fermentation Article Microbiological and Metagenomic Characterization of a Retail Delicatessen Galotyri-Like Fresh Acid-Curd Cheese Product John Samelis 1,* , Agapi I. Doulgeraki 2,* , Vasiliki Bikouli 2, Dimitrios Pappas 3 and Athanasia Kakouri 1 1 Dairy Research Department, Hellenic Agricultural Organization ‘DIMITRA’, Katsikas, 45221 Ioannina, Greece;
[email protected] 2 Hellenic Agricultural Organization ‘DIMITRA’, Institute of Technology of Agricultural Products, 14123 Lycovrissi, Greece;
[email protected] 3 Skarfi EPE—Pappas Bros Traditional Dairy, 48200 Filippiada, Greece;
[email protected] * Correspondence:
[email protected] (J.S.);
[email protected] (A.I.D.); Tel.: +30-2651094789 (J.S.); +30-2102845940 (A.I.D.) Abstract: This study evaluated the microbial quality, safety, and ecology of a retail delicatessen Galotyri-like fresh acid-curd cheese traditionally produced by mixing fresh natural Greek yogurt with ‘Myzithrenio’, a naturally fermented and ripened whey cheese variety. Five retail cheese batches (mean pH 4.1) were analyzed for total and selective microbial counts, and 150 presumptive isolates of lactic acid bacteria (LAB) were characterized biochemically. Additionally, the most and the least diversified batches were subjected to a culture-independent 16S rRNA gene sequencing analysis. LAB prevailed in all cheeses followed by yeasts. Enterobacteria, pseudomonads, and staphylococci were present as <100 viable cells/g of cheese. The yogurt starters Streptococcus thermophilus and Lactobacillus delbrueckii were the most abundant LAB isolates, followed by nonstarter strains of Lactiplantibacillus, Lacticaseibacillus, Enterococcus faecium, E. faecalis, and Leuconostoc mesenteroides, Citation: Samelis, J.; Doulgeraki, A.I.; whose isolation frequency was batch-dependent. Lactococcus lactis isolates were sporadic, except Bikouli, V.; Pappas, D.; Kakouri, A. Microbiological and Metagenomic for one cheese batch.