patients of the same age in the individual groups tested, we were not able to prove significant clustering in a metagenomic analysis. For this reason, we are currently conducting a more extensive study under physiological and pathological conditions in patients with GERD, whose results will be presented.

Druh

O - Ostatní výsledky

CEP obor

—

OECD FORD obor

30219 - Gastroenterology and hepatology

Projekt

<a href="/cs/project/NU20-03-00126" target="_blank" >NU20-03-00126: Hostitelský mikrobiom ve vztahu k rozvoji Barrettova jícnu a adenokarcinomu jícnu</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2020

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů