Antibacterial activity produced by Enterococcus spp. isolated from an artisanal Mexican dairy product, Cotija cheese

Heterologous Expression of Bacteriocins from the Metagenome Mining of Cotija Cheese

Bacteriocins are a heterologous group of ribosomal peptides with antibacterial activity. They are of interest to the pharmaceutical and food industries due to their potential to fight antibiotic-resistant pathogens and improve microbial food safety, respectively. Metagenomic data mining for antibacterial activity is valuable for the information it provides from unstudied genomic sequences. Furthermore, the higher biosynthetic yield obtained by the heterologous expression of putative bacteriocins allows their subsequent purification and characterization. This work aimed to express antilisterial bacteriocins in Escherichia coli after obtaining their gene sequences by in silico mining the bacterial metagenome of Cotija cheese. This artisanal Mexican cheese is manufactured with unpasteurized milk and ripens for at least 3 months. Analyzing the Cotija cheese bacterial shotgun metagenome allowed us to select two sequences (QC1 and QC2) encoding novel Class IId bacteriocins belonging to the lactococcin family. These genes were expressed as (His)6-fusion proteins in E. coli BL21 (DE3) and showed high antimicrobial activity against Listeria monocytogenes, with a minimum inhibitory concentration of 78 µg/mL. QC1 and QC2 were tested against several pathogenic bacteria and showed activity exclusively against L. monocytogenes. QC2 has a novel sequence that showed no matches against the UniProt database. It was purified by Ni2+ affinity chromatography and retained its activity after heating at 70 °C for 30 min. As the sequences were obtained by genomic mining on a fermented food metagenome, QC1 and QC2 have potential applications as sanitizers in industrial food facilities where L. monocytogenes contamination is the most prevalent.

Transcriptional Analysis and Identification of a Peptidoglycan Hydrolase (PGH) and a Ribosomal Protein with Antimicrobial Activity Produced by Lactiplantibacillus paraplantarum

The growing challenge of antibiotic resistance has intensified the search for new antimicrobial agents. Promising alternatives include peptidoglycan hydrolases (PGHs) and certain ribosomal proteins, both of which exhibit antimicrobial activity. This study focuses on a Lactiplantibacillus paraplantarum strain, isolated from fermented meat, capable of inhibiting pathogens such as Listeria innocua, Salmonella Typhimurium, Escherichia coli, Staphylococcus aureus, and Weissella viridescens. The highest growth and antimicrobial activity were observed at a high nitrogen concentration (5.7 g/L). Two antimicrobial proteins were identified: the 50S ribosomal protein L14 (RP uL14) and 6-phospho-N-acetylmuramidase (MupG), a PGH. Partial purification and characterization of these proteins were achieved using SDS-PAGE, zymography, and LC-MS/MS. Transcriptional data (RT-qPCR) showed that higher nitrogen concentrations enhanced MupG expression, while increased carbon concentrations boosted RP uL14 expression. These findings highlight the importance of nutritional sources in maximizing the production of novel antimicrobial proteins, offering a potential path to develop effective alternatives against antibiotic-resistant bacteria.

Microbiological quality and native lactic acid bacteria diversity of artisanal Mexican cheeses: A review

This review aims to provide an overview of artisanal Mexican cheeses microbiota focused on microbiological quality and safety, as well as native Lactic acid Bacteria (LAB) diversity. For the search, key words of artisanal Mexican cheeses varieties was carried out through several online databases and original articles were screened and data about populations of indicator microorganisms, presence of pathogens, and native LAB identified were extracted. Several artisanal Mexican cheeses exceeded the permissible limit established in Mexican regulation (NOM-243-SSA1-2010) for indicator microorganisms, as well as in some types of cheese, the presence of pathogens was confirmed. However, other varieties of artisanal Mexican cheeses possess unique physicochemical characteristics, and during their manufacturing particular steps are used that contribute to ensuring their quality and safety. Additionally, strains able to control the growth of pathogenic and spoilage bacteria are part of the microbiota of some artisanal Mexican cheeses. About native LAB diversity, it is composed by species of Lactobacillus, Enterococcus, Streptococcus, Leuconostoc, Weisella, Lactococcus, Pediococus, Aerococus, Carnobacterium, Tetragenococus, among others genera. Otherwise, artisanal Mexican cheeses represent an important source of specific LAB with several approaches within human health because they showed potential for the development of functional foods, nutraceutical, and bioprotective cultures.

Microbiological Evaluation of Two Mexican Artisanal Cheeses: Analysis of Foodborne Pathogenic Bacteria in Cotija Cheese and Bola de Ocosingo Cheese by qPCR

Cotija and Bola de Ocosingo are artisanal ripened cheeses produced in Mexico. Both are made with raw bovine milk from free-grazing cows and with no starter cultures. Unlike culture-based techniques, molecular methods for pathogen detection in food allow a shorter turnaround time, higher detection specificity, and represent a lower microbiological risk for the analyst. In the present investigation, we analyzed 111 cheese samples (95 Cotija and 16 Bola de Ocosingo) by qPCR (TaqMan®) after an enrichment-culture step specific to each foodborne bacterium. The results showed that 100% of the samples were free of DNA from Listeria monocytogenes, Brucella spp., Escherichia coli enterotoxigenic (ETEC), and O157:H7; 9% amplified Salmonella spp. DNA; and 11.7%, Staphylococcus aureus DNA. However, the threshold cycle (Ct) values of the amplified targets ranged between 23 and 30, indicating DNA from non-viable microorganisms. Plate counts supported this assumption. In conclusion, 100% of the cheeses analyzed were safe to consume, and the enrichment step before DNA extraction proved essential to discern between viable and non-viable microorganisms. Hygienic milking, milk handling, cheese manufacturing, and ripening are crucial to achieve an adequate microbiological quality of cheeses made with raw milk.

Human Milk-Derived Enterococcus faecalis HM20: A Potential Alternative Agent of Antimicrobial Effect against Methicillin-Resistant Staphylococcus aureus (MRSA)

The increasing global impact of skin diseases, fueled by methicillin-resistant Staphylococcus aureus (MRSA), emphasizes the necessity for alternative therapies with lower toxicity, such as lactic acid bacteria (LAB). This study aims to isolate potential LAB from human milk and evaluate their efficacy against MRSA using various methods, including well diffusion, microdilution, crystal violet assay, enzymatic characterization, SDS-PAGE, and scanning electron microscopy (SEM). Among the 26 LAB screened, the human milk-derived strain HM20 exhibited significant antimicrobial activity against S. aureus CCARM 3089 (MRSA), which is a highly resistant skin pathogen. Through 16S rRNA sequencing, strain HM20 was identified as closely related to Enterococcus faecalis ATCC 19433T, which was subsequently designated as Enterococcus faecalis HM20. The minimum inhibitory concentration (MIC) of the cell-free supernatant (CFS) of HM20 against S. aureus KCTC 3881 and S. aureus CCARM 3089 was determined to be 6.25% and 12.5%, respectively. Furthermore, the effective inhibition of biofilm formation in S. aureus KCTC 3881 and S. aureus CCARM 3089 was observed at concentrations of 12.5% and 25% or higher, respectively. The antibacterial effect of the CFS was attributed to the presence of organic acids, hydrogen peroxide, and bacteriocins. Additionally, the antimicrobial peptides produced by HM20 were found to be stable under heat treatment and analyzed to have a size below 5 kDa. SEM image observations confirmed that the CFS of HM20 caused damage to the cell wall, forming pores and wrinkles on S. aureus KCTC 3881 and S. aureus CCARM 3089. This comprehensive investigation on strain HM20 conducted in this study provides foundational data for potential developments in functional materials aimed at addressing skin infections and antibiotic-resistant strains in the future.

Role of Feeding and Novel Ripening System to Enhance the Quality and Production Sustainability of Curd Buffalo Cheeses

The buffalo dairy sector is extending its boundaries to include new buffalo cheese productions beyond mozzarella, overcoming some barriers that make cheeses expensive and unsustainable. This study aimed to evaluate the effects of both the inclusion of green feed in the diet of Italian Mediterranean buffaloes and an innovative ripening system on buffalo cheese quality, providing solutions capable of guaranteeing the production of nutritionally competitive and sustainable products. For this purpose, chemical, rheological, and microbiological analyses were carried out on cheeses. Buffaloes were fed with or without the inclusion of green forage. Their milk was used to produce dry ricotta and semi-hard cheeses, ripened according to both respective traditional (MT) and innovative methods (MI); these are based on automatic adjustments of climatic recipe guided by the continuous control of pH. Green feed enhances the nutritional profile of the final products (high content of MUFAs and PUFAs). As far as the ripening method is concerned, to our knowledge, this is the first study that tests aging chambers, commonly used for meat, for the maturing of buffalo cheeses. Results pointed out the MI validity also in this field of application, as it shortens the ripening period without negatively compromising any of desirable physicochemical properties and the safety and hygiene of the final products. Conclusively, this research highlights the benefits of diets rich in green forage on productions and provides support for the ripening optimization of buffalo semi-hard cheeses.

Probiotic Properties and Proteomic Analysis of Pediococcus pentosaceus 1101

Pediococcus pentosaceus 1101 was identified by using 16S rRNA and MALDI-Biotyper. The strain was exposed to conditions that resemble the gastrointestinal tract (GT) to evaluate its probiotic properties. That included the growth kinetics, proteolytic and inhibitory activities within a pH range, survival at low pH and in the presence of bile salts, antagonistic activity, cell-adhesion properties, and antibiotic resistance. The evaluation was followed by a genomic and proteomic analysis that involved the identification of proteins obtained under control and gastrointestinal conditions. The strain showed antagonistic activity against Gram-negative and Gram-positive bacteria, high resistance to acidity (87% logarithmic survival rate, pH 2) and bile salts (99% logarithmic survival rate, 0.5% w/v), and hydrophobic binding, as well as sensitivity to penicillin, amoxicillin, and chloramphenicol. On the other hand, P. pentosaceus 1101 has a genome size of 1.76 Mbp, with 1754 coding sequences, 55 rRNAs, and 33 tRNAs. The proteomic analysis showed that 120 proteins were involved in mechanisms in which the strain senses the effects of acid and bile salts. Moreover, the strain produces at least one lytic enzyme (N-acetylmuramoyl-L-alanine amidase; 32 kDa) that may be related to the antimicrobial activity. Therefore, proteins identified might be a key factor when it comes to the adaptation of P. pentosaceus 1101 into the GT and associated with its technological and probiotic properties.

Microbiological Characteristics and Behavior of Staphylococcus aureus, Salmonella spp., Listeria monocytogenes and Staphylococcal Toxin during Making and Maturing Cotija Cheese

Cotija cheese is an artisanal matured Mexican cheese from unpasteurized milk. This work determined the microbiological characteristics and behavior of Staphylococcus aureus, Salmonella spp., Listeria monocytogenes and staphylococcal toxin during cheese elaboration and ripening. Sixteen 20-kg cheeses were used, eight inoculated with 6 log CFU/mL of each pathogen, and eight uninoculated, and samples were taken at each stage of the process. In the uninoculated samples, the survival of S. aureus and L. monocytogenes decreased after 30 days of ripening. The average counts of S. aureus in milk, curd, and serum were 7 log MPN /mL, and 8.7 log MPN /g in cheese, decreasing from day 15. Salmonella spp. counts (initial inoculum: 7.2 log MPN /mL) decreased after 24 h, and L. monocytogenes counts (8.7 log MPN/g at 24 h) decreased from day 15 in the cheese. Salmonella spp. and L. monocytogenes were not detected in any sample after 60 days of ripening, unlike S. aureus, which was detected at the end of the study. Lactic acid bacteria counts were 9 log CFU/mL in milk and whey and 7.2 log CFU/g in cheese. Pathogens behavior during the ripening process reduces the health risks by consuming products made with unpasteurized milk when subjected to ripening.

Bacteriocins Produced by LAB Isolated from Cheeses within the Period 2009-2021: a Review

A survey is presented concerning original research articles published in well-reputed scientific journals on the isolation of lactic acid bacteria (LAB) from cheeses worldwide, where researchers evaluated the bacteriocin production by such isolates in searching for novel functional peptides that can exhibit potential for biotechnological applications. Seventy-one articles were published in the period of study, with contributions being American (45%), Asiatic (28%), and European (21%), being Brazil-USA-Mexico, Turkey-China, and France-Italy the countries that contributed the most for each said continent, respectively. Most of the isolated LAB belong to the genera Enterococcus (35%), Lactobacillus (30%), Lactococcus (14%), and Pediococcus (10%), coming from soft (64%), hard (27%), and semi-hard (9%) cheeses, predominantly. Also, scholars focused mainly on the food biopreservation (81%) and pharmaceutical field (18%) potential applications.

Characterization of antibacterial activity of a N-acetylmuramoyl-L-alanine amidase produced by Latilactobacillus sakei isolated from salami

Lactic acid bacteria are the predominant group within meat products, whose metabolites such as bacteriocins and peptidoglycan hydrolases inhibit pathogenic or spoilage bacteria. Fermented meat products, as a salami, is a good source to analyze the viable microbiota, due to these products present a low risk to consumer health. The aim of this work was to identify the lactic acid bacteria with broad antibacterial activity present in salami, purify the protein responsible for this activity, achieve antagonistic spectrum and perform the biochemical characterization. Five strains from salami were selected, isolated and identified by 16S rRNA gene sequencing. The antimicrobial activity was evaluated by antagonism assay and zymography, using spoilage microorganisms commonly found in meat products. The strain that showed a broad antibacterial activity was Latilactobacillus sakei and the antibacterial activity was given by a protein with 75-kDa of molecular mass, identified by LC/MALDI-TOF/TOF. The sequence analysis showed 67% of identity with a N-acetylmuramoyl-L-alanine amidase protein with five non-identical LysM domains. The purified protein showed an optimal pH of 8.0 and heat resistance at 80 °C for 10 min. L. sakei strain displayed antibacterial activity against Gram-negative and Gram-positive spoilage microorganisms. The results of this study provide the information to use Latilactobacillus sakei as a starter culture which will provide the necessary metabolites to combat undesirable microorganisms. Additionally, the conditions and properties for the best application and use of the antibacterial protein produced by this strain. This protein may have a potential use in the food industry as a new antibacterial agent.

Optimization of bacterial cytokine protein production by response surface methodology for environmental bioremediation

In natural and engineered systems, most microorganisms would enter a state of dormancy termed as “viable but non-culturable” (VBNC) state when they are exposed to unpredictable environmental stress. One of the major advances in resuscitating from such a state is the discovery of a kind of bacterial cytokine protein called resuscitation-promoting factor (Rpf), which is secreted from Micrococcus luteus. In this study, the optimization of Rpf production was investigated by the response surface methodology (RSM). Results showed that an empirical quadratic model well predicted the Rpf yield, and the highest Rpf protein yield could be obtained at the optimal conditions of 59.56 mg L⁻¹ IPTG, cell density 0.69, induction temperature 20.82 °C and culture time 7.72 h. Importantly, Phyre2 web portal characterized the structure of the Rpf domain to have a shared homology with lysozymes, and the highest lysozyme activity was at pH 5 and 50 °C. This study broadens the knowledge of Rpf production and provided potential strategies to apply Rpf as a bioactivator for environmental bioremediation.

A group of secreted proteins from M. luteus, recognized as resuscitation promoting factors (Rpf) can resuscitate the viable but non-culturable (VBNC) state bacteria which have the potential function of environmental bioremediation.

Quality and Probiotic Lactic Acid Bacteria Diversity of Rabbit Meat Bekasam-Fermented Meat

Rabbit meat bekasam is a traditional fermentation product from Indonesia. This study aimed to determine the chemical and microbiological characteristics of rabbit meat bekasam during the fermentation process in order to isolate, characterize (in vitro and in vivo), and identify lactic acid bacteria (LAB) as the probiotic candidate. The chemical contents of bekasam on 7-day fermentation were investigated in explorative and experimental methods in a completely randomized design. A proximate analysis reported a decrease in the moisture content, fat and carbohydrate content, and an increase in protein content. Also, lactic acid content was increased from 0.48% to 1.12%, and pH was decreased from 5.3 to 4.3. Other properties indicated different values, such as bacteria (2.75×10⁶ to 4.45×10⁷ CFU/g), total LAB (3.82×10⁶ to 4.67×10⁸ CFU/g), total yeast (9.89×10⁶ to 3.82×10⁸ CFU/g) and total mould (4.34×10¹ to 4.86×10³ CFU/g). The experiment produced nine LAB isolates, including two probiotics subjected to further 16S rRNA gene analysis, which indicated that Lactobacillus buchneri was the potential probiotic isolate. After being tested on BALB/c mice, L. buchneri could improve the immune system by inhibiting the growth of Coliform and Salmonella.

Lactic acid bacteria isolated from dairy products as potential producers of lipolytic, proteolytic and antibacterial proteins

Regular consumption of fermented dairy products helps maintain a healthy microbiota and prevent gut dysbiosis-linked diseases. The lactic acid bacteria (LAB) present in food enhance the digestibility of proteins, moderate the release of fatty acids, and support human health through inhabiting the gastrointestinal tract. These desirable properties of LAB are attributed, in part, to their metabolic processes involving enzymes such as lipases, proteases, and antibacterial proteins. The LAB strains presenting higher enzymatic activities may offer improved functionality for applications in foods. The first aim of this work was to isolate and identify LAB from diverse dairy products and select those with enhanced enzymatic activities. Secondly, this work aimed to investigate the subcellular organization and identity of these enzymes after semi-purification. Out of the total 137 LAB strains isolated and screened, 50.3% and 61.3% of the strains exhibited lipolytic and proteolytic activities, respectively. Seven strains displaying high enzymatic activities were selected and further characterized for the cellular organization of their lipases, proteases, and antibacterial proteins. The lipolytic and proteolytic activities were exhibited predominantly in the extracellular fraction; whereas, the antibacterial activities were found in various cellular fractions and were capable of inhibiting common undesirable microorganisms in foods. In total, two lipases, seven proteases, and three antibacterial proteins were identified by LC-MS/MS. Characterization of LAB strains with high enzymatic activity has potential biotechnological significance in fermentative processes and in human health as they may improve the physicochemical characteristics of foods and displace strains with weaker enzymatic activities in the human gut microbiota.

Enhancement of the antibacterial activity of an E. faecalis strain by the heterologous expression of enterocin A

The genus Enterococcus occurs as native microbiota of fermented products due to its broad environmental distribution and its resistance to salt concentrations. Enterococcus faecalis F, a non-pathogenic strain isolated from a ripened cheese, has demonstrated useful enzymatic capabilities, a probiotic behavior and antibacterial activity against some food-borne pathogens, mainly due to peptidoglycan hydrolase activity. Its use as a natural pathogen-control agent could be further enhanced through the production of a bacteriocin, e.g. Enterocin A, because of its remarkable antilisterial activity. In this work, a markerless allelic insertion method was used to obtain an enterococcal strain capable of producing a functional enterocin. Agar diffusion tests showed that the recombinant strain was active against Staphylococcus aureus, Listeria monocytogenes and the pathogenic strain E. faecalis V583. When grown in liquid culture together with L. monocytogenes, it attained a two-log reduction of the pathogen counts in lesser time relative to the native strain. Because the DNA construction is integrated into the chromosome, the improved strain avoids the use of antibiotics as selective pressure; besides, it does not require an inductor because of the inclusion of a constitutive promoter in the construction. Its technological and antibacterial capabilities make the improved E. faecalis strain a potential culture for use in the food industry.

Cloning and Characterization of a Novel N-acetylglucosaminidase (AtlD) from Enterococcus faecalis

The atlD gene from an Enterococcus faecalis strain isolated from a Mexican artisanal cheese was cloned, sequenced and expressed in Escherichia coli in order to perform a biochemical characterization. A partial amino acid sequence of the heterologous protein was obtained by LC-MS/MS, and it corresponded to a novel peptidoglycan hydrolase designated AtlD. Its molecular mass was 62-75 kDa, as determined by SDS-PAGE, zymography, Western blot, and exclusion chromatography. Electrofocusing rendered an isoelectric point (pI) of 4.8. It exhibited N-acetylglucosaminidase activity, with an optimal pH and temperature between 6-7 and 50°C, respectively. It retained 85% activity with NaCl at 1,000 mM, but it was susceptible to divalent ions, particularly Zn2+. It showed antibacterial activity against Listeria monocytogenes, Staphylococcus aureus, and enterococcal strains of clinical origin. Due to the fact that it showed activity versus pathogenic bacteria, and because of its capabilities under ionic strength, temperature, and pH values present in food matrices, it could be applied as an additive in the food industry. This study will aid in the design of new antibacterial agents of natural origin to combat food-borne diseases, and it could be used as an industrial or hospital hygiene agent as well.

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening

Enterococcus spp. are present in the native microbiota of many traditional fermented foods. Their ability to produce antibacterial compounds, mainly against Listeria monocytogenes, has raised interest recently. However, there is scarce information about their proteolytic and lipolytic potential, and their biotechnological application is currently limited because enterococcal strains have been related to nosocomial infections. In this work, next-generation sequencing and optimised bioinformatic pipelines were used to annotate the genomes of two Enterococcus strains-one E. faecium and one E. faecalis-isolated from the Mexican artisanal ripened Cotija cheese. A battery of genes involved in their proteolytic system was annotated. Genes coding for lipases, esterases and other enzymes whose final products contribute to cheese aroma and flavour were identified as well. As for the production of antibacterial compounds, several peptidoglycan hydrolase- and bacteriocin-coding genes were identified in both genomes experimentally and by bioinformatic analyses. E. faecalis showed resistance to aminoglycosides and E. faecium to aminoglycosides and macrolides, as predicted by the genome functional annotation. No pathogenicity islands were found in any of the strains, although traits such as the ability of biofilm formation and cell aggregation were observed. Finally, a comparative genomic analysis was able to discriminate between the food strains isolated and nosocomial strains. In summary, pathogenic strains are resistant to a wide range of antibiotics and contain virulence factors that cause host damage; in contrast, food strains display less antibiotic resistance, include genes that encode class II bacteriocins and express virulence factors associated with host colonisation rather than invasion.

Safety Evaluation of Enterocin Producer Enterococcus sp. Strains Isolated from Traditional Turkish Cheeses

The purpose of this study was to determine the antimicrobial activity and the occurrence of bacteriocin structural genes in Enterococcus spp. isolated from different cheeses and also investigate of their some virulence factors. Enterococcus strains were isolated from 33 different cheeses. Enterococcus faecium (6 strains) and Enterococcus faecalis (5 strains) enterocin-producing strains were identified by 16S rDNA analyses. entA, entB, entP and entX structural genes were detected in some isolates. Multiple enterocin structural genes were found in 7 strains. None of the tested enterococci demonstrated β-haemolytic activity and only one strain has gelatinase activity. Six strains showed multiple antibiotic resistance patterns and in addition, vanA and several virulence genes were detected in many strains. Only E. faecalis MBE1-9 showed tyrosine decarboxylase activity and tdc gene was only detected in this strain.

Expression, purification, and characterization of a bifunctional 99-kDa peptidoglycan hydrolase from Pediococcus acidilactici ATCC 8042

Pediococcus acidilactici ATCC 8042 is a lactic acid bacteria that inhibits pathogenic microorganisms such as Staphylococcus aureus through the production of two proteins with lytic activity, one of 110 kDa and the other of 99 kDa. The 99-kDa one has high homology to a putative peptidoglycan hydrolase (PGH) enzyme reported in the genome of P. acidilactici 7_4, where two different lytic domains have been identified but not characterized. The aim of this work was the biochemical characterization of the recombinant enzyme of 99 kDa. The enzyme was cloned and expressed successfully and retains its activity against Micrococcus lysodeikticus. It has a higher N-acetylglucosaminidase activity, but the N-acetylmuramoyl-L-alanine amidase can also be detected spectrophotometrically. The protein was then purified using gel filtration chromatography. Antibacterial activity showed an optimal pH of 6.0 and was stable between 5.0 and 7.0. The optimal temperature for activity was 60 °C, and all activity was lost after 1 h of incubation at 70 °C. The number of strains susceptible to the recombinant 99-kDa enzyme was lower than that susceptible to the mixture of the 110- and 99-kDa PGHs of P. acidilactici, a result that suggests synergy between these two enzymes. This is the first PGH from LAB that has been shown to possess two lytic sites. The results of this study will aid in the design of new antibacterial agents from natural origin that can combat foodborne disease and improve hygienic practices in the industrial sector.