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• MakaleAçık Erişim2025/r/bayburt/16178
  Bayburt Yöresel Fermente Süt Ürünlerinden Bakteriyosin Üreticilerinin İzolasyonu, Tanımlanması ve Bakteriyosinlerin Karakterizasyonu

  Kaya, Halil İbrahim

  Laktik asit bakterileri (LAB), diğer antimikrobiyallerin dışında özellikle ürettikleri bakteriyosinler nedeniyle de antimikrobiyal aktiviteye sahiptir. Bakteriyosinlerin gıda üretiminde kullanılması, gıda güvenliğinin iyileştirilmesi ve raf ömrünün uzatılmasına önemli katkılar sağlamaktadır. Bakteriyosinlerin temel özelliklerinden biri, üreticilerin çeşitliliğine göre yapısal varyasyonlara sahip olmaları ve buna bağlı olarak farklı antimikrobiyal aktivite spektrumlarına sahip olmalarıdır. Bu nedenle, yeni bakteriyosinlerin araştırılması ve karakterize edilmesi gerekmektedir. Bu çalışmada, Bayburt'un yerel fermente süt ürünlerinden bakteriyosin üreten LAB izole edilmiş ve bu bakteriler tanımlanmıştır. Daha sonra bakteriyosin üreten suşların antimikrobiyal spektrumu belirlenmiş ve farklı sıcaklık ve enzimlere karşı duyarlılıkları karakterize edilmiştir. Bakteriyosin üreten LAB sırasıyla Lactobacillus plantarum, Pediococcus pentosaceus ve Enterococuus faecium olarak tanımlanmıştır. Bu suşların sırasıyla 7, 6 ve 4 farklı indikatöre karşı antibakteriyel olduğu bulunmuştur. LAB tarafından üretilen bütün bakteriyosinlerin proteolitik enzimlerle muamele edildiklerinde bakteriyosinlerden kaynaklı aktivitelerini kaybettikleri ve protein yapısında oldukları belirlenmiştir. Bunların sırasıyla, 100 oC 10 dakika, 80 oC 10 dakika ve 80 oC 15 dakika ısıl işlem sonrasında stabil olduğu, yani antimikrobiyal aktivitelerini koruduğu tespit edilmiştir.

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  İncele
• MakaleAçık Erişim2025Scopus SJRQ3/r/bayburt/11320
  Identification 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.

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  AtıfScopus2·WoS1·OpenAlex1

  İncele
• Derleme MakaleAçık Erişim2025Scopus SJRQ1/r/bayburt/10965
  Expanding 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.

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  AtıfScopus22·WoS21·OpenAlex22

  İncele
• MakaleAçık Erişim2023Scopus SJRQ1/r/bayburt/11907
  Diversity of Clostridium spp. causing late blowing in Kaşar cheese and their behaviour against various antimicrobials

  Kaya, Halıl Ibrahim; Simsek, Omer; Akgunoglu, Ozlem

  One of the problems encountered during storage of Kaşar cheese is blowing. The diversity of Clostridium spp. having a role in blowing was screened and the sensitivity of Clostridium spp. strains against nisin, NaCl, CuSO4, and EDTA was determined and compared. According to 16S rDNA sequence similarity, 12 Clostridium spp. isolates were Clostridium sporogenes while 3 were Clostridium jeddahense. Gas formation by Clostridium spp. spores can be significantly inhibited by reducing the pH below 5.5 and adding 400 IU mL−1 nisin when the number of spores are below 300 spore mL−1. It was determined that the late-blowing problem in Kaşar cheese is caused by C. sporogenes and C. jeddahense strains, but the success of preventive agents is closely related to the amount of spores.

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  AtıfScopus7·WoS4·OpenAlex6

  İncele
• MakaleAçık Erişim2023Scopus SJRQ3/r/bayburt/11797
  The effect of heart failure on gut microbial richness and diversity; [O efeito da insuficiência cardíaca estável na riqueza e diversidade microbiana intestinal]

  Kilic, Oguz; Kaya, Halil Ibrahim; Secme, Mucahit; Kilinc, Mehmet; Sevgican, Cihan Ilyas; Buber, Ipek; Dodurga, Yavuz; Simsek, Omer; Ergin, Cagrı; Kilic, Ismail Dogu

  Introduction and objective: With recent advances in genome sequencing technology, a large body of evidence has accumulated over the last few years linking alterations in microbiota with cardiovascular disease. In this study, we aimed to compare gut microbial composition using 16S ribosomal DNA (rDNA) sequencing techniques in patients with coronary artery disease (CAD) and stable heart failure (HF) with reduced ejection fraction and patients with CAD but with normal ejection fraction. We also studied the relationship between systemic inflammatory markers and microbial richness and diversity. Methods: A total of 40 patients (19 with HF and CAD, 21 with CAD but without HF) were included in the study. HF was defined as left ventricular ejection fraction <40%. Only stable ambulatory patients were included in the study. Gut microbiota were assessed from the participants’ fecal samples. The diversity and richness of microbial populations in each sample were assessed by the Chao1-estimated OTU number and the Shannon index. Results: The Chao1-estimated OTU number and Shannon index were similar between HF and control groups. There was no statistically significant relationship between inflammatory marker levels (tumor necrosis factor-alpha, interleukin 1-beta, endotoxin, C-reactive protein, galectin-3, interleukin 6, and lipopolysaccharide-binding protein) and microbial richness and diversity when analyzed at the phylum level. Conclusion: In the current study, compared to patients with CAD but without HF, stable HF patients with CAD did not show changes in gut microbial richness and diversity. At the genus level Enterococcus sp. was more commonly identified in HF patients, in addition to certain changes in species levels, including increased Lactobacillus letivazi.

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  AtıfScopus8·OpenAlex7

  İncele
• MakaleAçık Erişim2020/r/bayburt/14935
  Tarhanadan 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.

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• MakaleAçık Erişim2020Scopus SJRQ2/r/bayburt/13291
  Characterization 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.

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  AtıfScopus29·WoS25·OpenAlex33

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