Genome comparison and physiological characterization of eight Streptococcus thermophilus strains isolated from Italian dairy products

Eight Streptococcus thermophilus strains of dairy origin isolated in Italy were chosen to investigate autochthonous bacterial diversity in this important technological species. In the present study a comparative analysis of all the 17 S. thermophilus genomes publicly available was performed to identify the core and the variable genes, which vary among strains from 196 to 265. Additionally, correlation between the isolation site and the genetic distance was investigated at genomic level. Results highlight that the phylogenetic reconstruction differs from the geographical strain distribution. Moreover, strain M17PTZA496 has a genome of 2.15 Mbp, notably larger than that of the others, determined by lateral gene transfer (including phage-mediated incorporation) and duplication events. Important technological characters, such as growth kinetics, bacteriocin production, acidification kinetics and surface adhesion capability were studied in all the Italian strains. Results indicate a wide range of variability in adhesion properties that significantly clustered strains into four groups. Genomic differences among strains in relation to these characters were identified but a clear correlation between genotype and phenotype was not always found since most of the genomic modifications arise from single nucleotide polymorphisms. This research represents a step forward in the identification of strains-specific functions in Streptococcus thermophilus and it has also the potential to provide valuable information to predict strain specific behaviors in industrial processes

Phenotypic and Genotypic Characterization of Staphylococcus aureus Strains from Italian Dairy Products

Staphylococcus aureus is a known major cause of foodborne illnesses, and milk and dairy products are often contaminated by enterotoxigenic strains of this bacterium. In the present study, 122 S. aureus isolates collected from different dairy products were characterised by phenotypic properties, by the distribution of genes encoding staphylococcal enterotoxins (sea, sec, sed, seg, seh, sei, sej, and sel) and by randomly amplified polymorphic DNA PCR (RAPD-PCR). Moreover, strain resistance to vancomycin and methicillin (oxacillin) was studied. The differences in the RAPD-PCR profiles obtained with the primers M13 and AP4 revealed the presence of a great genetic heterogeneity among the different S. aureus strains. Using the primer AP4 and M13, eight groups were distinguished by RAPD-PCR cluster analysis, although, except in few cases, it was not possible to correlate the isolates of different animal species (cow or ovine) with the presence of se genes. None of the isolates showed resistance to vancomycin or methicillin

Isolation, Identification, and Characterisation of Beer-Spoilage Lactic Acid Bacteria from Microbrewed Beer from Victoria, Australia

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A survey of yeasts in traditional sausages of southern Italy

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Comparative evaluation of cheese whey microbial composition from four Italian cheese factories by viable counts and 16S rRNA gene amplicon sequencing

The microbiota of cheese whey from four dairy companies located in the North-East of Italy was evaluated during winter and spring using both culture-dependent and culture-independent methods. Although no significant differences were observed (p > 0.05) for any of the six microbial categories analysed by plate counting among the dairy companies, significant differences at the family and genus level were revealed by linear discriminant analysis (LDA). In particular, variations in the abundance of the families Pseudomonadaceae and Enterobacteriaceae, as well as of the genus Acinetobacter were observed and positively correlated with plate count results (p < 0.05). The combined use of culture-dependent and culture-independent approaches gave a better description of the hygienic conditions and food safety aspects and could therefore be suggested as a useful integrated approach. \ua9 2020 Elsevier Lt

Intraspecies Genomic Groups in Enterococcus faecium and Their Correlation with Origin and Pathogenicity

http://aem.asm.org/Seventy-eight Enterococcus faecium strains from various sources were characterized by random amplified polymorphic DNA (RAPD)-PCR, amplified fragment length polymorphism (AFLP), and pulsed-field gel electrophoresis (PFGE) analysis of SmaI restriction patterns. Two main genomic groups (I and II) were obtained in both RAPD-PCR and AFLP analyses. DNA-DNA hybridization values between representative strains of both groups demonstrated a mean DNA-DNA reassociation level of 71%. PFGE analysis revealed high genetic strain diversity within the two genomic groups. Only group I contained strains originating from human clinical samples or strains that were vancomycin-resistant or beta-hemolytic. No differentiating phenotypic features between groups I and II were found using the rapid ID 32 STREP system. The two groups could be further subdivided into, respectively, four and three subclusters in both RAPD-PCR and AFLP analyses, and a high correlation was seen between the subclusters generated by these two methods. Subclusters of group I were to some extent correlated with origin, pathogenicity, and bacteriocinogeny of the strains. Host specificity of E. faecium strains was not confirmed

Interrelationships among physical and chemical traits of cheese: Explanatory latent factors and clustering of 37 categories of cheeses

ABSTRACT: Cheese presents extensive variability in physical, chemical, and sensory characteristics according to the variety of processing methods and conditions used to create it. Relationships between the many characteristics of cheeses are known for single cheese types or by comparing a few of them, but not for a large number of cheese types. This case study used the properties recorded on 1,050 different cheeses from 107 producers grouped into 37 categories to analyze and quantify the interrelationships among the chemical and physical properties of many cheese types. The 15 cheese traits considered were ripening length, weight, firmness, adhesiveness, 6 different chemical characteristics, and 5 different color traits. As the 105 correlations between the 15 cheese traits were highly variable, a multivariate analysis was carried out. Four latent explanatory factors were extracted, representing 86% of the covariance matrix: the first factor (38% of covariance) was named Solids because it is mainly linked positively to fat, protein, water-soluble nitrogen, ash, firmness, adhesiveness, and ripening length, and negatively to moisture and lightness; the second factor (24%) was named Hue because it is linked positively to redness/blueness, yellowness/greenness, and chroma, and negatively to hue; the third factor (17%) was named Size because it is linked positively to weight, ripening length, firmness, and protein; and the fourth factor (7%) was named Basicity because it is linked positively to pH. The 37 cheese categories were grouped into 8 clusters and described using the latent factors: the Grana Padano cluster (characterized mainly by high Size scores); hard mountain cheeses (mainly high Solids scores); very soft cheeses (low Solids scores); blue cheeses (high Basicity scores), yellowish cheeses (high Hue scores), and 3 other clusters (soft cheeses, pasta filata and treated rind, and firm mountain cheeses) according to specific combinations of intermediate latent factors and cheese traits. In this case study, the high variability and interdependence of 15 major cheese traits can be substantially explained by only 4 latent factors, allowing us to identify and characterize 8 cheese type clusters

Major Causes of Variation of External Appearance, Chemical Composition, Texture, and Color Traits of 37 Categories of Cheeses

: Cheeses are produced by many different procedures, giving rise to many types differing in ripening time, size, shape, chemical composition, color, texture, and sensory properties. As the first step in a large project, our aim was to characterize and quantify the major sources of variation in cheese characteristics by sampling 1050 different cheeses manufactured by over 100 producers and grouped into 37 categories (16 with protected designation of origin, 4 traditional cheese categories, 3 pasta filata cheese categories, 5 flavored cheese categories, 2 goat milk categories, and 7 other categories ranging from very fresh to very hard cheeses). We obtained 17 traits from each cheese (shape, height, diameter, weight, moisture, fat, protein, water soluble nitrogen, ash, pH, 5 color traits, firmness, and adhesiveness). The main groups of cheese categories were characterized and are discussed in terms of the effects of the prevalent area of origin/feeding system, species of lactating females, main cheese-making technologies, and additives used. The results will allow us to proceed with the further steps, which will address the interrelationships among the different traits characterizing cheeses, detailed analyses of the nutrients affecting human health and sensorial fingerprinting