Browsing by Author "Ilikkan, Ozge Kahraman"

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A Novel Synbiotic Edible Film Based On Aquafaba, Psyllium Husk Powder, Peg 400, And Lactiplantibacillus Plantarum 299v And Applicability On Kashar Cheese
(JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION, 2024-12) Ilikkan, Ozge Kahraman; Bagdat, Elif Seyma; Yilmaz, Ilkay; Beyter, Nurten; Yuzay, Isinay Ebru
In this study, it was aimed to compare a novel synbiotic edible film based on aquafaba, psyllium husk powder, and PEG 400 with or without Lactiplantibacillus plantarum 299v. Therefore, primarily, optimization of the edible film was carried out by Box-Behnken design in response surface methodology (rsm). The characterization of edible films with or without probiotic bacteria was performed by FTIR, viscosity, pH, total solid content, water and oxygen solubility, film thickness, color L*, a*, b*, transparency, and film tensile strength. It was determined that there was no statistically significant difference in viscosity, pH, lightness L*, water vapor, and oxygen permeability values with the addition of probiotic lactic acid bacteria to the optimized coating film samples. In addition, it was observed that the probiotic bacteria count did not decrease below 108 cfu/g for 60 days of storage. The resulting edible film formulation with (PL) and without (PS) probiotics was used to coat Kashar cheese, while control cheeses (C) were not coated. As a result, it was observed that the microbiological quality of the coated cheeses was as good as control or better than control especially at the end of storage in terms of mold/ yeast and coliforms. Sensory evolution revealed coating films with or without probiotics did not change the texture, flavor, odor, or appearance of cheeses. Physicochemical properties such as pH, % titratable acidity, % dry matter, % fat, and % salt were detected.
Analysis of Probiotic Bacteria Genomes: Comparison of CRISPR/Cas Systems and Spacer Acquisition Diversity
(2021) Ilikkan, Ozge Kahraman; 0000-0001-5843-6868; 35068602; Q-9641-2019
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes constitute an adaptive (acquired) defense system of bacteria and archaea. Here 72 probiotic bacteria genomes were investigated in terms of the presence of CRISPR/Cas systems and phage/plasmid invaders through spacer analysis. 49 CRISPR/Cas systems were detected within probiotic strains, namely,17 type II-A, 10 type I-C, 8 type I-E, 5 Type I-U (I-G), 4 type III-A, 2 type I-B, 1 type I-A, 1 type IV-B, and 1 type II-C. The predicted target of spacers was determined in 25 strains and consequently, three different spacer and target patterns were revealed. The diversity of CRISPR spacers provides insight and understanding to determine strain-specific invaders of probiotic bacteria as well as their relationships between strains. CRISPR systems were clarified in many studies for genomic characterization. However, recently, endogenous genome editing with CRISPR has provided an approach for various genome editing projects. Thus, in the future, producing strain-specific phage-resistant starter cultures or probiotics by endogenous genome editing methods according to phage/plasmid survey can be utilized for industrial and pharmaceutical applications. Therefore, this study intended a comprehensive investigation of CRISPR systems of probiotic bacteria.
Comparison of bacterial and fungal biodiversity of Turkish kefir grains with high-throughput metagenomic analysis
(2021) Ilikkan, Ozge Kahraman; Bagdat, Elif Seyma; 0000-0001-5843-6868; Q-9641-2019
Kefir is a health-promoting fermented drink having complex microbiota. This complex microbiota consists of bacteria and yeast association that is bound together with a polysaccharide called kefiran. To date, the complex microbiota of fermented foods was enlightened with culture-depended methods, however, recently, metagenomic studies have been started to use to reveal microbial diversity of fermented foods such as kefir. In this present study, we investigated the microbiome of two artisanal Turkish kefir grains (namely, A and G) by high throughput sequencing at the species level. Additionally, physicochemical analyses were carried out besides enumerations of lactobacilli, lactococci, total aerobic, and bifidobacteria in fermented milk kefirs. In these two kefir grains, different bacterial and fungal populations were revealed. In kefir grain A, Bifidobacterium longum was the dominant species while in kefir grain G, Lactobacillus kefiranofaciens was dominant. Concerning fungal diversity, in kefir grain A, Naumovozyma dairensis was the dominant yeast, while in kefir grain G, Zygosaccharomyces rouxii was dominant. High-throughput sequencing studies have revealed that kefir grains were typically dominated by lactobacilli. But, in this study, Bifidobacterium longum was found as a dominant bacterium in kefir for the first time.
Comprehensive Analysis Of The Crispr-Cas Systems In Streptococcus Thermophilus Strains Isolated From Traditional Yogurts
(ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, 2024-12) Ozcan, Ali; Yibar, Artun; Kiraz, Deniz; Ilikkan, Ozge Kahraman
Phage resistance is crucial for lactic acid bacteria in the dairy industry. However, identifying all phages affecting these bacteria is challenging. CRISPR-Cas systems offer a resistance mechanism developed by bacteria and archaea against phages and plasmids. In this study, 11 S. thermophilus strains from traditional yogurts underwent analysis using next-generation sequencing (NGS) and bioinformatics tools. Initial characterization involved molecular ribotyping. Bioinformatics analysis of the NGS raw data revealed that all 11 strains possessed at least one CRISPR type. A total of 21 CRISPR loci were identified, belonging to CRISPR types II-A, II-C, and III-A, including 13 Type II-A, 1 Type III-C, and 7 Type III-A CRISPR types. By analyzing spacer sequences in S. thermophilus bacterial genomes and matching them with phage/plasmid genomes, notable strains emerged. SY9 showed prominence with 132 phage matches and 30 plasmid matches, followed by SY12 with 35 phage matches and 25 plasmid matches, and SY18 with 49 phage matches and 13 plasmid matches. These findings indicate the potential of S. thermophilus strains in phage/plasmid resistance for selecting starter cultures, ultimately improving the quality and quantity of dairy products. Nevertheless, further research is required to validate these results and explore the practical applications of this approach.
Evaluating The Multifaceted Impact Of Cephalaria Extract On Dough Quality: Antioxidant, Antimicrobial, And Cytotoxic Properties
(INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY, 2024-12) Bagdat, Elif Seyma; Bozkurt, Fatih; Ilikkan, Ozge Kahraman; Sagdic, Osman; Tornuk, Fatih
Cephalaria syriaca, known as cephalaria, is an annual, pilose plant with pink-purple flowers growing wild in wheat fields. Viscoelastic properties of gluten-free doughs can be improved by adding cephalaria. However, this addition results in some undesirable properties in bread such as bitter taste and dark internal colour. This study aimed to reduce these effects by obtaining cephalaria obtained from distilled water and ethanol extracts and to increase the potential use of extracts in bread production. Different proportions of water and ethanol extracts obtained from oil-free cephalaria were added to bread by creating a model with Mixture Design, and the optimum concentration was determined by farinograph trials. The antioxidative, antimicrobial, and cytotoxic effects of extract and the effect of cephalaria on yeast activity were examined. Cephalaria extracts had no measurable antimicrobial effect and no antifungal effect on Rhizopus stolonifer, while an antifungal effect was found against A. niger and P. expansum. The IC50 value was found to be 4.15 mg mL(-1 )for ethanol extract while the water extract had no effect on cells. The addition of extract had no negative effect on the number of yeasts in sourdough fermentation. The study has improved the usage of cephalaria by using water and ethanol extracts in dough.