Bacterial metagenome profiling of hand-made herby cheese samples utilizing high-throughput sequencing to detect geographical indication and marketing potential

Rustemoglu, Mustafa; Erkan, Mehmet Emin; Cengiz, Gazal; Hajyzadeh, Mortaza

doi:10.1016/j.heliyon.2023.e13334

Cited by 3 publications

(2 citation statements)

References 40 publications

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“…W. jogaejeotgali, initially found in traditionally fermented Korean jogae jeotgal [57], exhibits resistance to osmotic stress and tolerance to acidic conditions. Recent discoveries have placed W. jogaejeotgali as part of the cheese microbiome [26,58], though other species of this genus have been also isolated from dairy environments in previous studies [51,59]. Furthermore, our findings align with previous studies on Feta, Domiati, and Halloumi cheeses, indicating a consistent presence of non-starter lactobacilli in mature samples [12,60,61].…”

Section: Identification Of Sfela Microbiome At Species Level Using Sh...supporting

confidence: 89%

Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics

Tsouggou,

Slavko,

Tsipidou

et al. 2024

Foods

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Sfela is a white brined Greek cheese of protected designation of origin (PDO) produced in the Peloponnese region from ovine, caprine milk, or a mixture of the two. Despite the PDO status of Sfela, very few studies have addressed its properties, including its microbiology. For this reason, we decided to investigate the microbiome of two PDO industrial Sfela cheese samples along with two non-PDO variants, namely Sfela touloumotiri and Xerosfeli. Matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS), 16S rDNA amplicon sequencing and shotgun metagenomics analysis were used to identify the microbiome of these traditional cheeses. Cultured-based analysis showed that the most frequent species that could be isolated from Sfela cheese were Enterococcus faecium, Lactiplantibacillus plantarum, Levilactobacillus brevis, Pediococcus pentosaceus and Streptococcus thermophilus. Shotgun analysis suggested that in industrial Sfela 1, Str. thermophilus dominated, while industrial Sfela 2 contained high levels of Lactococcus lactis. The two artisanal samples, Sfela touloumotiri and Xerosfeli, were dominated by Tetragenococcus halophilus and Str. thermophilus, respectively. Debaryomyces hansenii was the only yeast species with abundance > 1% present exclusively in the Sfela touloumotiri sample. Identifying additional yeast species in the shotgun data was challenging, possibly due to their low abundance. Sfela cheese appears to contain a rather complex microbial ecosystem and thus needs to be further studied and understood. This might be crucial for improving and standardizing both its production and safety measures.

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Section: Identification Of Sfela Microbiome At Species Level Using Sh...supporting

confidence: 89%

Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics

Tsouggou,

Slavko,

Tsipidou

et al. 2024

Foods

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“…According to our results, E. coli and C. freundii were the dominant species in populations of coliform bacteria contaminating cheese. The dominance of E. coli in bacterial metagenome profile of dairy products was noted recently (Rüstemoğlu et al, 2023).…”

Section: Discussionmentioning

confidence: 94%

Coliforms Diversity and Antibiotic Resistance in Kazakhstan Cheese

Kuzeubayeva,

Ussenbayev,

Aydin

et al. 2024

American Journal of Animal and Veterinary Sciences

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Coliform bacteria contaminate dairy products and pose public health concerns including food poisoning and toxemia. We aimed to determine the species diversity of coliforms and to evaluate the resistance to antibiotics of E. coli in various types of cheese sold by local producers in Kazakhstan. We collected 197 samples from different cheeses sold by producers in the Kostanay (n = 89), East Kazakhstan (n = 70) and Akmola (n = 38) regions and studied by classical microbiological and mass spectrometric methods for contamination with coliforms in certificated for bacterial pathogens' research laboratories. Such investigation of cheese was experienced the first time in Central Asia. We isolated five coliform bacteria species (Escherichia coli, Citrobacter freundii, Serratia liquefaciens, Enterobacter cloacae and Citrobacter braakii) in 45.2% of the samples. E. coli and C. freundii were dominant. Antibacterial resistance of E. coli isolates (n = 65) to 19 antibiotics was investigated by the disc-diffusion and molecular genetic (PCR) methods. Isolates were sensitive to drugs of the aminoglycosides group and resistant to 60% of the β-lactams group drugs (ampicillin, cefpodoxime, cefoperazone) and to an agent out of four of the fluoroquinolones group (enrofloxacin). Some E. coli strains were multi-drug resistance to tetracyclines, beta-lactams and fluoroquinolones. PCR of E. coli isolates revealed genes that encoded the resistance to β-lactams in 15.4%, to sulfonamides in 30.8% and quinolones in 9.3% of cheese samples, providing sufficient biotic potential for the transfer of these genes to intestinal biocenosis bacteria of humans.

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The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

Fusco,

Chieffi,

Fanelli

et al. 2023

Front. Microbiol.

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Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.

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Bacterial metagenome profiling of hand-made herby cheese samples utilizing high-throughput sequencing to detect geographical indication and marketing potential

Cited by 3 publications

References 40 publications

Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics

Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics

Coliforms Diversity and Antibiotic Resistance in Kazakhstan Cheese

The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

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