Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods

Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects

Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.

Profile of lactic acid bacteria (MALDI-TOF-MS) and physico-chemical and microbiological characteristics of the raw milk and fresh artisanal cheese from Serra Geral, Minas Gerais, Brazil

Artisanal cheese from Serra Geral, Minas Gerais, Brazil, stands out for its cultural asset and socio-economic relevance. However, standards of identity and quality and the peculiar terroir associated with the edaphoclimatic conditions have not been established. Therefore, the production flow diagram and the physico-chemical and microbiological quality of the raw milk, pingo (natural starter culture), production benches, water and fresh cheese were investigated for the first time. In addition, lactic acid bacteria (LAB) from cheese and its production environment were identified by MALDI-TOF. For that, 12 cheese making facilities were selected. The raw milk and pingo showed adequate physico-chemical characteristics for cheesemaking; however, high microbial counts were found. In the water, total and thermotolerant coliforms were also identified. The fresh cheeses were classified as 'high moisture and fat' and 'soft mass'. Most physico-chemical parameters were satisfactory; however, there were high counts of total coliforms, Staphylococcus spp. and coagulase-positive staphylococci. There were high counts of LAB in the raw milk, pingo, bench surface and fresh cheese. A total of 84 microbial biotypes from MRS agar were isolated. Lactococcus lactis was the predominant LAB, followed by Lactococcus garvieae. Leuconostoc mesenteroides (benches), Leuconostoc pseudomesenteroides (fresh cheese), and Enterococcus faecium (pingo) were identified sporadically. These results indicate the risks to public health associated with the consumption of the fresh cheese, and measures to improve its safety are needed.

Novel yeasts with potential probiotic characteristics isolated from the endogenous ferment of artisanal Minas cheese

Artisanal Minas cheese (QMA) is traditionally elaborate using raw milk and endogenous ferment (pingo - whey or rala - grated ripened cheese). In the present study, 91 yeast strains were isolated and identified from pingo and rala. Eight yeast species were identified by the MALDI-TOF mass spectrometry and confirmed by sequencing of the ITS region. The yeasts' protease and lipase activities were evaluated in addition to probiotic properties such as tolerance to low pH and bile salts, hydrophobicity, autoaggregation, co-aggregation with pathogens, and antimicrobial susceptibility. The rala ferment showed a greater variety of species. Yarrowia lipolytica was the dominant specie (52.7% of isolates), followed by the Kluyveromyces lactis and Kodamaea ohmeri (9.9 and 6.6%, respectively). From the total yeasts evaluated, 74 strains showed positive enzymatic activity: 52 strains showed lipolytic (51 Y. lipolytica and one Trichosporon japonicum) and 44 proteolytic activities (18 Y. lipolytica, 13 K. ohmeri, 11 K. lactis, and 2 Wickerhamiella sp.). All evaluated isolates demonstrated tolerance to pH 2.0, and 69 isolates supported the presence of bile salts. From them, 12 isolates showed the capacity of autoaggregation (> 30%) and hydrophobicity (> 90.0%) and were then selected for co-aggregation and antibiotic resistance assays. All selected isolates showed co-aggregation with Salmonella Enteritidis, Escherichia coli, and Listeria monocytogenes greater than 30%. None of the yeast showed sensibility to the evaluated antibiotics and antagonistic activity against the evaluated pathogens. The results demonstrated that pingo and rala have different yeast composition with different enzymatic activity, which may affect the characteristics of the cheese. Furthermore, some yeast strains: Y. lipolytica (9 strains isolated from rala) and K. ohmeri (3 strains isolated from pingo) demonstrated attractive probiotic potential.

Distinct Bacterial Communities in São Jorge Cheese with Protected Designation of Origin (PDO)

São Jorge cheese is an iconic product of the Azores, produced from raw cow's milk and natural whey starter (NWS). Although it is produced according to Protected Designation of Origin (PDO) specifications, the granting of the PDO label depends crucially on sensory evaluation by trained tasters. The aim of this work was to characterize the bacterial diversity of this cheese using next-generation sequencing (NGS) and to identify the specific microbiota that contributes most to its uniqueness as a PDO by distinguishing the bacterial communities of PDO and non-PDO cheeses. The NWS and curd microbiota was dominated by Streptococcus and Lactococcus, whereas Lactobacillus and Leuconostoc were also present in the core microbiota of the cheese along with these genera. Significant differences (p < 0.05) in bacterial community composition were found between PDO cheese and non-certified cheese; Leuconostoc was found to play the chief role in this regard. Certified cheeses were richer in Leuconostoc, Lactobacillus and Enterococcus, but had fewer Streptococcus (p < 0.05). A negative correlation was found between contaminating bacteria, e.g., Staphylococcus and Acinetobacter, and the development of PDO-associated bacteria such as Leuconostoc, Lactobacillus and Enterococcus. A reduction in contaminating bacteria was found to be crucial for the development of a bacterial community rich in Leuconostoc and Lactobacillus, thus justifying the PDO seal of quality. This study has helped to clearly distinguish between cheeses with and without PDO based on the composition of the bacterial community. The characterization of the NWS and the cheese microbiota can contribute to a better understanding of the microbial dynamics of this traditional PDO cheese and can help producers interested in maintaining the identity and quality of São Jorge PDO cheese.

High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community

Microbial starter cultures are used in the production of many cheeses around the world, such as Parmigiano-Reggiano, in Italy, Époisses, in France, and Canastra, in Brazil, providing many of the unique features of these cheeses. Bacteriophages (phages) are ubiquitous and well known to modulate the structure of bacterial communities, and recent data indicate that cheeses contain a high abundance of naturally occurring phages. Here, we analyze the viral and bacterial metagenomes of Canastra cheese: a traditional artisanal Brazilian cheese produced using an endogenous starter culture and raw milk. Over 1,200 viral operational taxonomic units were recovered using both isolated viral-like particles and complete metagenomic DNA. Common viral families identified included Siphoviridae and Myoviridae, with 40% of putative phage genomes unidentified at the family level of classification. We observed very high phage diversity, which varied greatly across different cheese producers, with 28% of phage genomes detected in only one producer. Several metagenome-assembled genomes were recovered for lactic acid-producing bacteria, as well as nonstarter bacterial species, and we identified several phage-bacterium interactions, at the strain level of resolution, varying across distinct cheese producers. We postulate that at least one bacterial strain detected could be endogenous and unique to the Canastra cheese-producing region in Brazil and that its growth seems to be modulated by autochthonous phages present in this artisanal production system. This phage-host relationship is likely to influence the fermentation dynamics and ultimately the sensorial profile of these cheeses, with implications for other similar cheese production systems around the world. IMPORTANCE Our work demonstrated a dynamic yet stable microbial ecosystem during cheese production using an endogenous starter culture. This was observed across several distinct producers and was marked by genomic evidence of continued phage-bacterium interactions, such as the presence of bacterial defense mechanisms. Furthermore, we provide evidence of unique microbial signatures for each individual cheese producer studied in the region, a fact that may have profound consequences on product traceability. This was the first effort to describe and understand the bacteriophage composition and ecological dynamics within the Brazilian Canastra cheese production system. The study of this prototypical backslopping production system provides a solid background for further mechanistic studies of the production of many cheeses around the world.

Seasonal variation in the Canastra cheese mycobiota

Canastra cheese is the most well-known artisanal cheese produced in Brazil. Although its production includes a step to remove fungi from the cheese surface, in recent years some cheesemakers have preserved the autochthonous fungi grown during ripening due to an interest in the sensory characteristics attributed to these microorganisms. In this work, the mycobiota of artisanal cheeses produced in the Canastra region was characterized based on ITS marker gene analysis. A total of 96 artisanal cheeses from 16 different farms across 9 cities were collected during two different periods (dry and wet seasons). The Canastra cheese mycobiota was significantly impacted by the season, the city of production and the farm but altitude did not affect the fungal community of the cheeses analyzed. Debaryomyces prosopidis was most abundant in the majority of samples across both seasons. During the wet season, Trichosporon asahii, Kluyveromyces lactis and Fusarium solani were the next most abundant species, followed by Torulaspora delbrueckii and Acremonium citrinum. These results highlight the importance of manufacturing practices and seasonality on the fungal composition of Canastra cheeses. These insights are particularly important in light of recent new regulation in Brazil, removing previous obstacles for surface fungi to persist on cheese. These new regulations will allow new approaches to cheese production, and ultimately, novel products.

Flavour Profile of Traditional Dry Sausage Prepared with Partial Substitution of NaCl with KCl

The effects of partial substitution of NaCl with 0%, 20%, 30% and 40% KCl on the physical characteristics, bacterial community and flavour profile of traditional dry sausage were investigated in this study. With the increase in KCl substitution ratio, the moisture content, astringency, bitterness and umami increased significantly, and the saltiness gradually decreased (p < 0.05). The high-throughput sequencing results showed that the dry sausages with KCl substitution had relatively high abundances of Staphylococcus. For volatile compounds, increasing the KCl substitution ratio reduced the formation of aldehydes, ketones and some alcohols, but promoted the formation of acids and esters (p < 0.05). Sensory evaluation and partial least square regression analysis showed that the dry sausages with 20% and 30% KCl were similar in overall physical and microbial properties, flavour profiles and sensory attributes, and the sausages with 40% KCl were characterized by taste defects. Overall, partial substitution of NaCl with 30% KCl could ensure the acceptable flavour and sensory attributes of dry sausages.

Microorganisms present in artisanal fermented food from South America

Artisanal fermented products (foods and beverages) are produced in an artisanal way in many countries around the world. The main purpose of fermentation is to preserve the food, improve its safety, increase the nutritional and health-promoting value and add specific flavours. In South America, there is a great variety of fermented food produced in an artisanal way. Different raw materials are used such as potatoes, sweet potato, cassava, maize, rice, milk (cow, ewe, goat) and meat (beef, goat, lamb, llama and guanaco). Some of these fermented foods are typical of the region and are part of the culture of native communities, e.g. tocosh, masa agria, puba flour, charqui, chicha, champu and cauim among others (indigenous foods). However, other fermented foods produced in South America introduced by mainly European immigration, such as cheeses and dry sausages, and they are also produced in many different parts of the world. In this work, the microbial composition of the different artisanal fermented products produced in South America is reviewed, taking into consideration the associated raw materials, fermentation conditions and methodologies used for their production.

Further culture-independent characterization of the lactic microbiota of Serro artisanal cheese

This study aimed to provide a further characterization of the lactic microbiota present in Minas artisanal cheese (MAC) from the Serro region by using culture-independent methods, as a complementary analysis of a previous study. The total DNA extracted from MAC samples (n = 55) was subjected to repetitive extragenic palindromic-PCR (rep-PCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Rep-PCR analysis showed that core microbiota of Serro MAC was closely related, independent of the production town, farm size, or time of production. The sequencing of PCR-DGGE bands identified the prevalence of Lactococcus lactis in all samples, and Streptococcus salivarius was also identified. Thus, we conclude that when more accurate methods are unavailable, rep-PCR can be used as a culture-independent method to demonstrate if the microbiota is closely related or not among the samples. PCR-DGGE results also matched to the main findings of high-throughput sequencing, previously presented, confirming its confidence to detect the main microbial groups present in the raw milk cheeses.

Staphylococcus aureus from Minas Artisanal Cheeses: Biocide Tolerance, Antibiotic Resistance and Enterotoxin Genes

Staphylococcus aureus is a common contaminant in artisanal raw-milk cheeses. Tolerance of S. aureus to biocides is a threat to disinfection in the cheese production environment, while antibiotic resistance and enterotoxin production are additional health concerns. This study aimed to evaluate the tolerance of S. aureus isolated from Minas artisanal cheeses to the biocides benzalkonium chloride, hexadecylpyridinium chloride, cetrimide, triclosan, hexachlorophene, and chlorhexidine, and the simultaneous occurrence of genes coding for antibiotic resistance (mecA, aacA-aphD, and tetK), efflux pumps [qacA/B and smr (qacC/D)], and enterotoxins (sea, seb, sec, sed, see, seg, seh, sei, and sej). Among the tested isolates, 38.2% were resistant to at least one biocide, and 73.1% were positive for one or more antibiotic resistance gene. Most of the biocide-tolerant and antibiotic-resistant isolates harbored efflux pump genes, and were positive for at least one staphylococcal enterotoxin gene. The study highlights the need for correct hygiene monitoring programs to ensure the safety of these products.

Biodiversity and succession of lactic microbiota involved in Brazilian buffalo mozzarella cheese production

The biodiversity and succession of lactic acid bacteria (LAB) involved in the production and storage of Brazilian buffalo mozzarella cheese were evaluated. The isolates were characterized by Gram staining and catalase test, by the ability to grow at different conditions: temperatures, pH, concentrations of NaCl, and production of CO₂ from glucose. The biodiversity and succession of 152 LAB isolated during cheese production were evaluated by 16S rRNA gene sequencing, Random Amplified Polymorphic DNA (RAPD-PCR), and Restriction Fragment Length Polymorphism (RFLP-PCR) techniques. Most of the strains grow well at 30 °C and are tolerant to 6.5% of NaCl, and in general, the best pH for growing was 9.6. Leuconostoc mesenteroides, Lacticaseibacillus casei, Limosilactobacillus fermentum, and Enterococcus sp. were prevalent and present in almost all steps of production. The LAB strains are typically found in the traditional Italian cheese, except the Leuconostoc citreum species. Sixty clusters were obtained by RAPD-PCR with 85% of similarity (114 isolates) while most of the LAB was clustered with 100% of similarity by the RFLP-PCR technique. The applied techniques enabled a valuable elucidation of the LAB biodiversity and succession, contributing to a better understanding of the specific microbial cultures with a technological aptitude of this cheese.

Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques

The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.

Artisanal Brazilian Cheeses-History, Marketing, Technological and Microbiological Aspects

This review focused on the historical, marketing, technological, and microbiological characteristics of artisanal Brazilian cheese. Brazilian cheese production was introduced and developed from the influence of immigrants considering the combination of climate, races of the animals, quality and specificity of milk, technological cheese-making processes and environmental microbiology, among other factors. It resulted in cheese products with specific physicochemical, microbiological, and sensory quality, which represent the heritage and identities of the different Brazilian regions. The production of artisanal cheese increased in many Brazilian regions, mainly in the southeast, especially due to the traditional production and innovative development of new varieties of cheese. The microbiological quality and safety of raw-milk artisanal cheese continues to be a concern and many studies have been focusing on this matter. Special attention needs to be given to the cheeses produced by raw milk, since numerous reports raised concerns related to their microbiological safety. This fact requires attention and the implementation of strict hygiene practices on the production and commercialization, besides appropriate governmental regulations and control. However, more studies on the relationship between technological processes and microbiological properties, which results in a superior culinary quality and safety of artisanal Brazilian cheeses, are needed.

Microbiological and Metagenomic Characterization of a Retail Delicatessen Galotyri-Like Fresh Acid-Curd Cheese Product

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, whose isolation frequency was batch-dependent. Lactococcus lactis isolates were sporadic, except for one cheese batch. However, Lactococcus lactis, Enterobacteriaceae, Vibrionaceae, Salinivibrio, and Shewanellaceae were detected at fairly high relative abundances culture-independently, despite the fact that their viable counts in the cheeses were low or undetectable. Metagenomics confirmed the prevalence of S. thermophilus and Lb. delbrueckii. Overall, this delicatessen Galotyri-like cheese product was shown to be a rich pool of indigenous nonstarter LAB strains, which deserve further biotechnological investigation.

Brazilian Artisanal Cheeses: Diversity, Microbiological Safety, and Challenges for the Sector

Artisanal cheeses made with raw milk are highly appreciated products in Brazil. Most of these cheeses are produced in small facilities across different production regions in the country, some of which have been granted a protected designation of origin and are award winners. The most prominent state that manufactures these products is Minas Gerais (MG), but production is also gaining strength in other Brazilian states. The major challenge faced by artisanal cheese production is related to microbial risks associated with foodborne pathogens when the quality of the raw milk is unsatisfactory. Regulations created for the dairy industry are constantly been revised and adapted, considering the small-scale production of Brazilian artisanal cheeses, in order to guarantee safety at all steps of cheese production and commercialization. This text presents a summary of the huge diversity of artisanal cheeses produced in the country, grouped by geographical regions, and reviews the current challenges faced by producers and government considering the safety of these cheeses.

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.

Microbiological quality and safety of Brazilian artisanal cheeses

The establishment of norms that regulates the production and trade of Brazilian Artisanal Cheeses (BAC) has been stimulating many small farmers for this activity. The predominance of lactic acid bacteria (LAB) is a typical characteristic of BAC, which confers desirable attributes to artisanal cheeses. However, these products can be contaminated by other microbial groups, including those that indicate hygienic failures during production and may cause spoilage, or even microorganisms that pose risks to consumers' health. A systematic review of the literature published from January 1996 to November 2020 was carried out to identify scientific data about production characteristics and microbiological aspects of BAC, with a major focus on quality and safety status of these traditional products. Studies that fulfilled the inclusion criteria indicated that artisanal chesses produced in Brazil still do not satisfactorily meet the microbiological criteria established by the national laws, mainly due to the high counts of coagulase-positive Staphylococcus and coliforms. Despite low prevalence, pathogens such as Salmonella and Listeria monocytogenes were isolated in some BAC. This review contributed to better understanding microbiological aspects of BAC, the data compiled by the authors highlight the need to improve hygiene practices along the production chain of these traditional cheeses.

Microbial shifts through the ripening of the "Entre Serras" Minas artisanal cheese monitored by high-throughput sequencing

Minas Gerais is a Brazilian state known as the largest cheese producer in Brazil. Minas Artisanal Cheese (MAC) is produced in different regions of this Brazilian state using raw cow milk to which a natural starter culture ("pingo") is added. "Entre Serras" is one of these regions, in which the MAC production had decreased (even stopped) for decades until recently, when artisanal cheeses production has been resurrected. Here, we aimed to gain insights on the bacterial diversity of "Entre Serras" MAC. 16S rRNA gene amplicon sequencing was used to assess the bacterial community in cheeses produced by four farms (A, B, C, and D) over 60 days of ripening. Overall, Lactococcus lactis was the predominant species found, regardless of the producer/farm. Enterococcus, Streptococcus, Lactobacillus and Leuconostoc genera were also prevalent in the samples microbiota and their levels varied according to the producer/farm. Cheeses produced by Farms A and B presented high contaminant levels (mainly Enterobacteriaceae and S. aureus), which may be attributed to poor hygiene during cheese production and/or herd health management. Chao1 indices varied significantly when the estimated species richness values of the producers/farms were compared (p < 0.05). A principal coordinate analysis also revealed distinct microbial communities for some farms (p < 0.001). However, no statistical significance was identified when samples were grouped by ripening time. Core microbiota analysis indicated that "Entre Serras" MAC microbiota includes not only LAB, but also spoilage and potentially pathogenic bacteria. We provide the first insights on the bacterial diversity of "Entre Serras" MAC, helping the understanding of the inter-regional microbiological diversity of the samples.

High-throughput sequencing approach to reveal the bacterial diversity of traditional yak jerky from the Tibetan regions

A high-throughput sequencing approach was used to investigate the bacterial community diversity of traditional Tibetan yak jerky, which was collected from three different regions in Tibet and with different natural drying times. Tibetan yak jerky from different regions had different bacterial communities, which was mainly reflected in the relative abundance levels of unclassified Cyanobacteria, Psychrobacter and Acinetobacter. The unclassified Cyanobacteria was the dominant genus of Qamdo yak jerky, Acinetobacter was the dominant genus of Shigatse yak jerky, and Psychrobacteria was the dominant genus of Nyingchi yak jerky. With increasing natural drying time, the diversity of bacterial communities in yak jerky decreased, and unclassified Cyanobacteria become the dominant genus. Spearman's correlation analysis and canonical correspondence analysis revealed that physicochemical factors (moisture content, water activity, shear force and pH) were significantly correlated with bacterial community. Our results will be beneficial to improve and standardize the safety and quality of traditional Tibetan yak jerky.

Biopreservation and probiotic potential of a large set of lactic acid bacteria isolated from Brazilian artisanal cheeses: From screening to in product approach

The increasing interest in products with functional properties has encouraged the search for new lactic acid bacteria (LAB) present in natural sources, as traditional fermented foods. In this study, a large set of wild LAB isolates (n = 220) from Brazilian artisanal cheeses (BAC) were assessed for their probiotic and biopreservation potential. First, the rational selection was performed. From the tested isolates, 92 (41.8 %) were resistant to low pH (2 and 3). These isolates were submitted to bile salt (0.4 % Oxgall powder) resistance, and 22 were selected and submitted to adhesion assays. The autoaggregation values ranged from 68.5-99% and were considered moderate to high (20-70 %). Hydrophobicity values varied significantly between LAB (5.0-64.3%), and seven isolates presented values higher than 40 %. All selected LAB (n=22) were capable of adhering to Caco-2 (> 70 %) cells, and none isolate displayed any tested gene for biogenic amine production. Most isolates (18/22) showed less than 1 log CFU reduction after passage through the simulated gastrointestinal tract (GIT) conditions. A total of twenty isolates satisfied key in vitro criteria to be considered as probiotics. A hierarchical cluster analysis (HCA) was performed, and two clusters were observed, showing high variability between Lactobacillus plantarum isolates regarding adhesion properties and survival to GIT stress and one influence of the source of isolation on these properties. After screening, the antimicrobial activity of Lb. plantarum (1QB77) was tested in microcheeses in which survival of two relevant pathogenic bacteria (Staphylococcus aureus and Listeria monocytogenes) was monitored along ripening and after a simulated GIT passage, concomitantly. L. plantarum (1QB77) has shown the ability to reach high counts (∼ 9 log CFU/g) at the end of ripening. This isolate was also able to reduce counts of S. aureus and L. monocytogenes in microcheeses in approx. 2.3 and 2.5 log CFU/g, respectively, until the 21st day of ripening; and about 3.2 and 3.5 log CFU/g after simulated GIT passage. Overall, the assessment of the probiotic properties of a large set of LAB was fundamental for gaining insights on the technological, functional, and potential regional traits of wild LAB isolates that can be used to develop starter cultures for tailored applications.

Uma análise histórico-crítica sobre o desenvolvimento das normas brasileiras relacionadas a queijos artesanais

RESUMO Diferentes tipos de queijos artesanais são produzidos, comercializados e consumidos no Brasil, o que impulsiona o constante desenvolvimento de normas por órgãos oficiais, como o Mapa. A criação do Suasa e do Sisbi-POA foi fundamental para esse setor, por permitir um sistema de equivalência na fiscalização e por ampliar a distribuição. Ainda, o Mapa passou a permitir que queijos artesanais produzidos com leite cru pudessem ser maturados em um período inferior a 60 dias, desde que comprovada sua inocuidade. A redução do tempo de maturação é um tema controverso e polêmico, já que não há critérios específicos que estudos científicos devem contemplar, o que permite múltiplas interpretações de dados. Com a criação e a regulamentação do selo Arte, a fiscalização dos produtos artesanais foi designada aos órgãos de agricultura, pecuária e de saúde pública, em complementação à atribuição já prevista pelo Mapa e pelo Sisbi-POA. Ainda, o selo Arte atribui aos órgãos de inspeção uma função orientadora, atividade que deveria ser prioritariamente executada por agências de extensão e associações. As normas que balizam a produção e comercialização de produtos artesanais devem ser frequentemente atualizadas, devido aos constantes avanços científicos na área e para assegurar a oferta de produtos com qualidade e inócuos aos consumidores.

DNA extraction method influences human milk bacterial profiles

AIMS

To evaluate four DNA extraction methods to elucidate the most effective method for bacterial DNA recovery from human milk (HM).

METHODS AND RESULTS

Human milk DNA was extracted using the following methods: (i) Qiagen MagAttract Microbial DNA Isolation Kit (kit QM), (ii) Norgen Milk Bacterial DNA Isolation Kit (kit NM), (iii) Qiagen MagAttract Microbiome DNA/RNA Isolation Kit (kit MM) and (iv) TRIzol LS Reagent (method LS). The full-length 16S rRNA gene was sequenced. Kits MM and method LS were unable to extract detectable levels of DNA in 9/11 samples. Detectable levels of DNA were recovered from all samples using kits NM (mean = 0·68 ng μl^-1 ) and QM (mean = 0·55 ng μl^-1 ). For kits NM and QM, the greatest number of reads were associated with Staphylococcus epidermidis, Streptococcus vestibularis, Propionibacterium acnes, Veillonella dispar and Rothia mucilaginosa. Contamination profiles varied substantially between kits, with one bacterial species detected in negative extraction controls generated with kit QM and six with kit NM.

CONCLUSIONS

Kit QM is the most suitable of the kits tested for the extraction of bacterial DNA from human milk.

SIGNIFICANCE AND IMPACT OF THE STUDY

Choice of extraction method impacts the efficiency of bacterial DNA extraction from human milk and the resultant bacterial community profiles generated from these samples.

Artisan minas cheese of Serro: proteolysis during ripening

The Artisan Minas Cheese (AMC) is the oldest and most traditional Brazilian cheese, it is produced in several regions of the state of Minas Gerais, such as the Serro region. The most striking features of the AMC-Serro are the use of raw milk and natural bacteria from the whey, popularly known as pingo, as well as the use of the rind washing process. The aim of the present study was to evaluate the proteolysis of the AMC-Serro from three different producers, during 60 days of maturation, and to relate the proteolysis to the producing farms, the production season and the rind washing during ripening. For this purpose, TRICINE-SDS-PAGE, proteolysis extension and depth indices, moisture, and texture (firmness) were evaluated. It was concluded that the temperature and moisture of the cheeses, that were determined by the location of the ripening room, the production season and the rind washing, were the most important factors. The degree of proteolysis also had an impact on the water loss during ripening, with effect on cheese safety. The results obtained in this study may be used to better understand the transformations during ripening of AMC-Serro and help the small traditional farmers to improve their product's quality and stability.

Amplicon sequencing reveals the bacterial diversity in milk, dairy premises and Serra da Canastra artisanal cheeses produced by three different farms

In this work, the amplicon sequencing of the 16 S rRNA gene was employed to investigate the bacterial diversity in ingredients, processing environment, and ripened cheeses collected from three farms producing Serra da Canastra artisanal cheese. The data obtained indicated a remarkable variability in the bacteria consortia of the milk, whey, and environmental samples collected in farms 1, 2, and 3, despite their location in the same city. On the other hand, the starter culture and final product (ripened cheese) presented more constant and similar microbiota no matter the farm. The findings suggest that Streptococcus and Lactococcus have competitive advantages throughout Serra da Canastra cheese-making/ripening, which is crucial for their high relative abundance in the final products. An exploratory assessment based on sequencing data available in the literature showed that the Serra da Canastra cheeses sequences clustered with specific cheese varieties that are also made from raw milk but ripened for very different periods. The findings of this study highlight that despite the variability of milk and whey microbiota among the three farms, the starter culture ("pingo") has strong relevance in shaping the microbiota of the final product.

Phylogenetic distribution of the bacteriocin repertoire of lactic acid bacteria species associated with artisanal cheese

The microbiota contributes to artisanal cheese bioprotection and biopreservation through inter and intraspecific competition. This work aimed to investigate the phylogenetic distribution of the repertoire of bacteriocin structural genes of model lactic acid bacteria (LAB) in order to investigate its respective role in the artisanal cheeses microenvironment. A phylogenetic analysis of the rRNA 16S gene from 445 model strains of LAB was conducted using bayesian inference and the repertoire of bacteriocin genes was predicted from these strains by BAGEL software. Bacterial strains were clustered in five monophyletic clades (A, B, C, D and E) with high posterior probability values (PP > 0.99). One bacteriocin structural gene was predicted for 88.5% of the analyzed strains. The majority of the species encoded different classes of bacteriocins. Greater diversity of bacteriocin genes was found for strains included in clade A, comprising Lactococcus lactis, Streptococcus agalactiae, Streptococcus thermophilus, Streptococcus macedonicus, Enterococcus faecalis and Enterococcus faecium. In addition, Lactococcus lactis presented higher diversity of bacteriocin classes, encoding glycocins, lanthipeptides, sactipeptides, cyclic and linear azole-containing peptides, included in bacteriocins class I, besides class II and III. The results suggest that the distribution of bacteriocin structural genes is related to the phylogenetic clades of LAB species, with a higher frequency in some specific clades. Information comprised in this study contributes to comprehend the bacterial competition mechanisms in the artisanal cheese microenvironment.

Brazilian Artisanal Cheeses: An Overview of their Characteristics, Main Types and Regulatory Aspects

A large variety of cheeses exist in Brazil, reflecting historical and cultural aspects. Brazilian artisanal cheeses present differences in the processing, ripening time (when applied), type of milk used, texture, size, shape, color, moisture content, flavor, the use or not of starter cultures, among others. This review describes the main artisanal cheeses produced in Brazil, focusing on general and particular characteristics associated with their making process and geographical identity. Overall, the high variability of the physicochemical data and deficiency of information on sensorial properties of Brazilian artisanal cheeses were noticed. On the other hand, culture-dependent methods were mostly used to expand the knowledge into the microbiology of these cheeses, whereas their microbial diversity has been recently discovered through the use of 16S rRNA gene sequencing-based methods. The certification of a geographical indication for Brazilian artisanal cheeses may encompass an essential milestone for adding value to these products. Regardless of their significance in the diet, culture, and economy of producing regions, taken together, the reviewed literature discloses the need of insightful studies to generate scientific data to support the expansion of the market, while ensuring the protection of historic aspects related to the production of Brazilian artisanal cheeses.

AFLP protocol comparison for microbial diversity fingerprinting

Over the last decade, several methods based on genomic DNA have been developed for the identification and genotyping of prokaryotic and eukaryotic organisms. These genomic methods differ regarding taxonomic range, discriminatory power, reproducibility, and ease of interpretation and standardization. The amplified fragment length polymorphism (AFLP) technique is a very powerful DNA fingerprinting technique for DNA of any source or complexity, varying in both size and base composition. In addition, this method shows high discriminatory power and good reproducibility allowing it to be efficient in discriminating at both the species and strain levels. The development and application of AFLP have allowed significant progress in the study of biodiversity and taxonomy of microorganisms. In the last years, the Applied Biosystems AFLP Microbial Fingerprinting Kit, now out of production, was widely used in various studies to perform AFLP characterization of selected bacteria strains (described by Vos et al. (Nucleic Acids Res 23(21):4407-4414, 1995)). Its replacement gives the possibility for laboratories to continue the use of the previous AFLP data as a reference for bacteria genetic fingerprinting analysis in biodiversity studies. To overcome this issue a result comparison, by using an improved AFLP protocol and the AFLP commercial kit, was performed. In particular, previous results on different species (Listeria monocytogenes, Lactobacillus plantarum, and Streptococcus thermophilus) obtained with the commercial kit were compared with the improved AFLP procedure to validate the protocol. When compared with the AFLP Microbial Fingerprinting Kit, the improved protocol shows high reproducibility, resolution, and overall, is a faster method with lower costs.

Microbial shifts in Minas artisanal cheeses from the Serra do Salitre region of Minas Gerais, Brazil throughout ripening time

The Minas artisanal cheese is a traditional product in its way of producing. Produced in the Minas Gerais state, Brazil, this cheese is made using raw cow's milk with the addition of an endogenous starter culture called "pingo", responsible for inoculating specific microorganisms that could enhance flavor and sensorial aspects. There are seven regions able to produce and commercialize this product - Araxá, Campo das Vertentes, Canastra Cerrado, Serra do Salitre, Serro and Triângulo Mineiro. This study aimed to assess the bacterial community of raw milk, endogenous starter culture and to uncover possible shifts in the bacterial community of the rind and core of cheeses at sixty days of ripening located in the Serra do Salitre region by Illumina MiSeq 16S rRNA gene amplicon sequencing. Raw milk and starter culture are responsible for inoculating specific bacteria into the cheese, with Planococcaceae and Streptococcaceae being prevalent throughout ripening time. The Planococcaceae family seems to develop strong interactions with the Leuconostocaceae family on the surface of these cheeses, and is associated with environmental aspects of the region, probably leading to a microbial signature of these products. Additionally, abiotic factors such as geographical location, moisture and acidity are major drivers in the microbial shift.

Metagenomics of pasteurized and unpasteurized gouda cheese using targeted 16S rDNA sequencing

BACKGROUND

The microbiome of cheese is diverse, even within a variety. The metagenomics of cheese is dependent on a vast array of biotic and abiotic factors. Biotic factors include the population of microbiota and their resulting cellular metabolism. Abiotic factors, including the pH, water activity, fat, salt, and moisture content of the cheese matrix, as well as environmental conditions (temperature, humidity, and location of aging), influence the biotic factors. This study assessed the metagenomics of commercial Gouda cheese prepared using pasteurized or unpasteurized cow milk or pasteurized goat milk via 16S rDNA sequencing.

RESULTS

Results were analyzed and compared based on milk pasteurization and source, spatial variability (core, outer, and under the rind), and length of aging (2-4 up to 12-18 months). The dominant organisms in the Gouda cheeses, based on percentage of sequence reads identified at the family or genus levels, were Bacillaceae, Lactococcus, Lactobacillus, Streptococcus, and Staphylococcus. More genus- or family-level (e.g. Bacillaceae) identifications were observed in the Gouda cheeses prepared with unpasteurized cow milk (120) compared with those prepared with pasteurized cow milk (92). When assessing influence of spatial variability on the metagenomics of the cheese, more pronounced differences in bacterial genera were observed in the samples taken under the rind; Brachybacterium, Pseudoalteromonas, Yersinia, Klebsiella, and Weissella were only detected in these samples. Lastly, the aging length of the cheese greatly influenced the number of organisms observed. Twenty-seven additional genus-level identifications were observed in Gouda cheese aged for 12-18 months compared with cheese only aged 2-4 months.

CONCLUSIONS

Collectively, the results of this study are important in determining the typical microbiota associated with Gouda cheese and how the microbiome plays a role in safety and quality.

The potential use of probiotic and beneficial bacteria in the Brazilian dairy industry

Scientific studies demonstrate the importance of intestinal microbiota to human health and how probiotic microorganisms can positively affect health when administered regularly and in adequate amounts. Probiotic bacteria can be part of fermented products and their functional importance is associated mainly with their metabolism. They are thought to benefit individuals to maintain their health and also to strengthen resistance against various types of diseases. The acceptance of probiotic cultures and products by consumers increased when these bacteria were marketed as natural cultures that help in digestion and health. Considering this, the food industry has an increasing demand for new candidates as probiotic cultures, and the dairy industry has a particular interest for fermented milks and other dairy products, since these are the most common food vehicles for probiotic cultures. Therefore, the dairy industries are increasingly seeking to improve their products with these beneficial bacteria. However, the legal peculiarities and excess of control agencies in Brazil makes the registration of these products and the collection of data very complex. Prospective analysis suggests that probiotic foods have the potential to effect a considerable expansion of the dairy industry, allowing the dairy sector to grow and for these products to be increasingly sought by consumers globally. For this, not only actions on research and innovation are necessary, but also official clarifications on the claims for considerations of microbiological security and functionality of these products. This review aims to elucidate important probiotic research regarding the isolation and characterization of beneficial cultures in Brazil, and to demonstrate the relevance of the dairy chain as a potential source of novel cultures for the development of new probiotic products to expand the Brazilian dairy industry.

Intrinsic Parameters and Bacterial Growth Prediction in a Brazilian Minimally Ripened Cheese (Coalho) during Refrigerated Storage

This study evaluated the microbiological and physicochemical characteristics in different commercial brands of a Brazilian minimally ripened (coalho) cheese during 60 days of storage under refrigeration. Combinations of maximum and minimum values of water activity and pH determined in cheese samples at refrigeration temperature (7°C) were used in a bacterial growth prediction analysis. Maximum growth rate (Grmax) was estimated for different pathogenic and/or spoilage bacteria using the ComBase Predictor. Results of microbiological characterization analyses showed persistent high counts for all monitored microbial groups ( Lactobacillus spp., Lactococcus spp., Enterococcus spp., Staphylococcus spp., Enterobacteriaceae, proteolytic and lipolytic microorganisms, and fungi) in cheese samples; no dominant microbial group was observed over time. Values of pH (6.03 ± 0.16 to 7.28 ± 0.55), acidity (0.15% ± 0.09% to 0.66% ± 0.26%), sodium chloride (1.05% ± 0.19% to 1.97% ± 0.75%), and water activity (0.948 ± 0.020 to 0.974 ± 0.012) did not vary in cheese samples during storage. Estimated Grmax values for the tested bacteria were in the range of 0.004 to 0.044 log CFU/h. Highest Grmax values (0.005 to 0.044 log CFU/h) were predicted for the psychrotrophic Aeromonas hydrophila, Listeria monocytogenes, Pseudomonas spp., and Yersinia enterocolitica. Grmax values predicted for Escherichia coli, Salmonella spp., and Staphylococcus aureus were in the range of 0.004 to 0.016 log CFU/h. These results indicate unsatisfactory microbiological characteristics of commercially available coalho cheese. Physicochemical characteristics of commercial coalho cheese stored under refrigeration allow bacterial growth to occur, indicating higher risk for fast growth of contaminant bacteria in this product.