Sürdürülebilir Kalkınma Amaçları
Yayınlar
- MakaleAçık Erişim2025Scopus SJRQ3Identification of additional probiotic attributes in yeasts isolated from tarhana fermentation
Erdem, Belgin; Kaya, Halil İbrahim; Tulumoğlu, Şener; Coteli, Ebru; Şimşek, Ömer
Fermented foods constitute a valuable source of probiotics for both bacteria and yeasts. To date, however, there has been a limited amount of research conducted on Saccharomyces cerevisiae, Kazakhstania servazzi, Kluyveromyces marxianus and Torulaspora delbrueckii isolated from tarhana. The objective of the research is to identify additional probiotic characteristics other than the leavening activity exhibited by yeasts that were previously isolated from tarhana fermentation. In this study, yeasts were subjected to subsequent acid and bile salt tolerance, bile salt hydrolysis, antagonistic activity, aggregation activity (auto-aggregation and co-aggregation), cholesterol assimilation, folate production, biofilm production, and hemolysis activity. S. cerevisiae PCF122, S. cerevisiae PCF107, and S. cerevisiae PCF134 strains grew at pH 2 and 2,5 but remained at pH 3. Except for S. cerevisiae PCF115 and T. delbrueckii PCF150, all yeasts were found to be 0,5% and 1,0% oxalate tolerant. All yeasts hydrolyze oxalate (bile salt), but only S. cerevisiae PCF115 and T. delbrueckii PCF150 produced EPS. Yeasts also exhibited significant amounts of autoaggregation (46–87%). After 24 and 48 h incubation, all strains assimilated cholesterol at rates ranging from 10,4% to 87,5% and 10,6–91%, respectively. The highest folate production was determined at S. cerevisiae PCF108 (56 µg/mL) and the lowest was at S. cerevisiae PCF110 and K. marxianus PFC120 (18 µg/mL). In conclusion, yeasts that existed in tarhana fermentation showed cholesterol assimilation, folate production, and aggregation activity which are additional probiotic attributes that would have consumer health promotion, beside these yeast leaven the tarhana dough.
AtıfScopus2WoS1OpenAlex1
İncele - Derleme MakaleAçık Erişim2025Scopus SJRQ1Expanding Layers of Bacteriocin Applications: From Food Preservation to Human Health Interventions
Demirgül, Furkan; Kaya, Halil İbrahim; Ucar, Redife Aslıhan; Mitaf, Naciye Afranur; Şimşek, Ömer
Bacteriocins, ribosomally synthesized by bacteria, have long been recognized for their role in ensuring food safety and security due to their antibacterial effects against foodborne pathogens and spoilage bacteria. However, recent advancements have unveiled their expanding potential beyond food applications, with increasing evidence of their efficacy against clinically significant pathogenic bacteria, biofilm formation, viral infections, and even cancer. These emerging discoveries have continuously added new layers to the application of bacteriocins, extending their relevance from food preservation to broader human health interventions. To further harness this expanding potential, various innovative strategies have been developed to overcome traditional limitations associated with bacteriocin use. Instead of directly employing bacteriocins or bacteriocin-producing bacterial cultures, novel approaches, such as incorporating them into films and packaging materials or coupling them with nanoparticles, have demonstrated enhanced effectiveness. In this review, we examine the evolving landscape of bacteriocin applications and shed light on the expanding functional spectrum of bacteriocins for both food safety and human health, although some important challenges and limitations remain. By analyzing the recent literature and innovative technological advancements, we highlight how bacteriocins are continuously evolving, opening new frontiers for their use and reinforcing their significance beyond their conventional roles.
AtıfScopus22WoS21OpenAlex22İncele - MakaleYalnız künye2022Scopus SJRQ1Comparison of the probiotic characteristics of Lactic Acid Bacteria (LAB) isolated from sourdough and infant feces
Kaya, Yasemin; Erten, Tayyibe; Vurmaz, Melike; İspirli, Hümeyra; Şimşek, Ömer; Dertli, Enes
Probiotics are beneficial microorganisms with certain characteristics such as survival under gastrointestinal conditions, adhesion to intestinal surface and different functions which result in several health benefits to host. With this regards, this study aimed to isolate Lactic Acid Bacteria (LAB) from sourdough and human feces as two different environments and to test their potential probiotic functions. In total nine distinct isolates were assessed with several probiotic functions such as in vitro adhesion to human colon cells, antimicrobial activities and survival under harsh gastrointestinal conditions. In general, distinct strains showed strong antimicrobial activity against the pathogenic and fungal strains tested in this study. Importantly, the adhesion levels to HT29 cells were determined between 0.29 % and 9.54% and Lactobacillus paracasei F7B showed the highest adhesion. All isolates tolerated the bile salt after 24 h and the infant feces isolates showed good survival characteristics at pH 4.
AtıfScopus18WoS15OpenAlex18İncele - MakaleAçık Erişim2020Tarhanadan izole edilen laktobasiller tarafından üretilenbakteriyosinlerin karakterizasyonu
Kaya, Halil İbrahim; Şimşek, Ömer
Tarhana Anadolu’da kış için hazırlanan ve sık tüketilen fermente bir gıdadır. Fermente tarhana hamuru laktik asit bakterileri (LAB) ve maya türlerinden oluşan mikrofloraya sahiptir. Bu florada bazı LAB’de bakteriyosin üretimiyle antimikrobiyal aktivite gösterirler. Çalışmamızın amacı tarhanadan izole edilmiş L. namurensis PFC70, L. plantarum PFC74 ve L. paralimentarius PFC97 suşlarının bakteriyosinlerinin belirlenmesi ve karakterizasyonudur. PFC70, PFC74 ve PFC97 suşlarının Micrococcus luteus DSM1790 suşuna karşı 400, 1600, 1600 AU/mL antimikrobiyal aktiviteye sahip olduğu belirlenmiştir. Suşların kültür üst sıvılarındaki metabolitlerin yüksek sıcaklığa ve proteaz enzimlerine karşı hassas, düşük pH koşullarında stabil, bakteriyosin tabiatında olduğu anlaşılmıştır. Üretici hücrelerin genomunda yapılan PZR taramasında, PFC74 bakteriyosininin plantarisin benzeri olduğu belirlenmiştir. Bakteriyosinler, amonyum sülfat çöktürmesi, katı faz ekstraksiyonu ve ters faz sıvı kromotografisi ile saflaştırılmış ve trisin-SDS PAGE ile moleküler büyüklükleri 5 kDa altında olduğu tespit edilmiştir. PFC70 vePFC74 bakteriyosini bakteriyosidal, PFC97 ise bakteriyostatik etkili bulunmuştur. Bu sonuçlar PFC70 suşunun yeni bir bakteriyosin üreticisi olduğunu göstermiştir.
- MakaleAçık Erişim2020Scopus SJRQ2Characterization of pediococcus acidilactici PFC69 and lactococcus lactis PFC77 bacteriocins and their antimicrobial activities in tarhana fermentation
Kaya, Halil İbrahim; Şimşek, Ömer
Tarhana is a traditional cereal product fermented by lactic acid bacteria (LAB) and yeast strains that has gained special interest recently as an infant nutrition. Tarhana contains wheat flour, yogurt, and various vegetables that might create a microbiological toxicological risk, especially for Bacillus cereus and Staphylococcus aureus. In this study, characterization of the metabolites responsible for antibacterial activity of Pediococcus acidilactici PFC69 and Lactococcus lactis PFC77 strains obtained from tarhana was performed, and antibacterial effects were detected against B. cereus ATCC 11778 and S. aureus ATCC 29213 during the fermentation. A total of 12,800 AU/mL antibacterial activity was observed for the supernatants of the PFC69 and PFC77 strains that were found to be stable at high temperature and in low pH conditions and sensitive to proteases, suggesting the antimicrobial metabolite is a bacteriocin. These bacteriocins were further purified and their molecular sizes were determined as 4.5 and 3.5 kDa, respectively. Importantly, inoculation of PFC69 and PFC77 to tarhana dough significantly decreased B. cereus ATCC 11778 and S. aureus ATCC 29213 amounts from the fifth day of fermentation compared to the control dough samples. P. acidilactici PFC69 and L. lactis PFC77 strains were concluded as bioprotective cultures for tarhana and these strains were offered for other cereal-based fermentations.
AtıfScopus29WoS25OpenAlex33İncele - MakaleAçık Erişim2020Scopus SJRQ2Structural and technological characterization of ropy exopolysaccharides produced by Lactobacillus plantarum strains isolated from Tarhana
Zehir Şentürk, Duygu; Dertli, Enes; Erten, Hüseyin; Şimşek, Ömer
Exopolysaccharide producing starter cultures enable manufacturing “clean labeled” foods with improved textural and nutritional properties. The structural and technological analyses were performed on the ropy exopolysaccharides of six Lactobacillus plantarum. The incubation temperature, time and pH affected the exopolysaccharide production and high exopolysaccharide was produced in the presence of sucrose and maltose. The viscosity of exopolysaccharide was high at acidic conditions except PFC311E that showed viscous at neutral pH. Lactobacillus plantarum strains produced between 120 and 400 mg/L exopolysaccharide in which the highest was observed at L. plantarum PFC311. Exoploysaccharides were degraded over 300 °C except PFC311E that degraded at 295.7 °C. The NMR analyses revealed that the exopolysaccharides were synthesized by α1-6, α1-3 and α1-4 bonds with glucose, galactose and fructose moieties. In conclusion, L. plantarum PFC311 produced ropy exopolysaccharide with different structural, rheological and thermal properties and reveals potential to be used in food industry.
AtıfScopus42WoS37OpenAlex36İncele - Proje2019Nadir Bir Ekzopolisakkarit Olarak Alternanın Fonksiyonel Etkilerinin Belirlenmesi, Alternan Üretiminden Sorumlu Alternansükraz Enziminin Ekspresyonu ve Aktivitesinin Tespiti
Yılmaz, Mustafa Tahsin; Şimşek, Ömer; Dertli, Enes
Laktik Asit Bakterileri (LAB)?nin starter kültür olarak islevlerine ilave olarak son dönemde bu önemli mikrobiyal grubun ürettigi fonksiyonel metabolitler üzerinde durulmaktadır. Bu metabolitlerin basında da LAB türleri tarafından in situ olarak üretilip gıda maddelerinin fizikokimyasal niteliklerini gelistirebilen ekzopolisakkaritler (EPS) gelmektedir. LAB türlerinde yapısal olarak glukoz/fruktoz?dan olusabilen homopolimerik EPS üretimi ucuz substrat ve yüksek miktarda üretim nedeniyle temel olarak ?-glukan üretimi çerçevesinde sekillenmektedir ve sükrozun substrat olarak kullanılması ile ?-glukan üretiminden glukansükrazlar sorumludur. LAB türlerinde glukansükrazların aktivitesi ile alternan gibi farklı yapılarda ?-glukan üretimi gerçeklesebilmektedir. Son dönemde LAB türlerinde ortaya çıkartılan ?-glukan üretebilen bir diger enzim grubu da sükrozda inaktif ancak amiloz gibi ?-1- 4 glikozidik bagı içeren substratlara etki edip açıga çıkan glukoz ünitelerini farklı baglar ile baglayabilen glukanotransferazlardır. Her iki enzim grubu ile de farklı yapılarda fonksiyonel etkileri olabilecek polisakkarit/oligosakkaritlerin üretimi gerçeklesebilmekte olup, bu enzimlerin aktivitelerinin belirlenerek üretebildikleri polisakkarit/oligosakkaritlerin karakterizasyonu ve bu bilesenlerin fonksiyonel etkilerinin tespiti son derece önemli bir husustur. Bu baglamda bu projenin amacı eksi hamurdan izole edilen alternan üreticisi oldugu gösterilen Lactobacillus reuteri E81?de alternan üretiminin eksi hamur üretimi açısından fonksiyonel etkilerini ortaya koymak, alternan üretiminden sorumlu glukansükrazın ve yine aynı bakteride açıga çıkartılan 4,6-?-glukanotransferazın aktivitesinin ve sırasıyla verici-alıcı reaksiyonları ve farklı substratlarda üretebildikleri oligosakkaritlerin karakterizasyonu ve bu oligosakkaritlerin bagısıklık düzenleyici ve prebiyotik potansiyellerinin belirlenmesidir. Proje kapsamında öncelikle Lactobacillus reuteri E81 eksi hamurdan izole edilip ürettigi alternanın fizikokimyasal karakterizasyonu gerçeklestirilmis ve bakterinin bütün genom sekansı açıga çıkartılmıstır. L. reuteri E81?in genom analizi bu bakteri de glukansükraz (gtfA) enzimine ilaveten 4,6-?-glukanotransferaz (gtfB) enzimini kodlayabilecek bir genin genomda yer aldıgını göstermistir. Ilk olarak eksi hamur ve ekmeginin nitelikleri açısından alternan üretiminin fonksiyonel etkilerinin anlasılabilmesi için gtfA geni L. reuteri E81?den silinmis ve L. reuteri E81 ve alternan üretemeyen L. reuteri E81 ?gtfA ile eksi hamur üretilip eksi hamurun fizikokimyasal özellikleri ve eksi hamur ekmeginin yapısal karakteristikleri üzerine alternan üretiminin etkileri açıga çıkartılmıs ve alternan üretiminin hamunun viskoelastik yapısının gelisimine katkı sagladıgı ortaya konmustur. Ikinci olarak L. reuteri E81?den gtfA ve gtfB genleri Escherichia coli BL21 (DE3) hücrelerinde üretilip glukansükraz (GTFA) ve 4,6-?- glukanotransferaz (GTFB) enzimlerinin aktivitesi ortaya konmus ve ürettikleri ?-glukanların yapıları Nükleer Manyetik Rezonans (NMR) spektroskopisi ile belirlenmistir. Takiben GTFA enziminin sükroz ve farklı seker alıcılarla ve GTFB enziminin ise ?-1-4 bagı içeren farklı substratlardan üretebildikleri oligosakkaritler Ince Tabaka Kromatografisi (TLC), NMR ve Sıvı Kromatografisi-Kütle Spektroskopisi (LC-MS) analizleri ile karakterize edilmis ve her iki enzimin farklı reaksiyonlarda özgün oligosakkaritleri üretme kabiliyetinde oldukları gösterilmistir. Son olarak GTFA ve GTFB ile üretilen bu oligosakkaritlerin fonksiyonel etkileri in vitro olarak HT-29 kolon hücrelerinde IL-10, IL-4, IL-12 ve TNF-? sitokinlerinin indüklenme potansiyelleri ve probiyotik ve patojen bakterilerin gelisimi üzerine potansiyel etkileri incelenerek ortaya konmus ve oligosakkarit düzeyinde fonksiyonel etkinin degisiklik gösterebildigi açıga çıkartılmıstır.
- MakaleAçık Erişim2019Scopus SJRQ1Characterization of a 4,6‑α‑glucanotransferase from Lactobacillus reuteri E81 and production of malto-oligosaccharides with immune-modulatory roles
İspirli, Hümeyra; Şimşek, Ömer; Skory, Christopher; Sağdıç, Osman; Dertli, Enes
A wide number of Lactic Acid Bacteria (LAB) species produce α-glucans with their ability to synthesize glucansucrases (GS) which use sucrose as substrate for the glucan production. Recently another group of enzymes in LAB gained special interest for their ability to produce α-glucans targeting the substrates containing α1-4-linkages and synthesizing new (α1-6) or (α1-3)–linkages as α‑glucanotransferases. In this study, a putative 4,6‑α‑glucanotransferase (GTFB) from sourdough isolate Lactobacillus reuteri E81 was identified and expressed in Escherichia coli. The biochemical characterization of the GTFB-E81 confirmed its function as it cleaved the α1-4-linkages in different substrates and produced new gluco-oligomers/polymers containing α1-6 linkages together with the α1-4-linkages detected by NMR analysis. GTFB-E81 produced malto-oligosaccharides targeting maltose and maltoheptaose as substrates with up to DP 8 detected by TLC and ESI-MS/MS analysis. The functional roles of these malto-oligosaccharides were determined by testing their immune-modulatory functions in HT29 cells and they triggered the production of anti-inflammatory 1L-4 and pro-inflammatory IL-12 cytokines.
AtıfScopus43WoS40OpenAlex42İncele - MakaleAçık Erişim2018Scopus SJRQ3Genome sequences of five Lactobacillus sp. isolates from traditional Turkish sourdough
Dertli, Enes; Skory, Christopher D.; Şimşek, Ömer
A high level of variation in microflora can be observed in profiles of lactic acid bacteria (LAB) from sourdoughs. Here, we present draft genome sequences of Lactobacillus reuteri E81, L. reuteri LR5A, L. rhamnosus LR2, L. plantarum PFC-311, and the novel Lactobacillus sp. strain PFC-70, isolated from traditional Turkish backslopped wheat sourdoughs.
AtıfScopus8WoS8OpenAlex9İncele
