Case Control Study
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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 by the 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.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/
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
Core Tip

Core Tip: In this study, we aimed to characterize the microbiota of gastric cancer (GC) on two levels: 16S rRNA gene and its transcript. Our study showed that only a small portion of bacterial sequences overlapped using those two approaches. Moreover, our study revealed that obtained results comparing the case group with the controls depend on the chosen modality. We also showed that Reyranella and Sediminibacterium was associated with the Lauren classification and RNA level was more sensitive to detect low abundant bacteria. This study provides novel insights into microbiome study as well as new founding related to complex GC pathogenesis.