Short communication: High-throughput sequencing approach to investigate Italian artisanal cheese production

Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity

Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.

A comprehensive study on the autochthonous microbiota, volatilome, physico-chemical, and morpho-textural features of Montenegrin Njeguški cheese

The present study aims to deepen the knowledge of the microbiota, gross composition, physico-chemical and morpho-textural features, biogenic amines content and volatilome of Njeguški cheese, one of the most popular indigenous cheeses produced in Montenegro. Cheese samples were collected in duplicate from three different batches produced by three Montenegrin artisan producers. For the first time, the microbiota of Njeguški cheese was investigated using both culture-dependent techniques and metagenomic analysis. Coagulase positive staphylococci viable counts were below the detection limit of the analysis (<1 log cfu g-1). Salmonella spp., Listeria monocytogenes and staphylococcal enterotoxins were absent. However, relatively high viable counts of Enterobacteriaceae, Escherichia coli, Pseudomonadaceae and eumycetes were detected. Metataxonomic analysis revealed a core microbiome composed of Lactococcus lactis, Streptococcus thermophilus, Debaryomyces hansenii, and Kluyveromyces marxianus. Furthermore, the detection of opportunistic pathogenic yeasts such as Magnusiomyces capitatus and Wickerhamiella pararugosa, along with the variable content of biogenic amines, suggests the need for increased attention to hygienic conditions during Njeguški cheese production. Significant variability was observed in humidity (ranging from 38.37 to 45.58 %), salt content (ranging from 0.70 to 1.78 %), proteins content (ranging from 21.42 to 25.08 %), ash content (ranging from 2.97 to 4.05 %), hardness, springiness, and color among samples from different producers. Gas chromatography-mass spectrometry analysis showed a well-defined and complex volatilome profile of the Njeguški cheese, with alcohols (ethanol, isoamyl alcohol, phenetyl alcol), esters and acetates (ethyl acetate, ethyl butanoate, isoamyl acetate), ketones (acetoin, 2-butanone), and acids (acetic, butanoic, hexanoic acids) being the main chemical groups involved in aroma formation. This research will provide new insights into the still poorly explored identity of Njeguški cheese, thus serving as a first baseline for future studies aimed at protecting its tradition.

Chemical, microbiological, textural, and sensory characteristics of pilot-scale Caciofiore cheese curdled with commercial Cynara cardunculus rennet and crude extracts from spontaneous and cultivated Onopordum tauricum

The aim of this study was the chemical, microbiological, textural, and sensory characterization of pilot-scale prototypes of an Italian ewe's raw milk cheese (Caciofiore) curdled with commercial Cynara cardunculus rennet, used as a control, and crude extracts obtained from flowers of either spontaneous or cultivated Onopordum tauricum. Hence, the control and experimental cheese prototypes produced in two rounds of cheesemaking trials were assayed, at the end of their 60-day maturation, for the following features: pH, titratable acidity, dry matter, fat, total and soluble nitrogen (TN and SN, respectively), ash, salt, protein, lactose, viable plate counts and composition of the bacterial and fungal populations, color, texture, volatile organic compounds (VOCs), and olfactory attributes by sensory analysis (the latter for the sole prototypes curdled with the commercial rennet and the extract obtained from cultivated O. tauricum). The data overall collected showed a very low impact of the type of thistle rennet on the analyzed cheese traits, with significant differences being exclusively found for SN/TN%, titratable acidity, color, and adhesiveness. By contrast, a higher impact of the cheesemaking round was seen, with significant differences being observed for salt content, load of presumptive lactobacilli, thermophilic cocci, and Escherichia coli, and levels of the following VOCs: 2,3-butanedione, 2-pentanone, 1-butanol, 2-heptanone, 3-methyl-1-butanol, 2-heptanol, 2-nonanone, dimethyl trisulfide, 2-methyl propanoic acid, butanoic acid, and 3-methyl butanoic acid. Sensory analysis revealed a strong ewe's cheese odor, accompanied by other olfactory notes, such as pungent, sour curd, sweet, and Parmesan cheese-like notes, in all the analysed cheese prototypes. Moreover, key odor active compounds, including butanoic acid, ethyl butanoate, 2,3-butanedione, 1-octen-3-one, and dimethyl trisulfide, were identified by GC-olfactometry analysis. Regarding the odor attributes as determined by sensory analysis, again the type of rennet had an almost negligible impact, with significant differences being only perceived for 1 or 2 out of 20 odor attributes, depending on the analytical conditions applied. Although some aspects deserve further investigation, the results herein collected confirm that O. tauricum can be regarded as an alternative source of thistle rennet for the manufacture of Caciofiore cheese, and more in general, Mediterranean ewe's milk cheeses.

Diversity of the Microbiota of Traditional Izmir Tulum and Izmir Brined Tulum Cheeses and Selection of Potential Probiotics

High-throughput DNA sequencing (HTS) was used to study the microbial diversity of commercial traditional Izmir Tulum (IT) and Izmir Brined Tulum (IBT) cheeses from Izmir, Türkiye. Simultaneously, cultivation-dependent methods were used to isolate, identify and characterize bacterial strains displaying probiotic potential. At the phylum level, Firmicutes dominated the microbiota of both cheese types comprising >98% of the population. Thirty genera were observed, with Streptococcus being the most abundant genus and with Streptococcus thermophilus and S. infantarius subsp. infantarius being the most abundant species. Genera, including Bifidobacterium and Chryseobacterium, not previously associated with IT and IBT, were detected. IT cheeses displayed higher operational taxonomic units (OTUs; Richness) and diversity index (Simpson) than IBT cheeses; however, the difference between the diversity of the microbiota of IT and IBT cheese samples was not significant. Three Lacticaseibacillus paracasei strains isolated from IBT cheeses exhibited probiotic characteristics, which included capacity to survive under in vitro simulated gastrointestinal conditions, resistance to bile salts and potential to adhere to HT-29 human intestinal cells. These findings demonstrate that Tulum cheeses harbor bacterial genera not previously reported in this cheese and that some strains display probiotic characteristics.

Characterization of microbiota of naturally fermented sauerkraut by high-throughput sequencing

Sauerkraut is a traditionally fermented cabbage, with a unique taste and beneficial properties, in northeast China. The taste and flavor of sauerkraut vary from region to region, owing to the differences in microorganisms. Illumina MiSeq sequencing was used to identify and quantify the microbial community composition of the broth and leaves of the naturally fermented Suan-cai collected from northeast China. The alpha and beta diversity of the samples from three areas in Heilongjiang province shown that the complexity of bacterial diversity of the three samples was C, A and B in turn. The Lactobacillus widely existed in fermented sauerkraut, of these, Latilactobacillus sakei, Loigolactobacillus coryniformis subsp. torquens, Lactiplantibacillus plantarum subsp. plantarum, and Secundilactobacillus malefermentans were more abundant in the sauerkraut leaves than in fermentation broth. Other genera of lactic acid bacteria Pediococcus and Leuconostoc, which have potential probiotic properties, were also present. However, some harmful bacteria such as Arcobacter and Acinetobacter were also detected.

Determination of the microbial community of traditional Mongolian cheese by using culture-dependent and independent methods

Mongolian cheese is not only a requisite source of food for the nomadic Mongolian but also follows a unique Mongolian dairy artisanal method of production, possessing high nutritional value and long shelf-life. In this study, the ancient technique for the production of Mongolian cheese was investigated. The nutritional value of Mongolian cheese was characterized by its high-protein content (30.13 ± 2.99%) and low-fat content (9.66 ± 3.36%). Lactobacillus, Lactococcus, and Dipodascus were the predominant bacterial and fungal genera, and Lactobacillus helveticus, Lactococcus piscium, and Dipodascus geotrichum were the predominant species in the Mongolian cheese. The microbiota of products from different cheese factories varies significantly. The high-temperature (85°C-90°C) kneading of coagulated curds could eliminate most of the thermosensitive microorganisms for extending the shelf-life of cheese. The indigenous spore-forming microbes, which included yeasts, belonging to Pichia and Candida genera, and molds, belonging to Mucor and Penicillium genera, which originated from the surroundings during the process of cooling, drying, demolding, and vacuum packaging could survive and cause the package to swell and the cheese to grow mold. The investigation of production technology, nutrition, microbiota, and viable microbes related to shelf-life contributes to the protection of traditional technologies, extraction of highlights (nutritional profiles and curd scalding) for merchandise marketing, and standardization of Mongolian cheese production, including culture starters and aseptic technique.

Lactic Acid Bacteria in Raw-Milk Cheeses: From Starter Cultures to Probiotic Functions

Traditional cheeses produced from raw milk exhibit a complex microbiota, characterized by a sequence of different microorganisms from milk coagulation and throughout maturation. Lactic acid bacteria (LAB) play an essential role in traditional cheese making, either as starter cultures that cause the rapid acidification of milk or as secondary microbiota that play an important role during cheese ripening. The enzymes produced by such dynamic LAB communities in raw milk are crucial, since they support proteolysis and lipolysis as chief drivers of flavor and texture of cheese. Recently, several LAB species have been characterized and used as probiotics that successfully promote human health. This review highlights the latest trends encompassing LAB acting in traditional raw milk cheeses (from cow, sheep, and goat milk), and their potential as probiotics and producers of bioactive compounds with health-promoting effects.

Characterization of Microbial Shifts during the Production and Ripening of Raw Ewe Milk-Derived Idiazabal Cheese by High-Throughput Sequencing

Simple Summary

Idiazabal is a traditional cheese produced from raw ewe milk in the Basque Country (Southwestern Europe). The sensory properties of raw milk cheeses have been attributed, among other factors, to microbial shifts that occur during the production and ripening processes. In this study, we used high-throughput sequencing technologies to investigate the microbiota of Latxa ewe raw milk and the dynamics during cheese production and ripening processes. The microbiota of raw milk was composed of lactic acid bacteria (LAB), environmental bacteria and non-desirable bacteria. Throughout the cheese making and ripening processes, the growth of LAB was promoted, whereas that of non-desirable and environmental bacteria was inhibited. Moreover, some genera not reported previously in raw ewe milk were detected and clear differences were observed in the bacterial composition of raw milk and cheese among producers, in relation to LAB and environmental or non-desirable bacteria, some of which could be attributed to the production of flavour related compounds.

Abstract

In this study, we used high-throughput sequencing technologies (sequencing of V3–V4 hypervariable regions of 16S rRNA gene) to investigate for the first time the microbiota of Latxa ewe raw milk and the bacterial shifts that occur during the production and ripening of Idiazabal cheese. Results revealed several bacterial genera not reported previously in raw ewe milk and cheese, such as Buttiauxella and Obesumbacterium. Both the cheese making and ripening processes had a significant impact on bacterial communities. Overall, the growth of lactic acid bacteria (LAB) (Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Streptococcus and Carnobacterium) was promoted, whereas that of non-desirable and environmental bacteria was inhibited (such as Pseudomonas and Clostridium). However, considerable differences were observed among producers. It is noteworthy that the starter LAB (Lactococcus) predominated up to 30 or 60 days of ripening and then, the growth of non-starter LAB (Lactobacillus, Leuconostoc, Enterococcus and Streptococcus) was promoted. Moreover, in some cases, bacteria related to the production of volatile compounds (such as Hafnia, Brevibacterium and Psychrobacter) also showed notable abundance during the first few weeks of ripening. Overall, the results of this study enhance our understanding of microbial shifts that occur during the production and ripening of a raw ewe milk-derived cheese (Idiazabal), and could indicate that the practices adopted by producers have a great impact on the microbiota and final quality of this cheese.

Mycobiota Composition of Robiola di Roccaverano Cheese along the Production Chain

Robiola di Roccaverano is a Protected Designation of Origin (PDO) cheese from the Piedmont region of Italy. In this study, the mycobiota occurring during Robiola di Roccaverano production was elucidated. Samples of milk, Natural Milk Cultures (NMC), curd, 5- and 15-days ripened cheese were collected from one dairy plant and the mycobiota was analyzed by the metataxonomic approach. Milk samples showed a high diversity and Cladosporium, Kluyveromyces marxianus, Geotrichum candidum and Debaryomyces hansenii were found with higher relative abundance. This mycobiota remains quite stable in NMC and curd matrices although the relative abundance of K. marxianus and G. candidum yeasts increased significantly and shaped the fungal composition of 5- and 15-day ripened cheese.

Shifts of microbiota during cheese production: impact on production and quality

The high-throughput DNA sequencing (HTS) method is used to identify microbes in cheese and their potential functional properties. The technique can be applied to the microbiota of the cheese processing environment, raw milk, curd, whey, and starter cultures, and be used to improve the quality, safety, and other physicochemical properties of the final product. The HTS method is also utilized to study the microbiota shift of different types of cheeses during processing, as the composition and functional properties of the microbiome provide unique characteristics to different cheeses. Although there are several reviews that focused on microbiota of various types of cheeses, this review focuses on evaluating the microbiota shift of different types of cheese production and highlights key bacteria in each step of the processing as well as microbiota of various types of cheeses. KEY POINTS: • High-throughput sequencing can be applied to identify microbiota in cheese. • Microbiota in cheese is changed during making process and aging. • Starter culture plays an important role to establish microbiota in cheese.