Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Citation - WoS: 18Citation - Scopus: 21Genomic, Probiotic, and Metabolic Potentials of Liquorilactobacillus Nagelii AGA58, a Novel Bacteriocinogenic Motile Strain Isolated From Lactic Acid-Fermented Shalgam(Soc Bioscience Bioengineering Japan, 2023-01) Yetiman, Ahmet Evren; Ortakci, FatihThis study aimed to perform genomic, probiotic, and metabolic characterization of a novel Liquorilactobacillus nagelii AGA58 isolated from a lactic acid-fermented shalgam beverage to understand its metabolic potentials and probiotic features. AGA58 is gram-positive, motile, catalase-negative and appears as short rods under the light-microscope. The AGA58 chromosome comprises a single linear chromosome of 2,294,635 bp that is predicted to carry 2135 coding sequences, including 45 tRNA genes, 3 mRNA, and 3 rRNA operons. The genome has a GDC content of 36.9%, including 55 pseudogenes and a single intact prophage. AGA58 is micro-anaerobic due to achieving a shorter doubling time and faster growth rate than micro-aerophilic conditions. It carries flagellar biosynthesis protein-encoding genes predicting motile behavior, which was confirmed with the in vitro motility test. AGA58 is an obligatory homofermentative lactobacillus that can ferment hexose sugars such as galactose, glucose, fructose, sucrose, mannose, N-acetyl glucosamine, maltose, and trehalose to lactate through glycolysis. No acid production from pentoses implies that five-carbon sugars are being utilized for purine and pyrimidine synthesis. Putative pyruvate metabolism revealed formate, malate, oxaloacetate, acetate, acetaldehyde, acetoin, and lactate forms from pyruvate. AGA58 is predicted to encode the LuxS gene and biosynthesis of class IIa and Blp family class-II bacteriocins suggesting this bacterium's antimicrobial potential, linked to antagonism tests that AGA58 can inhibit Escherichia coli ATCC 43895, Salmonella enterica serovar Typhimurium ATCC 14028, and Klebsiella pneumonia ATCC 13883. Moreover, AGA58 is tolerant to acid and bile concentrations simulating the human gastrointestinal conditions depicting the probiotic potential of the organism as the first report in literature within the same species. (c) 2022, The Society for Biotechnology, Japan. All rights reserved.Article Citation - Scopus: 2Evaluating the Microbial Growth Kinetics and Artificial Gastric Digestion Survival of a Novel Pichia Kudriavzevii FOL-04(Field Crops Central Research Institute, 2022-06-15) Gumustop, Ismail; Ortakci, FatihPresent study aims to explore Pichia kudriavzevii FOL-04 (FOL-04)’s: i) survival against artificial gastric juice (AGJ) and artificial bile juice (ABJ), ii) growth kinetics in shake flask (SF) and fed-batch trials (FBT). Survival of FOL-04 as measured by relative cell density (RCD) against AGJ and ABJ was screened at four different pH-levels (control, 3, 2, 1.5) and ox-bile concentrations (control, 0.2%, 1%, 2%), respectively. Growth kinetics was calculated by periodic measurement of OD<inf>600</inf> in SF (225 rpm, 30°C) or in FBT using exponential feeding regimen where pH, dissolved-oxygen and temperature were controlled at 5.5, 21%, and 30°C, respectively. The doubling-time, maximum specific growth rate, and final cell densities achieved for SF and FBT were 81.7min, 1.67, 11.79 and 170.4 min, 4.75, 37.95, respectively. RCDs calculated were similar for pH=3 and control vs both were significantly higher(p<0.05) than pH=1.5 and 2 with the latter two pH-levels were not significantly different(p>0.05). RCDs were similar across control, 0.2%, and 1% ox-bile levels(p>0.05). However, 2% ox-bile yielded significantly lower RCD (p<0.05) compared to all except 1%. FOL-04 is a potential probiotic candidate showing robustness against AGJ and ABJ and remarkable biomass increase was achieved when grown under FBT which could pave the way for developing a yeast-based probiotic using this strain. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 29Citation - Scopus: 36Characterization of Genomic, Physiological, and Probiotic Features Lactiplantibacillus Plantarum DY46 Strain Isolated From Traditional Lactic Acid Fermented Shalgam Beverage(Elsevier, 2022-04) Yetiman, Ahmet E.; Keskin, Abdullah; Darendeli, Busra Nur; Kotil, Seyfullah Enes; Ortakci, Fatih; Dogan, MahmutLactiplantibacillus plantarum is a significant probiotic where it could be found in ubiquitous niches. In this study, a new Lb. plantarum strain DY46 was isolated from a traditional lactic-acid-fermented beverage called shalgam. The whole genome of the DY46 was sequenced and obtained sequences were assembled into a 3.32 Mb draft genome using PATRIC (3.6.8.). The DY46 genome consists of a single circular chromosome of 3,332,827 bp that is predicted to carry 3219 genes, including 61 tRNA genes, 2 rRNA operons. The genome has a GC content of 44.3% includes 98 predicted pseudogenes, 25 complete or partial transposases and 3 intact prophages. The genes encoding enzymes related in the intact EMP (Embden-Meyerhof-Parnas) and PK (phosphoketolase) pathways were predicted using BlastKOALA which is an indicator of having facultative heterofermentative pathways. DY46 genome also predicted to carry genes of Pln E, Pln F and Pln K showing the antimicrobial potential of this bacterium which can be linked to in vitro antagonism tests that DY46 can inhibit S.enterica sv. Typhimurium ATCC14028, K. pneumonie ATCC13883, and P. vulgaris ATCC8427. Moreover, it is determined that all resistome found in its genome were intrinsically originated and the strain was found to be tolerant to acid and bile concentrations by mimicking human gastrointestinal conditions. In conclusion, L. plantarum DY46 is a promising bacterium that appears to have certain probiotic properties, confirmed by "in vitro" and "in silico" analyses, and is a potential dietary supplement candidate that may provide functional benefits to the host.