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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14411/18
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Article Citation - WoS: 6Citation - Scopus: 7Determination 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.Article Citation - WoS: 8Citation - Scopus: 8Bacterial Skin Microbiota of Seabass From Aegean Fish Farms and Antibiotic Susceptibility of Psychrotrophic <i>pseudomonas</I>(Mdpi, 2023) Aydin, Ali; Sudagidan, Mert; Mamatova, Zhanylbubu; Yurt, Mediha Nur Zafer; Ozalp, Veli Cengiz; Zornu, Jacob; Brun, EdgarFarming seabass (Dicentrarchus labrax) is an essential activity in the Mediterranean basin including the Aegean Sea. The main seabass producer is Turkey accounting for 155,151 tons of production in 2021. In this study, skin swabs of seabass farmed in the Aegean Sea were analysed with regard to the isolation and identification of Pseudomonas. Bacterial microbiota of skin samples (n = 96) from 12 fish farms were investigated using next-generation sequencing (NGS) and metabarcoding analysis. The results demonstrated that Proteobacteria was the dominant bacterial phylum in all samples. At the species level, Pseudomonas lundensis was identified in all samples. Pseudomonas, Shewanella, and Flavobacterium were identified using conventional methods and a total of 46 viable (48% of all NGS+) Pseudomonas were isolated in seabass swab samples. Additionally, antibiotic susceptibility was determined according to standards of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) in psychrotrophic Pseudomonas. Pseudomonas strains were tested for susceptibility to 11 antibiotics (piperacillin-tazobactam, gentamicin, tobramycin, amikacin, doripenem, meropenem, imipenem, levofloxacin, ciprofloxacin, norfloxacin, and tetracycline) from five different groups of antibiotics (penicillins, aminoglycosides, carbapenems, fluoroquinolones, and tetracyclines). The antibiotics chosen were not specifically linked to usage by the aquaculture industry. According to the EUCAST and CLSI, three and two Pseudomonas strains were found to be resistant to doripenem and imipenem (E-test), respectively. All strains were susceptible to piperacillin-tazobactam, amikacin, levofloxacin, and tetracycline. Our data provide insight into different bacteria that are prevalent in the skin microbiota of seabass sampled from the Aegean Sea in Turkey, and into the antibiotic resistance of psychrotrophic Pseudomonas spp.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: 3Citation - Scopus: 4Identification of Bacterial Diversity of Bee Collected Pollen and Bee Bread Microbiota by Metagenomic Analysis(Aves, 2022) Arserim Ucar, Dilhun Keriman; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Yegin, Zeynep; Ozalp, Veli Cengiz; Sudagidan, Mert; Uçar, Dilhun Keriman Arserim; Ozalp, Cengiz; Arserim-uçar, Dılhun KerimanThis 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 - WoS: 2Citation - Scopus: 2A 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 - WoS: 17Citation - Scopus: 19Bacterial Surface, Biofilm and Virulence Properties of <i>listeriamonocytogenes</I> Strains Isolated From Smoked Salmon and Fish Food Contact Surfaces(Elsevier, 2021) Sudagidan, Mert; Ozalp, Veli Cengiz; Ozturk, Orhan; Yurt, Mediha Nur Zafer; Yavuz, Orhan; Tasbasi, Behiye Busra; Aydin, AliBiofilm formation is one of the defense mechanisms of bacteria against disinfectants and antimicrobials. The aim of this study was to determine biofilm-forming L.monocytogenes from fish processing and salmon surfaces. Biofilm formation at 15, 25, 37, and 40 degrees C from 1 to 6-days period, adhesion to glass, polypropylene and stainless-steel surfaces, bacterial surface charge and hydrophobicity was determined. Adhesion behavior of the strains was evaluated using Surface Plasmon Resonance (SPR) technique. Totally 32 L.monocytogenes strains belonging to serogroups IIa (n:17), IIc(n:14) and IVb(n:1) were detected from 1320 swabs and 16 smoked salmons. Biofilm formation tests revealed that 21 strains form biofilm on microplate by increasing time and temperature. Although all strains strongly formed biofilm on glass surfaces, two strains slightly adhered polypropylene surfaces. High surface roughness of stainless-steel FeCrNi alloy (Ra = 4.15 nm) and CoCrMo alloy (Ra = 10.75 nm) increased biofilm formation of L.monocytogenes on stainless-steel surfaces. Zeta potential results showed that non-biofilm formers were more negatively charged after 6-days and hydrophobicity couldn't give a distinct distribution among biofilm formers and non-formers. SPR analysis method was evaluated to distinguish biofilm formers to adhere SPR gold chip surfaces. PCR results revealed that all strains were positive for hylA, iap, actA, plcA, plcB, fri, flaA, inlA, inlB, inlC, inlJ, and lmo1386 genes. Additionally, all strains were susceptible to penicillin, ampicillin, meropenem, erythromycin and trimethoprim-sulfamethoxazole. Biofilm-forming, virulence properties of L. monocytogenes strains isolated from fish processing surfaces and smoked salmons were evaluated and SPR was used to differentiate biofilm formers as a sensitive technique for biofilm studies.Article Citation - WoS: 16Citation - Scopus: 16Targeted mesoporous silica nanoparticles for improved inhibition of disinfectant resistant<i> Listeria</i><i> monocytogenes</i> and lower environmental pollution(Elsevier, 2021) Sudagidan, Mert; Yildiz, Gulsah; Onen, Selin; Al, Rabia; Temiz, S. Sevval Nur; Yurt, Mediha Nur Zafer; Ozalp, Veli C.Benzalkonium chloride (BAC) is a common ingredient of disinfectants used for industrial, medical, food safety and domestic applications. It is a common pollutant detected in surface and wastewaters to induce adverse effects on Human health as well as aquatic and terrestrial life forms. Since disinfectant use is essential in combatting against microorganisms, the best approach to reduce ecotoxicity level is to restrict BAC use. We report here that encapsulation of BAC in mesoporous silica nanoparticles can provide an efficient strategy for inhibition of mi-crobial activity with lower than usual concentrations of disinfectants. As a proof-of-concept, Listeria mono-cytogenes was evaluated for minimum inhibitory concentration (MIC) of nanomaterial encapsulated BAC. Aptamer molecular gate structures provided a specific targeting of the disinfectant to Listeria cells, leading to high BAC concentrations around bacterial cells, but significantly reduced amounts in total. This strategy allowed to inhibition of BAC resistant Listeria strains with 8 times less the usual disinfectant dose. BAC encapsulated and aptamer functionalized silica nanoparticles (AptBACNP) effectively killed only target bacteria L. monocytogenes, but not the non-target cells, Staphylococcus aureus or Escherichia coli. AptBACNP was not cytotoxic to Human cells as determined by in vitro viability assays.Article Citation - WoS: 19Citation - Scopus: 19Metagenomic and Chemical Analysis of Tarhana During Traditional Fermentation Process(Elsevier, 2021) Soyucok, Ali; Yurt, Mediha Nur Zafer; Altunbas, Osman; Ozalp, Veli Cengiz; Sudagidan, Mert; Zafer Yurt, Mediha NurTarhana is one of the favourable traditional fermented food consumed as a soup. Different flour, vegetables, spices and yogurt are main constituents and they compose of microbiota of Tarhana. In this study, bacterial communities in each fermentation process and in their constituents were identified by metagenomic analysis. Also, chemical properties (pH, acidity, salt content and dry matter) were analysed in each step. The results showed that in the dough formation, mainly Lactobacillus, Bacillus, Enterococcus and Streptococcus were present and after Day 4, Clostridium and Bacillus became dominant, after drying Clostridium disappeared and in the final product bacterial communities from Bacillus and Streptococcus genus were observed. Chemical analysis showed that pH decreased from 4.94 to 4.46, acidity increased by time at the beginning of fermentation from 7.5% to 22.5% in first 6 days period, then, became stable at 14% in drying process. Salt content increased by time from 1.74 to 3.08 g salt/100 g Tarhana in first 8 days and in drying process salt content was recorded as 2.81-2.90 and dry matter was obtained as 94 g dry matter/100 g Tarhana in the final product. This study elucidated the effects of ingredients, raw materials and how microbiota and chemical properties changes during fermentation steps of home-made traditional Tarhana production and thus preparation methods could be developed to obtain standardized Tarhana products for industrial production in future.Article Citation - WoS: 15Citation - Scopus: 20Determination 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 - WoS: 8Citation - Scopus: 9Surface Microbiota and Associated Staphylococci of Houseflies (musca Domestica) Collected From Different Environmental Sources(Academic Press Ltd- Elsevier Science Ltd, 2022) Sudagidan, Mert; Ozalp, Veli Cengiz; Can, Ozge; Eligul, Hakan; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Kocak, OnerHouseflies (Musca domestica) are important mechanical vectors for the transmission of pathogenic microorganisms. In this study, 129 houseflies (69 males and 60 females) were collected from 10 different environmental sources and a laboratory population was used. The surface microbiota of houseflies was identified by NextGeneration Sequencing. Staphylococci from the surfaces of houseflies were selectively isolated and their virulence genes, antibiotic susceptibilities, biofilm formation, and clonal relatedness were determined. Metagenomic analysis results demonstrated that Staphylococcus, Bacillus, and Enterococcus were mostly present on the surface of houseflies at the genus level. Additionally, the isolated 32 staphylococcal strains were identified as Staphylococcus sciuri (n = 11), S. saprophyticus (n = 9), S. arlettae (n = 6), S. xylosus (n = 4), S. epidermidis (n = 1) and S. gallinarum (n = 1). tetK, tetM, tetL, ermC, msrAB, and aad6 genes were found to carry by some of the staphylococcal strains. The strains were mostly resistant to oxacillin, penicillin, and erythromycin and three strains were multi-drug resistant. There was a statistical difference between housefly collection places and antibiotic resistance of isolated staphylococci to penicillin G, gentamicin, and erythromycin (p < 0.05). Biofilm test showed that 17 strains were strong biofilm formers, and it plays important role in the transmission of these bacteria on the surface of houseflies. Staphylococcal strains showed extracellular proteolytic and lipolytic activity in 31 and 12 strains, respectively. Closely related species were found in PFGE analysis from different environmental sources. By this study, surface microbiota and carriage of pathogenic staphylococci on the surfaces of houseflies and their virulence properties were elucidated.