TR-Dizin
Permanent URI for this collectionhttps://ada.atilim.edu.tr/handle/123456789/21
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Browsing TR-Dizin 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: 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: 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.