Nikitina D, Lehr K, Vilchez-Vargas R, Jonaitis LV, Urba M, Kupcinskas J, Skieceviciene J, Link A. Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals. World J Gastroenterol 2023; 29(7): 1202-1218 [PMID: 36926663 DOI: 10.3748/wjg.v29.i7.1202]
Corresponding Author of This Article
Jurgita Skieceviciene, PhD, Professor, Senior Researcher, Institute for Digestive Research, Lithuanian University of Health Sciences, Eivenių g. 4, Kaunas 44307, Lithuania. jurgita.skieceviciene@lsmu.lt
Research Domain of This Article
Gastroenterology & Hepatology
Article-Type of This Article
Case Control Study
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Nikitina D, Lehr K, Vilchez-Vargas R, Jonaitis LV, Urba M, Kupcinskas J, Skieceviciene J, Link A. Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals. World J Gastroenterol 2023; 29(7): 1202-1218 [PMID: 36926663 DOI: 10.3748/wjg.v29.i7.1202]
World J Gastroenterol. Feb 21, 2023; 29(7): 1202-1218 Published online Feb 21, 2023. doi: 10.3748/wjg.v29.i7.1202
Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals
Darja Nikitina, Konrad Lehr, Ramiro Vilchez-Vargas, Laimas Virginijus Jonaitis, Mindaugas Urba, Juozas Kupcinskas, Jurgita Skieceviciene, Alexander Link
Darja Nikitina, Juozas Kupcinskas, Jurgita Skieceviciene, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
Konrad Lehr, Ramiro Vilchez-Vargas, Alexander Link, Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg 39120, Germany
Laimas Virginijus Jonaitis, Mindaugas Urba, Juozas Kupcinskas, Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
Author contributions: Vilchez-Vargas R, Link A, Lehr K, Kupcinskas J, Skieceviciene J and Nikitina D contributed to the study design, analysis, and interpretation of the data; Nikitina D, Link A, and Skieceviciene J drafted the manuscript; Skieceviciene J, Kupcinskas J, Vilchez-Vargas R and Link A supervised the study procedures and revised the manuscript; Nikitina D, Lehr K, and Vilchez-Vargas R performed bioinformatic and statistical analyses; Urba M and Jonaitis LV obtained participant’s samples and provided clinical data; Skieceviciene J and Link A have contributed equally to this work and share last authorship; and all authors read and approved the final version of the manuscript.
Supported bythe MULTIOMICS project that has received funding from European Social Fund (No. 09.3.3-LMT-K-712-01 0130) under grant agreement with the Research Council of Lithuania; and 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”.
Institutional review board statement: The study was approved by the Kaunas Regional Biomedical Research Ethics Committee.
Informed consent statement: All study participants provided informed consent prior to study enrollment.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Data sharing statement: Technical appendix, statistical code, and dataset available from the corresponding author at jurgita.skieceviciene@lsmuni.lt.
STROBE statement: The authors have read the STROBE Statement-checklist of items, and the manuscript was prepared and revised according to the STROBE Statement-checklist of items.
Corresponding author: Jurgita Skieceviciene, PhD, Professor, Senior Researcher, Institute for Digestive Research, Lithuanian University of Health Sciences, Eivenių g. 4, Kaunas 44307, Lithuania. jurgita.skieceviciene@lsmu.lt
Received: October 27, 2022 Peer-review started: October 27, 2022 First decision: November 14, 2022 Revised: November 19, 2022 Accepted: December 21, 2022 Article in press: December 21, 2022 Published online: February 21, 2023 Processing time: 116 Days and 18.3 Hours
ARTICLE HIGHLIGHTS
Research background
There is currently no gold standard for analyzing the microbiome in 16S rRNA studies. Two common modalities are: Sequencing of DNA (16S rRNA gene) and sequencing of RNA (16S rRNA transcript). Gastric cancer (GC) remains one of the most common cancers in the world and microbiome takes important place in its carcinogenesis.
Research motivation
Microbiota studies are becoming more relevant and widespread. Comparison of different approaches for microbiome studying is necessary for correct interpretation of other studies results, as well as for a deeper understanding of bacterial composition.
Research objectives
To investigate how the choice of sequencing modality affects the bacterial profile of differences between case and controls as well as to characterize the microbiota of GC tissues using 16S rRNA gene and its transcript.
Research methods
The study included healthy tissues from the control group, as well as tumor and tumor adjacent tissues from GC patients. From all biopsies RNA and DNA were extracted. 16S rRNA V1-V2 region was sequenced for all samples. For significant differences between groups permutational multivariate analysis of variance and Mann-Whitney test followed by false-discovery rate test were used.
Research results
Only a small portion of bacterial sequences overlapped on DNA and RNA levels in all groups. Differences between GC and control groups also only partially overlayed on DNA and RNA levels. RNA sequencing was more sensitive for detecting differences in bacterial richness, low abundance bacteria, and changes in the relative abundance of Reyranella and Sediminibacterium according to the type of GC. In each study group differences between DNA and RNA bacterial profiles were identified.
Research conclusions
Chosen study material (16S rRNA transcript or 16S rRNA gene) greatly affects detectable microbiome profile as well as the differences between cases and controls.
Research perspectives
This study provides microbiome analysis applying two different methodologies using GC gastric tissues as example and could serve as a reference for future research.
