Browsing by Author "Acar, Elif Esma"
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Article Citation Count: 016S Bacterial Metagenomic Analysis of Herby Cheese (Otlu Peynir) Microbiota(Istanbul Univ-cerrahpasa, 2021) Sudağıdan, Mert; Yurt, Mediha Nur Zafer; Taşbaşı, Behiye Büşra; Acar, Elif Esma; Ömeroğlu, Esra Ersoy; Uçak, Samet; Aydın, AliCheese microbiota may contain various bacterial species due to the use of different types of milk, rennet, and herbs. In this study, the distribution of the dominant bacteria present in the microbiota of herby cheese samples (n = 13) were examined by the next generation sequencing (NGS) technique. DNA was extracted both directly from cheese samples and after pre-enrichment. The metagenomic analysis of the NGS results revealed that Firmicutes were dominant both in DNA directly extracted from herby cheese (KOP), and pre-enriched samples (OP), at the phylum level. At the genus level, Lactobacillus, Lactococcus, and Streptococcus were dominant in the KOP samples, whereas in the OP samples, Enterococcus, Streptococcus, and Bacillus were determined as the dominant bacterial genera. Although Lactococcus raffinolactis and Streptococcus salivarius were dominant in the KOP samples, Enterococcus faecalis and S. salivarius were dominant in the OP samples. The Shannon species diversity index and principal coordinates analysis (PCoA) were used to determine the distribution in KOP and OP samples at the genus level. The PCoA of KOP-10, KOP-11, KOP-2, and KOP-7, KOP-3, and KOP-6 samples showed the wide distribution, whereas KOP-5, KOP-8, KOP-9, and KOP-14 herby cheese samples were closely related. The OP samples, especially OP-7 and OP-14, showed wide distribution in comparison to other OP samples. Finally, the dominant bacterial communities were identified by DNAbased metagenomic analysis, and this is the first report to elucidate the microbiota of herby cheese produced in Turkey using the NGS technique.Article Citation Count: 2Bacterial and fungal microbiota of mould-ripened cheese produced in Konya(Wiley, 2023) Özalp, Veli Cengiz; Omeroglu, Esra Ersoy; Tasbasi, Behiye Busra; Acar, Elif Esma; Altunbas, Osman; Ozalp, Veli Cengiz; Sudagidan, Mert; Basic SciencesBacterial and fungal diversities of 24 mould-ripened cheeses originating from Konya-Turkiye were examined by metagenomic analysis. Firmicutes phylum, Enterococcus, Clostridium sensu stricto and Lactobacillus (Levilactobacillus) genera were the dominant bacteria. Ascomycota phylum and Penicillium and Pichia genera and Penicillium roqueforti and Pichia membranifaciens species were dominant fungi. Enterococcus faecium (n = 30) and Enterococcus faecalis (n = 6) were identified, and all strains were susceptible to penicillin, ampicillin, vancomycin, teicoplanin, chloramphenicol and linezolid. The highest resistance (n = 14) was against rifampin. Tetracycline resistance was determined in two strains. Biofilm-forming ability was found in nine E. faecium and 1 E. faecalis. E. faecium strains revealed 40-88.9%, and E. faecalis showed 59.2-100% homology by pulsed field gel electrophoresis.Article Citation Count: 1Boza Mikrobiyotasının Fermantasyon Sürecindeki Değişimi(2021) Kavruk, Murat; Yurt, Mediha Nur Zafer; Taşbaşı, Behiye Büşra; Acar, Elif Esma; Soyuçok, Ali; Altunbaş, Osman; Sudağıdan, Mert; Nutrition and DieteticsBoza, insan sağlığı için yararlı mikroorganizmaları içeren fermente bir içecektir. Çalışmamızda boza üretiminde ham madde olarak kullanılan (mısır unu, buğday unu, mayşe) ve boza fermantasyonunun 1. günü, 3. günü ve 4. gün son ürün boza’nın içerdiği mikrobiyota Yeni Nesil DNA Dizileme yöntemi ve metagenomik analiz ile ortaya çıkarılmıştır. Örneklerden doğrudan cins düzeyinde yapılan analiz sonucunda, mısır unu ve buğday ununda dominant olarak Streptophyta ve Pleomorphobacterium bulunurken; bozanın 1. gün, 3. gün ve son ürün ile boza mayasında dominant bakterilerin Leuconostoc ve Lactococcus cinsine ait olduğu tespit edilmiştir. Ön zenginleştirme yapılan örneklerin analizinde, mısır ununda dominant bakteriler Enterococcus, Klebsiella ve Micromonospora, buğday ununda ise Pantoea ve Bacillus olduğu, boza mayası, 1. gün boza, 3. gün boza ve satışa sunulan son üründe dominant bakteri Lactococcus olarak belirlenmiştir. Çalışmamızda örnekler arasındaki bakteriyel çeşitlilik, benzerlik ve farklılıklar Principal Coordinate Analiz ve dendrogram oluşturulması ile ortaya konmuştur. Boza üretiminde kullanılan ham maddelerin bozanın fermantasyon aşamalarındaki ürünler ile fermantasyon sürecinde mikrobiyotasına nasıl değiştiği ve son ürüne olan katkıları, DNA düzeyinde yapılan metagenomik analizler ile belirlenmiştir.Article Citation Count: 11Determination of bacterial community structure of Turkish kefir beverages via metagenomic approach(Elsevier Sci Ltd, 2022) Yegin, Zeynep; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Altunbas, Osman; Ucak, Samet; Sudagidan, MertBacterial microbiota of industrially produced kefir beverages (n:33) consumed in Turkey was studied using a culture-independent method and a metagenomic approach. DNA extraction from non pre enriched and pre-enriched kefir samples was used for 16S rRNA amplicon sequencing. Kefirs were dominated by Firmicutes, followed by Actinobacteria and Proteobacteria phyla. The most abundant genera in non pre-enriched kefir beverages were Lactococcus followed by Streptococcus, Bifidobacterium, Lactobacillus, and Leuconostoc. Pre-enriched kefirs were dominated by Streptococcus followed by Lactobacillus, Lactococcus, Bifidobacterium, and Leuconostoc at the genus level. Psychroserpens, Desulfonispora, Pediococcus, Micromonospora, Fructobacillus, Mycobacterium, Acetobacter, Pseudopedobacter, and Clostridium XI genera were found only in pre-enriched kefirs. Kefirs displayed pH differences from 4.04 to 4.49 and the acidity was 0.617e0.987. In two samples, the lowest pH values were obtained with abundance of Lactobacillus helveticus and Streptococcus salivarius. This study broadens our viewpoint and strengthens future applications of kefir beverages in industrial and medical fields. (C)& nbsp;2022 Elsevier Ltd. All rights reserved.Article Citation Count: 16Development of electrochemical aptasensors detecting phosphate ions on TMB substrate with epoxy-based mesoporous silica nanoparticles(Pergamon-elsevier Science Ltd, 2022) Özalp, Veli Cengiz; Ozalp, Veli Cengiz; Yilmaz, M. Deniz; Sudagidan, Mert; Aygun, Aysenur; Acar, Elif Esma; Sen, Fatih; Basic SciencesThis study, it is aimed to develop an electrochemical aptasensor that can detect phosphate ions using 3.3 & PRIME;5.5 & PRIME; tetramethylbenzidine (TMB). It is based on the principle of converting the binding affinity of the target molecule phosphate ion (PO43-) into an electrochemical signal with specific aptamer sequences for the aptasensor to be developed. The aptamer structure served as a gate for the TMB to be released and was used to trap the TMB molecule in mesoporous silica nanoparticles (MSNPs). The samples for this study were characterized by transmission electron spectroscopy (TEM), Brunner-Emmet-Teller, dynamic light scattering & electrophoretic light scattering, and induction coupled plasma atomic emission spectroscopy. According to TEM analysis, MSNPs have a morphologically hexagonal structure and an average size of 208 nm. In this study, palladium-carbon nano particles (Pd/C NPs) with catalytic reaction were used as an alternative to the biologically used horseradish peroxidase (HRP) enzyme for the release of TMB in the presence of phosphate ions. The limit of detection (LOD) was calculated as 0.983 mu M, the limit of determination (LOQ) was calculated as 3.276 mu M, and the dynamic linear phosphate range was found to be 50-1000 mu M. The most important advantage of this bio-based aptasensor assembly is that it does not contain molecules such as a protein that cannot be stored for a long time at room temperature, so its shelf life is very long compared to similar systems developed with antibodies. The proposed sensor shows good recovery in phosphate ion detection and is considered to have great potential among electrochemical sensors.Article Citation Count: 12Identification of bacterial communities of fermented cereal beverage Boza by metagenomic analysis(Elsevier, 2022) Ucak, Samet; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Altunbas, Osman; Soyucok, Ali; Sudagidan, MertBacterial microbiota of directly studied and pre-enriched Boza samples were investigated by metagenomic analysis. Virulence gene contents, biofilm formation, antibiotic susceptibility and clonal relationships of enterococci present in pre-enriched Boza samples were determined. Chemical properties of the samples were also investigated. Although directly studied samples showed a dominance by Lactococcus, Lactobacillus, Leuconostoc, and Streptococcus. NGS upon pre-enrichment of the same Boza samples demonstrated a dominance by Lactococcus, Enterococcus, Escherichia/Shigella, Bacillus, and Lactobacillus. All enterococci were identified as Enterococcus faecium and none of them was positive for vanA, vanB, vanC1, vanD, vanE, vanG, agg, gelE, efaAfs, cylA, ace, hyl, cob, cylB, and cylM genes. However, efaAfm, ccf, cpd, and esp genes were detected in the strains. Only one strain formed biofilm and seven strains showed low adherence. E. faecium strains were resistant to rifampin and erythromycin. PFGE revealed 54-100% clonal relationships of E. faecium strains. Percent acidity of Boza samples were 0.14%-0.51%, pH was 3.00-4.07, protein content was 0.35-1.23 mg/100 mg, total sugar content was 9.64-19.21 mg/100 mg Boza, crude ash content was 0.05-0.18 mg/100 mg dry sample, total dry matter was 13.79-28.04 mg/100 mg. Our results indicate to importance of the dynamics nature of microbial communities involved in Boza fermentation and virulence properties of enterococci.Article Citation Count: 0Identification of Bacterial Diversity of Bee Collected Pollen and Bee Bread Microbiota by Metagenomic Analysis(Aves, 2022) Özalp, Veli Cengiz; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Yegin, Zeynep; Ozalp, Veli Cengiz; Sudagidan, Mert; Basic SciencesThis study investigated the bacterial diversities of bee-collected pollen and bee bread of Apis mellifera in Turkey. The bacterial community structure of 14 bee pollen from Bingol, Konya, and Hakkari and 11 bee bread samples from Bingol were studied using 16 S rRNA amplicon sequencing and metagenomic analysis. The dominant bacterial phylum in pollen and bee bread samples was Firmicutes, followed by Proteobacteria. In pollen and bee bread samples, Bacillaceae, Clostridiaceae, Enterococcaceae, and Enterobacteriaceae were identified as dominant bacterial families. At the genus level, Bacillus, Clostridium sensu stricto, and Enterococcus were dominant bacteria in both pollen and bee bread samples. The most abundant species was Clostridium perfringens in both pollen and bee bread samples. Escherichia vulneris, Enterococcus faecalis, Bacillus cereus, Enterococcus casseliflavus, and Cronobacter malonaticus were identified with high reads in pollen samples. In bee bread samples, E. faecalis, Clostridium bifermentans, and Pantoea calida were abundant bacterial species. Alpha diversity showed that pol-3 sample had the highest diversity. Beta-diversity plots separated the pollen samples into four main groups and bee bread samples into three main groups. Our results indicated that the culture-independent metagenomic analysis will be a valuable tool for determining the microbial diversity of bee products produced in Bingol-Turkey one of the important centers of apiculture.Article Citation Count: 0Identification of Bacterial Vaginal Microbiota via Metagenomic Approach(Galenos Publ House, 2022) Özalp, Veli Cengiz; Sudagidan, Mert; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Tuna, Bilge Guvenc; Ozalp, Veli Cengiz; Basic SciencesAim: The aim of the current study was to identify vaginal bacterial microbiota of 38 Turkish women using the high -throughput next -generation sequencing and metagenomic approach at different taxonomic levels from the kingdom to the species level. Materials and Methods: Vaginal swab samples (n=38) were collected in the DNA/RNA shield collection tubes at Yeditepe University Hospital, Department of Obstetrics and Gynecology in June 2021 and DNA extraction was performed by ZymoBIOMICS DNA miniprep kit. The information related to age, marital status, preliminary diagnosis and anamnesis status of patients were collected. To determine the vaginal microbiota, a metagenomic approach was applied using 16S rRNA amplicon sequencing. Results: The dominant phylum Firmicutes was followed by Proteobacteria, Actinobacteria, Tenericutes, Fusobacteria, and Synergistetes in the vaginal samples. Lactobacillus was the most abundant genus followed by Prevotella, Enterobacter, Gardnerella, and Dialister. Lactobacillus iners was dominant at the species level in vaginal swab samples, followed by Gardnerella vaginalis, Enterobacter tabaci, Prevotella timonensis, Prevotella bivia, and Lactobacillus jensenii. Canonical correspondence analysis (CCA) showed that Proteobacteria and Fusobacteria were mainly related to married/single variable with the highest percentages, whereas Actinobacteria and Tenericutes were related to age variable at the phylum level. Campylobacter , Atopobium , Enterobacter , and Lactococcus were mainly found in married/single variable with the highest percentages, whereas Anaerococcus, Streptococcus, Sutterella , and Veillonella were related to age. Moreover, CCA showed that Campylobacter ureolyticus, Lb. jensenii , and Atopobium vaginae were associated with married/single variable, whereas Lactobacillus johnsonii and G. vaginalis were found in age variable with the highest percentages at the species level. Conclusion: Vaginal diseases are still a major public health concern. The vaginal microbiota, which has been studied in more depth in recent years, has been discovered to be more complicated than previously imagined thanks to technological developments. More patient investigations are needed to confirm and develop these findings.Article Citation Count: 0A metagenomic survey of bacterial communities from kurut: The fermented cow milk in Kyrgyzstan(Wiley-v C H verlag Gmbh, 2024) Yegin, Zeynep; Mamatova, Zhanylbubu; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Ucak, Samet; Sudagidan, MertKurut is a traditional dry dairy product mostly consumed in Central Asia. In this study, the distribution of the dominant bacteria present in kurut samples (n=84) originated from seven (Chuy, Issyk-Kul, Talas, Naryn, Jalal-Abad, Osh, and Batken) regions in Kyrgyzstan were analyzed with Illumina iSeq100 platform. The dominant phylum detected was Firmicutes followed by Proteobacteria, Actinobacteria, Cyanobacteria/Chloroplast, and Tenericutes. The most abundant family detected was Lactobacillaceae followed by Streptococcaceae, Enterococcaceae, Chloroplast, and Leuconostocaceae. At the genus level, Lactobacillus was the predominant one in samples and Streptococcus, Enterococcus, Lactococcus, and Streptophyta followed this. Further comprehensive characterization analyses in kurut samples may have potential applications both in industrial starter culture developments and also future therapeutic approaches based on potential strains with probiotic properties. imageArticle Citation Count: 13Microbial community of soda Lake Van as obtained from direct and enriched water, sediment and fish samples(Nature Portfolio, 2021) Özalp, Veli Cengiz; Sudagidan, Mert; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Ozalp, Veli Cengiz; Basic SciencesSoda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of ecologically and economically important microorganisms due to their unique geochemistry. Microbiota members of lakes are valuable models to study the link between community structure and abiotic parameters such as pH and salinity. Lake Van is the largest endroheic lake and in this study, bacterial diversity of lake water, sediment, and pearl mullet (inci kefali; Alburnus tarichi), an endemic species of fish which are collected from different points of the lake, are studied directly and investigated meticulously using a metabarcoding approach after pre-enrichment. Bacterial community structures were identified using Next Generation Sequencing of the 16S rRNA gene. The analysis revealed that the samples of Lake Van contain high level of bacterial diversity. Direct water samples were dominated by Proteobacteria, Cyanobacteria, and Bacteroidota, on the other hand, pre-enriched water samples were dominated by Proteobacteria and Firmicutes at phylum-level. In direct sediment samples Proteobacteria, whereas in pre-enriched sediment samples Firmicutes and Proteobacteria were determined at highest level. Pre-enriched fish samples were dominated by Proteobacteria and Firmicutes at phylum-level. In this study, microbiota members of Lake Van were identified by taxonomic analysis.