Browsing by Author "Kahraman-Ilikkan, Ozge"

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Comparative Genomics Of Four Lactic Acid Bacteria Identified With Vitek Ms (Maldi-Tof) And Whole-Genome Sequencing
(MOLECULAR GENETICS AND GENOMICS, 2024-11) Kahraman-Ilikkan, Ozge
Lactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and identification are essential. Recent advances in omics technologies and high-throughput sequencing have made the identification and characterization of bacteria. This study firstly aimed to demonstrate the sensitivity of the Vitek MS (MALDI-TOF) system in the identification of lactic acid bacteria and, secondly, to characterize bacteria using various bioinformatics approaches. Probiotic potency-related genes and secondary metabolite biosynthesis gene clusters were examined. The Vitek MS (MALDI-TOF) system was able to identify all of the bacteria at the genus level. According to whole genome sequencing, the bacteria were confirmed to be Lentilactobacillus buchneri, Levilactobacillus brevis, Lactiplantibacillus plantarum, Levilactobacillus namurensis. Bacteria had most of the probiotic potency-related genes, and different toxin-antitoxin systems such as PemIK/MazEF, Hig A/B, YdcE/YdcD, YefM/YoeB. Also, some of the secondary metabolite biosynthesis gene clusters, some toxic metabolite-related genes, and antibiotic resistance-related genes were detected. In addition, Lentilactobacillus buchneri Egmn17 had a type II-A CRISPR/Cas system. Lactiplantibacillus plantarum Gmze16 had a bacteriocin, plantaricin E/F.
Comparison Of Propionibacterium Genomes: CRISPR-Cas Systems, Phage/Plasmid Diversity, And Insertion Sequences
(2022) Kahraman-Ilikkan, Ozge; https://orcid.org/0000-0001-5843-6868; 35763226; Q-9641-2019
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems constitute the adaptive immune system in prokaryotes that provide resistance against invasive genetic elements. The genus Propionibacterium comprises gram-positive, facultative anaerobe, non-spore-forming bacteria, and is the source of some B group vitamins such as B12 as well as bacteriocins. Some of the selected species of the genus Propionibacterium spp. were reclassified into the three genera in 2016 (Acidipropionibacterium spp., Pseudopropionibacterium spp., Cutibacterium spp.). Therefore, this study compared CRISPR/Cas systems, Cas 1 and repeat sequences phylogeny, phage/plasmid surveys as well as insertion sequences of new genera members. In this study, a total of 34 genomes of 13 species were observed with a bioinformatic approach. CRISPR-Cas + + and CRISPRDetect were used to detect CRISPR/Cas systems, direct repeats, and spacers. 39 CRISPR-Cas systems were detected. Type I-E, Type I-U, and one incomplete III-B CRISPR-Cas subtypes were identified. Most of the strains had Cas1/Cas4 fusion proteins. Pseudopropionibacterium propionicum strains had two types I-U and one of the CRISPR loci had csx17 cas genes. Common phage invaders were Propionibacterium phage E6, G4, E1, Anatole, and Doucette. The BLSM62 similarity score of all Cas1 sequences was 48.4% while the pairwise identity of repeat sequences was 48.7%. Common insertion sequences were ISL3, IS3, IS30. The diversity analysis of the CRISPR/Cas system in the genus Propionibacterium provided a new perspective for determining the role of the CRISPR-Cas system in the evolution of new genera.
Metataxonomic Sequencing To Assess Microbial Safety Of Turkish White Cheeses
(2022) Kahraman-Ilikkan, Ozge; Bagdat, Elif Seyma; https://orcid.org/0000-0001-5843-6868; 35277850; Q-9641-2019
High-throughput sequencing has provided a way to monitor the large diversity of microorganisms in fermented foods that have complex microbiota. Up to date, many kinds of cheese have been characterized with the metataxonomic approach, but the safety of unpacked Turkish white cheeses, which are widely consumed in Turkey, has not been assessed. In this study, fifteen unpacked white cheeses sold in public bazaars in Ankara province have been collected and subjected to microbial enumeration as well as physicochemical analysis. Five white cheeses, which have relatively the highest foodborne pathogens, out of fifteen white cheeses, have been analyzed by next-generation sequencing and metataxonomic analysis. According to the results, abundant families were Lactobacillaceae, Oceanospirillaceae, Enterococcaceae, Pseudomonadaceae, and Vibrionaceae. Staphylococcus aureus, E. coli, and Salmonella, which are indicators of bad hygiene and sanitation conditions, were found in cheeses. In conclusion, culture-independent methods such as metataxonomic can be important to evaluate the safety of foods.