Sources of propionic acid bacteria contamination in the milking parlor environment on Alpine Dairy Farms

High quality raw milk is an important prerequisite for the production of long ripened raw milk cheeses. This implies not only the absence of pathogenic microorganisms in raw milk, but also low levels of spoilage bacteria, including dairy propionic acid bacteria (dPAB), that can cause blowing and sensory defects in cheese, resulting in severe economic losses for producers. Raw milk contamination with dPAB has been primarily associated with improperly cleaned milking systems, but they have been detected in feed, soil, feces and on the teat skin. The objective of this study was to identify potential sources of raw milk contamination with dPAB in the barn and milking parlor environments. We also wanted to know more about the prevalence of the dPAB species in these environments and the levels of contamination. For this purpose, 16 small scale Alpine dairy farms were visited in August 2022: samples were taken from the barn environment (e.g., swab samples, air, feed, bedding), the milking system (swab samples, residual cleaning water, cleaning sponges, milk filters) and milk samples were collected at various sampling points along the milking system. Samples were analyzed for dPAB contamination, and results showed contamination at multiple sampling locations. We observed potential adverse effects of improperly set cleaning parameters of the milking system, as well as of farm specific practices. In addition, we identified cleaning water residues as an important source of contamination. Based on these findings, we propose potential mitigation strategies to reduce the risk of raw milk contamination with cheese spoilage bacteria, thereby contributing to a more sustainable food production.

The Microbiota of Grana Padano Cheese. A Review

Grana Padano (GP) is the most appreciated and marketed cheese with Protected Designation of Origin in the world. The use of raw milk, the addition of undefined cultures (defined as 'sieroinnesto naturale'), the peculiar manufacturing proces, and the long ripening make the cheese microbiota play a decisive role in defining the quality and the organoleptic properties of the product. The knowledge on the microbial diversity associated with GP has been the subject, in recent years, of several studies aimed at understanding its composition and characteristics in order, on the one hand, to improve its technological performances and, on the other hand, to indirectly enhance the nutritional quality of the product. This review aims to briefly illustrate the main available knowledge on the composition and properties of the GP microbiota, inferred from dozens of studies carried out by both classical microbiology techniques and metagenomic analysis. The paper will essentially, but not exclusively, be focused on the lactic acid bacteria (LAB) derived from starter (SLAB) and the non-starter bacteria, both lactic (NSLAB) and non-lactic, of milk origin.

Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis

The composition of the bacterial community of Grana Padano (GP) cheese was evaluated by an amplicon-based metagenomic approach (DNA metabarcoding) and RAPD-PCR fingerprinting. One hundred eighteen cheeses, which included 118 dairies located in the production area of GP, were collected. Two hundred fifty-four OTUs were detected, of which 82 were further discriminated between dominant (32 OTUs; > 1% total reads) and subdominant (50 OTUs; between 0.1% and 1% total reads) taxa. Lactobacillus (L.) delbrueckii, Lacticaseibacillus (Lact.) rhamnosus, Lact. casei, Limosilactobacillus fermentum, Lactococcus (Lc.) raffinolactis, L. helveticus, Streptococcus thermophilus, and Lc. lactis were the major dominant taxa ('core microbiota'). The origin of samples significantly impacted on both richness, evenness, and the relative abundance of bacterial species, with peculiar pattern distribution among the five GP production regions. A differential analysis allowed to find bacterial species significantly associated with specific region pairings. The analysis of pattern similarity among RAPD-PCR profiles highlighted the presence of a 'core' community banding pattern present in all the GP samples, which was strictly associated with the core microbiota highlighted by DNA metabarcoding. A trend to group samples according to the five production regions was also observed. This study widened our knowledge on the bacterial composition and ecology of Grana Padano cheese.

A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods

The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products.

Biodiversity of dairy Propionibacterium isolated from dairy farms in Minas Gerais, Brazil

Dairy propionibacteria are used as ripening cultures for the production of Swiss-type cheeses, and some strains have potential for use as probiotics. This study investigated the biodiversity of wild dairy Propionibacteria isolates in dairy farms that produce Swiss-type cheeses in Minas Gerais State, Brazil. RAPD and PFGE were used for molecular typing of strains and MLST was applied for phylogenetic analysis of strains of Propionibacterium freudenreichii. The results showed considerable genetic diversity of the wild dairy propionibacteria, since three of the main species were observed to be randomly distributed among the samples collected from different farms in different biotopes (raw milk, sillage, soil and pasture). Isolates from different farms showed distinct genetic profiles, suggesting that each location represented a specific niche. Furthermore, the STs identified for the strains of P. freudenreichii by MLST were not related to any specific origin. The environment of dairy farms and milk production proved to be a reservoir for Propionibacterium strains, which are important for future use as possible starter cultures or probiotics, as well as in the study of prevention of cheese defects.

Heterologous production of antimicrobial peptides in Propionibacterium freudenreichii

Heterologous bacteriocin production in Propionibacterium freudenreichii is described. We developed an efficient system for DNA shuttling between Escherichia coli and P. freudenreichii using vector pAMT1. It is based on the P. freudenreichii rolling-circle replicating plasmid pLME108 and carries the cml(A)/cmx(A) chloramphenicol resistance marker. Introduction of the propionicin T1 structural gene (pctA) into pAMT1 under the control of the constitutive promoter (P4) yielded bacteriocin in amounts equal to those of the wild-type producer Propionibacterium thoenii 419. The P. freudenreichii clone showed propionicin T1 activity in coculture, killing 90% of sensitive bacteria within 48 h. The pamA gene from P. thoenii 419 encoding the protease-activated antimicrobial peptide (PAMP) was cloned and expressed in P. freudenreichii, resulting in secretion of the pro-PAMP protein. Like in the wild type, PAMP activation was dependent on externally added protease. Secretion of the antimicrobial peptide was obtained from a clone in which the pamA signal peptide and PAMP were fused in frame. The promoter region of pamA was identified by fusion of putative promoter fragments to the coding sequence of the pctA gene. The P4 and Ppamp promoters directed constitutive gene expression, and activity of both promoters was enhanced by elements upstream of the promoter core region.

Genus- and species-specific PCR-based detection of dairy propionibacteria in environmental samples by using primers targeted to the genes encoding 16S rRNA

PCR assays with primers targeted to the genes encoding 16S rRNA were developed for detection of dairy propionibacteria. Propionibacterium thoenii specific oligonucleotide PT3 was selected after partial resequencing. Tests allowed the detection of less than 10 cells per reaction from milk and cheese and 10(2) cells per reaction from forage and soil.

Identification and clustering of dairy propionibacteria by RAPD-PCR and CGE-REA methods

A total of 67 classical propionic acid bacteria (PAB) strains, 10 of which were from type culture collections and 57 from milk, typical Italian cheeses, acid whey and feed flour of different regions, were analysed by Randomly Amplified Polymorphic DNA (RAPD-PCR) and by Conventional Gel Electrophoresis Restriction Endonuclease Analysis (CGE-REA). The genotypic traits achieved using RAPD-PCR with three primers (OPL-01, OPL-02 and OPL-05) and SmaI CGE-REA patterns were compared by numerical analysis and allowed a clear distinction of four clusters corresponding to the currently described species of classical propionibacteria according to type and reference strains positions. No discrepancies exist in species recognition between the two methods; 36 isolates were identified as Propionibacterium freudenreichii, 15 as P. jensenii, four as P. acidipropionici and two as P. thoenii. Many differences, however, were observed in intraspecific clustering. Numerical comparison of RAPD-PCR profiles appeared to be a suitable method for highlighting the presence of particular phenotypic characters, while intraspecific differentiation obtained by CGE-REA analysis allowed association of strains at high similarity levels on the basis of their geographical origin.