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Article Citation - WoS: 4Citation - Scopus: 516s 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, Ali; Ozalp, Cengiz; Ersoy Omeroglu, Esra; Mediha Nur, Zafer YURTCheese 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 - WoS: 5Citation - Scopus: 6Bacterial and Fungal Microbiota of Mould-Ripened Cheese Produced in Konya(Wiley, 2023) Yurt, Mediha Nur Zafer; Omeroglu, Esra Ersoy; Tasbasi, Behiye Busra; Acar, Elif Esma; Altunbas, Osman; Ozalp, Veli Cengiz; Sudagidan, Mert; Ersoy Omeroglu, EsraBacterial 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 - WoS: 5Citation - Scopus: 5Determination of Bacterial Diversity of Propolis Microbiota(Wiley-v C H verlag Gmbh, 2023) Omeroglu, Esra Ersoy; Arserim-Ucar, Dilhun Keriman; Yegin, Zeynep; Caglayan, Nevzat; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Sudagidan, Mert; Keriman Arserim-Uçar, Dılhun; Busra Tasbasi, Behiye; Ersoy Omeroglu, Esra; Nur Zafer Yurt, MedihaPropolis is a natural resinous mixture produced by the excretions of honeybees. PCR amplification of the 16S rRNA gene region was achieved using DNA of pre-enriched propolis samples collected from Apis mellifera production hives (n=37) in Eastern Turkiye (Bingol and its regions). Next-generation sequencing and metabarcoding techniques were used to identify bacterial communities in propolis samples. Firmicutes dominated the phylum structure, with Proteobacteria, Actinobacteria, Tenericutes, and Spirochaetes following. The top three bacterial families were Bacillaceae, Enterobacteriaceae, and Enterococcaceae. Bacillus (dominantly B. badius and B. thermolactis at the species level) was recognized at the genus level, followed by Enterococcus and Clostridium sensu stricto. Our study comprehensively identified the bacterial diversity of propolis samples. Further investigations targeting to enlighten the microbiota of propolis and its potential application fields are required to gain better insight into ecological, nutritional, and medicinal perspectives.
