Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals  

作　　者：Darja Nikitina Konrad Lehr Ramiro Vilchez-Vargas Laimas Virginijus Jonaitis Mindaugas Urba Juozas Kupcinskas Jurgita Skieceviciene Alexander Link 

机构地区：[1]Institute for Digestive Research,Lithuanian University of Health Sciences,Kaunas 44307,Lithuania [2]Department of Gastroenterology,Hepatology and Infectious Diseases,Otto-von-Guericke University Hospital,Magdeburg 39120,Germany [3]Department of Gastroenterology,Lithuanian University of Health Sciences,Kaunas 44307,Lithuania

出　　处：《World Journal of Gastroenterology》2023年第7期1202-1218,共17页世界胃肠病学杂志（英文版）

基　　金：the MULTIOMICS project that has received funding from European Social Fund(No.09.3.3-LMT-K-712-010130)under grant agreement with the Research Council of Lithuania;the“LiLife”project as part of the“Autonomy in old Age”research group(No.ZS/2018/11/95324)under grant agreement with European Commission through the“European Funds for Regional development”.

摘　　要：BACKGROUND Helicobacter pylori and the stomach microbiome play a crucial role in gastric carcinogenesis,and detailed characterization of the microbiome is necessary for a better understanding of the pathophysiology of the disease.There are two common modalities for microbiome analysis:DNA(16S rRNA gene)and RNA(16S rRNA transcript)sequencing.The implications from the use of one or another sequencing approach on the characterization and comparability of the mucosal microbiome in gastric cancer(GC)are poorly studied.AIM To characterize the microbiota of GC using 16S rRNA gene and its transcript and determine difference in the bacterial composition.METHODS In this study,316 DNA and RNA samples extracted from 105 individual stomach biopsies were included.The study cohort consisted of 29 healthy control individuals and 76 patients with GC.Gastric tissue biopsy samples were collected from damaged mucosa and healthy mucosa at least 5 cm from the tumor tissue.From the controls,healthy stomach mucosa biopsies were collected.From all biopsies RNA and DNA were extracted.RNA was reverse transcribed into cDNA.V1-V2 region of bacterial 16S rRNA gene from all samples were amplified and sequenced on an Illumina MiSeq platform.Bray-Curtis algorithm was used to construct sample-similarity matrices abundances of taxonomic ranks in each sample type.For significant differences between groups permutational multivariate analysis of variance and Mann-Whitney test followed by false-discovery rate test were used.RESULTS Microbial analysis revealed that only a portion of phylotypes(18%-30%)overlapped between microbial profiles obtained from DNA and RNA samples.Detailed analysis revealed differences between GC and controls depending on the chosen modality,identifying 17 genera at the DNA level and 27 genera at the RNA level.Ten of those bacteria were found to be different from the control group at both levels.The key taxa showed congruent results in various tests used;however,differences in 7 bacteria taxa were found uniquely only at the DNA

关 键 词：Gastric cancer MICROBIOME Helicobacter pylori 16S rRNA gene 16S rRNA transcript 16S rDNA 

分 类 号：R735.2[医药卫生—肿瘤]