Publications
Application of Metagenomics approaches for Crohn’s Disease Istanbul University
Dec 8, 2022Journal Journal of Population Therapeutics & Clinical Pharmacology
Publisher Omar Sajer Naser1*, Elmira Davasaz Tabrizi2*, Dr. Ercan Arican3
DOI DOI: 10.47750/jptcp.2023.30.03.066
Issue 3
Volume 30
Crohn’s Disease (CD) also called the Chronic inflammation of the intestinal system, as well known as regional enteritis or regional ileitis generally occurs in the terminal segment of the ileum, the section of the small bowel farthest from the stomach (Barbara A. Schreiber, 2022). The study's aim was to identify the differences in the gut microbiome composition between patients with and without CD, as well as compare them with healthy control samples (a total of 35 human blood samples). This study is focusing on the mutations/variations in innate immunity and adaptive immunity genes, which increase the risk of inflammatory bowel disease. With that, it aimed to evaluate the effects of mutations on microbiota balance and dysbiosis observed in CD patients (Petagna L et al., 2020). As indicated in the results, we found the first principal coordinate which shows a percentage of 55.09% for the PC1 while showing a percentage of 22.26% for the C2. Moreover, the other principal coordinate shows a percentage of 55.09% for the PC1 while showing a percentage of 9.39% for the C2. Additionally, In the taxonomic classification, we found that bacterial community was found in samples C1 and C2 as similar to a CD. According to the results, all the microorganisms present are bacteria, but with differences in the phylum, order, family, genus, and species. Furthermore, it can be inferred that at the phylum level, the dominant bacteria are proteobacteria, at the class level, the dominant ones are gammaproteobacteria while at the order level, the dominant ones are pseudomonadellas. Keywords: Crohn’s disease. Gastrointestinal. Metagenomics
Bioinformatic challenge on prostate cancer and urinary microbiome
Sep 25, 2023Journal Reto bioinformático sobre el cáncer de próstata y el microbioma urinario
Publisher Elmira Davasaz Tabrizi1* Mushteba Sevil2 Omar Sajer Naser3 Ercan Arican4
DOI DOI: http://doi.org/10.5281/zenodo.10029976
Issue 6
Volume 18
The Bioinformatics Resource Center (BRC) program was developed by the National Institute of Allergy and Infectious Diseases (NIAID) to assist researchers in analyzing the increasing amount of genomic sequences and other omics-related data. In this work, whole-genome sequences of prostate cancer and genitourinary diseases (WGS) were examined for genes utilizing the BV-BRC Bioinformatics Resource Center. using the Usegalaxy program to combine the plasma and gut microbiome sequences from prostate cancer patients. Following that, chromosomes, plasmids, and unclassified sequences were subjected to ARG analysis. As a result of comprehensive genomic analysis of all samples, the S2 sequences were of good quality compared to the other sequences. As for virulence factors, intracellular survival is one of the important virulence factors, a common gene of Salmonella, which was represented in the prostate cancer samples but not in the urine microbiome samples. Keywords: Bioinformatic, Virulence factors, Antibiotic resistance gene, Prostate cancer.