Staphylococcal community of a small unit manufacturing traditional dry fermented sausages

Enhancement of fermented sausage quality driven by mixed starter cultures: Elucidating the perspective of flavor profile and microbial communities

The metabolic activities of microorganisms play a crucial role in the quality development of fermented sausage. This study investigated the effect of inoculation with different combinations of starter cultures (Lactiplantibacillus plantarum YR07, Latilactobacillus sakei L.48, Staphylococcus xylosus S.14, and Mammaliicoccus sciuri S.18) on the quality of sausages. Inoculation with mixed starter cultures promoted protein degradation to generate amino acids and the conversion to volatile compounds, which enhanced the flavor development in fermented sausages. The bacterial community analyses demonstrated that the inoculation of mixed starter cultures could inhibit the growth of spoilage and pathogenic bacteria, thereby reducing the total content of biogenic amines. The correlation analysis between the core bacteria and characteristic volatile compounds revealed that fermented sausages inoculated with Lactobacillus and coagulase negative staphylococci exhibited significant positive correlations with the majority of key characteristic volatile compounds. In four treatments, inoculation with L. plantarum YR07 and M. sciuri S.18 greatly promoted the formation of characteristic volatile compounds (3-hydroxy-2-butanone, hexanal, and 1- octen-3ol). Therefore, the combined inoculation of L. plantarum YR07 and M. sciuri S.18 is promising to enhance fermented sausage's flavor profile and safety.

Bacterial profile of pork from production to retail based on high-throughput sequencing

Pork is a common vehicle for foodborne pathogens, including Salmonella spp. and Yersinia enterocolitica. Cross-contamination can occur at any stage of the pork production chain, from farm to market. In the present study, high-throughput sequencing was used to characterize bacterial profiles and track their changes along the whole supply chain. Tracked meat samples (pig on the farm, carcass in the slaughterhouse, unprocessed carcass and processed meat in the processing plant, and fresh pork at the local retail stores) and their associated environmental samples (e.g., water, floor, feed, feces, and workers' gloves) were collected from sequential stages (n = 96) and subjected to 16S rRNA metataxonomic analyses. At the farm, a total of 652 genera and 146 exclusive genera were identified in animal and environmental samples (pig, drain, floor, fan, and feces). Based on beta diversity analysis, it was demonstrated that the microbial composition of animal samples collected at the same processing step is similar to that of environmental samples (e.g., drain, fan, feces, feed, floor, gloves, knives, tables, and water). All animal and environmental samples from the slaughterhouse were dominated by Acinetobacter (55.37 %). At the processing plant, belly meat and neck meat samples were dominated by Psychrobacter (55.49 %). At the retail level, key bacterial players, which are potential problematic bacteria and important members with a high relative abundance in the samples, included Acinetobacter (8.13 %), Pseudomonas (6.27 %), and Staphylococcus (2.13 %). In addition, the number of confirmed genera varied by more than twice that identified in the processing plant. Source tracking was performed to identify bacterial contamination routes in pork processing. Animal samples, including the processing plant's carcass, the pig from the farm, and the unwashed carcass from the slaughterhouse (77.45 %), along with the processing plant's gloves (5.71 %), were the primary bacterial sources in the final product. The present study provides in-depth knowledge about the bacterial players and contamination points within the pork production chain. Effective control measures are needed to control pathogens and major pollutants at each stage of pork production to improve food safety.

Autochthonous Cultures to Improve Safety and Standardize Quality of Traditional Dry Fermented Meats

Traditional dry fermented meat products are obtained artisanally in many countries, where they represent a gastronomic heritage well distinguished from industrial counterparts. This food category is most often obtained from red meat, a food commodity that is under attack because of evidence of increased risk of cancer and degenerative diseases with high consumption. However, traditional fermented meat products are intended for moderate consumption and gastronomic experience, and, as such, their production must be continued, which would also help safeguard the culture and economy of the geographical areas of origin. In this review, the main risks attributed to these products are considered, and how these risks are reduced by the application of autochthonous microbial cultures is highlighted by reviewing studies reporting the effects of autochthonous lactic acid bacteria (LAB), coagulase negative staphylococci (CNS), Debaryomyces hansenii and Penicillium nalgiovense on microbiological and chemical safety and on sensory attributes. The role of dry fermented sausages as a source of microorganisms that can be beneficial to the host is also considered. From the results of the studies reviewed here it appears that the development of autochthonous cultures for these foods can ensure safety and stabilize sensory characteristics and has the capacity to be extended to a larger variety of traditional products.

Effects of anaerobic and respiratory adaptation of Lacticaseibacillus casei N87 on fermented sausages production

Lacticaseibacillus casei N87 was used as starter culture for the production of fermented sausages. The strain was cultivated in anaerobic (A) and respiratory (growth in presence of oxygen and supplementation with haeme and menaquinone in the growth medium; R) conditions. Control without the starter culture inoculation and with the addition of 150 mg/kg of nitrate was also included. The effect on physico-chemical parameters (pH, Aw, weight loss, and color), microbial population, volatilome, proteolysis as well as the survival of the strain was evaluated during 90 days of ripening. Q-PCR and DGGE-PCR analyses demonstrated the ability of the strain used in this study to adapt to this environment and carry out the sausage's fermentation process. The inoculation of the strain did not have any effect on the Aw values, which decreased similarly in the different samples whereas the pH was lower in A samples (5.2) and the weight loss in R samples (2.5% less than the others). The color parameters of the samples inoculated with the starter cultures were comparable to those of the control added with nitrate. The concentration of aldehydes that usually are identified as marker of oxidation processes was similar in the samples inoculated with the starter cultures adapted under respiratory conditions and in the control. On the contrary, a higher level was detected in the samples inoculated with the starter cultivated under anaerobic conditions. The proteolysis that occurred during the ripening indicates the differentiation of the A samples from the others. Nonetheless, the volatile profiles of the inoculated fermented sausages were similar. The study demonstrated that aerobic adaptation of Lcb. casei N87 starter culture gave similar color parameters and amounts of aldehydes in sausages fermentations without nitrate compared to conventional fermentations with nitrate.

Diversity and Safety Aspects of Coagulase-Negative Staphylococci in Ventricina del Vastese Italian Dry Fermented Sausage

Ventricina del Vastese is a traditional dry fermented sausage from Central Italy not yet characterized for the occurrence, identity and safety of coagulase-negative staphylococci (CNS), a bacterial group technologically important for this kind of product. Therefore, in this study, 98 CNS isolates from four manufacturers were differentiated using repetitive element palindromic PCR (Rep-PCR) and identified using 16S rRNA gene sequencing. These were examined for genes encoding biogenic amine (BA) production, resistance to aminoglycosides, β-lactams, tetracyclines and staphylococcal enterotoxins (SEs). Staphylococcus succinus (55%) predominated, followed by S. xylosus (30%), S. epidermidis (7.4%), S. equorum (3.1%), S. saprophyticus (3.1%) and S. warneri (1%). One S. succinus subsp. casei isolate was slightly β-hemolytic. SEs and the histidine decarboxylase gene hdcA were not detected, whereas the tyrosine decarboxylase gene tdcA was detected in four S. xylosus isolates. The blaZ beta-lactamase gene in an S. equorum isolate, tetracycline resistance genes tetK in six S. succinus isolates and tetA in one S. succinus isolate also bearing tetK were found. The product examined is characterized by a peculiar CNS species ratio and a low occurrence and diversity of AR transferable genes than found in other studies, as a probable consequence of production only with meat from animals raised in small farms with extensive rearing systems in which antibiotic usage is infrequent.

Effect of Bacillus subtilis fortified inoculation on the microbial communities in different niches of Daqu

Daqu is the fermentation starter of Baijiu, which is one of the six most renowned distilled spirits. Studies have found that Bacillus is one of the dominant microbial genera in Daqu, and Bacillus subtilis is known to produce amylase, an important enzyme that influences the quality of Daqu. This study aims to explore the influence of B. subtilis inoculation on the microbial community structure in different niches of Daqu. We studied the microbial community structure of the natural inoculated Daqu (i.e., control Daqu) and the fortified Daqu (i.e., B. subtilis-inoculated Daqu) by amplicon sequencing. Our results showed that compared with the control Daqu rind microbial community, the relative abundance of Bacillus, Aspergillus, Thermomyces, and Rasamsonia in the fortified Daqu rind microbial community increased, and the relative abundance of Weissella, Lactobacillus, Leuconostoc, and Pichia decreased. Compared with the control Daqu core microbial community, the relative abundance of Bacillus in the fortified Daqu core microbial community also increased, but the relative abundance of Pseudomonas and Paecilomyces decreased. The effect of B. subtilis inoculation on the rind microbial community of Daqu was more significant. In addition, the bacterial community of Daqu was more susceptible to the effect of the B. subtilis inoculation than was the fungal community of Daqu. The correlation between the bacterial community of Daqu and the fungal community of Daqu increased significantly after the B. subtilis inoculation. These results provide an important theoretical basis for the production of fortified Daqu.

Transcriptomic Analysis of Staphylococcus equorum KM1031, Isolated from the High-Salt Fermented Seafood Jeotgal, under Salt Stress

Staphylococcus equorum is a potential starter for Korean high-salt fermented foods because of its salt tolerance and enzymatic activities that contribute to enhanced sensory properties of the food products. However, the mechanisms of salt tolerance of S. equorum are not fully understood. Here, RNA sequencing was performed on S. equorum strain KM1031 exposed to 7% NaCl (w/v) for 2 and 4 h to determine global gene expression changes. Salt pressure for 2 and 4 h resulted in significant differential expression of 4.8% (106/2209) and 6.1% (134/2209) of S. equorum KM1031 genes, respectively. Twenty-five core genes were differentially expressed on salt treatment for both 2 and 4 h, seven of which were related to osmoprotectant uptake and synthesis. We analyzed the genome of strain KM1031 and identified osmoprotectant uptake (Opu) systems, potassium importers, sodium exporters, and the glycine betaine synthesis system. The RNA sequencing results indicated that the OpuD system and glycine betaine synthesis might play the main roles in the salt tolerance of strain KM1031. Finally, the results of RNA sequencing were validated by quantitative real-time PCR of likely salt stress-related genes. This transcriptomic analysis provides evidence regarding the osmotic stress responses of S. equorum strain KM1031.

Incorporation of Selected Strains of Pediococcus spp. on Quality Characteristics of Dry Fermented Sausage during Fermentation and Ripening

This research investigated the physio-chemical and microbial quality characteristics of dry fermented sausage from selected Pediococcus strains: P. acidiliactici (PE1) and P. pentosaceus (PE2) as compared to commercial starter culture (COS) during fermentation and ripening. Treatments showed no substantial variation (p<0.05) in water activity (a_w) values across the study period. PE1 and PE2 treatments exhibited similar (p>0.05) pH values and presented remarkable (p<0.05) lower volatile basic nitrogen (VBN) and thiobarbituric acid reactive (TBARS) content than COS treatment throughout the ripening period. However, the pH values in COS batch were considerably lower than others. PE1 samples presented a significant highest (p<0.05) counts both in lactic acid bacteria (LAB) and total plate count (TPC) than COS and PE2 treatments at 7 days fermentation, and it resulted in a similar and higher TPC count as COS after the ripening period. After the ripening process, treatments are ordered based on LAB counts as follows: COS>PE1>PE2. All batches presented similar redness and yellowness attributes since the 7 days of fermentation and in lightness across the study period. Treatments were similar (p>0.05) in springiness and chewiness traits across the study period and in hardness characteristics in the ripened products. Cohesiveness was higher in PE1 and COS batches. No variation (p>0.05) in aroma and sourness sensory attributes of treatments. The color attribute was highest (p<0.05) in PE1 and PE2 treatments and PE1 had the highest overall acceptability. The overall outstanding merit exhibited by PE1 can be utilized in the commercial production of high-quality dry fermented sausage.

Health and safety aspects of traditional European meat products. A review

Meat products constitute one of the most important groups of traditional foods. Thanks to the unique and favorable organoleptic characteristics, and high quality, they are willingly chosen by consumers. Lately, there has been a growing concern over the health aspects of these products. Therefore, the aim of this study was to analyze the nutritional value and factors affecting quality and health safety of traditional meat products on the basis of available literature. The study findings have revealed various issues with uniformity of traditional meat products. Products of the same name may differ substantially considering nutritional value. Reports also indicate that there are some discrepancies which can be attributed to product character (traditional/conventional). They mainly concern the content of moisture, protein, salt, fat, and fatty acid profile. Research suggests that traditional meat products may also be associated with some health safety issues, such as the presence of pathogens, polycyclic aromatic hydrocarbons, nitrate and nitrite residues, N-nitrosamines, biogenic amines and heavy metals.

Composition, Succession, and Source Tracking of Microbial Communities throughout the Traditional Production of a Farmstead Cheese

Prior to the advent of milk pasteurization and the use of defined-strain starter cultures, the production and ripening of cheese relied on the introduction and growth of adventitious microbes from the environment. This study characterized microbial community structures throughout a traditional farmstead cheese production continuum and evaluated the role of the environment in microbial transfer. In total, 118 samples (e.g., raw milk, cheese, and environmental surfaces) were collected from milk harvesting through cheese ripening. Microbial communities were characterized based on amplicon sequencing of bacterial 16S rRNA and fungal internal transcribed spacer genes using the Illumina MiSeq platform. Results indicated that the environment in each processing room harbored unique microbial ecosystems and consistently contributed microbes to milk, curd, and cheese. The diverse microbial composition of milk was initially attributed to milker hands and cow teats and then changed substantially following overnight ripening in a wooden vat to one dominated by lactic acid bacteria, including Lactococcus lactis, Lactobacillus, and Leuconostoc, as well as fungi such as Exophiala, Kluyveromyces, and Candida. Additional microbial contributions were attributed to processing tools, but the composition of the cheese paste remained relatively stable over 60 days of ripening. In contrast, rind communities that were largely influenced by direct contact with bamboo aging mats showed a distinct succession pattern compared to the interior sections. Overall, these findings highlight the critical role of traditional tools and practices in shaping the microbial composition of cheese and broaden our understanding of processing environments as important sources of microbes in food. IMPORTANCE Throughout the 20th century, especially in the United States, sanitation practices, pasteurization of milk, and the use of commercial defined-strain starter cultures have enhanced the safety and consistency of cheese. However, these practices can reduce cheese microbial diversity. The rapid growth of the artisanal cheese industry in the United States has renewed interest in recapturing the diversity of dairy products and the microbes involved in their production. Here, we demonstrate the essential role of the environment, including the use of wooden tools and cheesemaking equipment, as sources of dominant microbes that shape the fermentation and ripening processes of a traditional farmstead cheese produced without the addition of starter cultures or direct inoculation of any other bacteria or fungi. These data enrich our understanding of the microbial interactions between products and the environment and identify taxa that contribute to the microbial diversity of cheese and cheese production.

Novel staphylococci nucH taxonomical marker used in identification of human-associated Staphylococcus succinus subsp. casei

The aim of our study was to assess the sequencing of unique nucH gene fragment based on performed bioinformatics analysis as a novel diagnostic method for the identification of difficult to identify staphylococcal human pathogenic strains. Initially, PCR-RFLP-rrn analysis specific to the spacers between 16SrDNA and 23SrDNA followed by HhaI restriction analysis was performed. Further, sequencing of nucH and 16S rDNA genes fragments was carried out. Blast analysis from the NCBI showed 99% similarity of nucH gene fragment with reference genomic DNA for S. succinus with the accession no. CP018199. This result was also confirmed by MALDI-TOF analysis. Sequencing analysis of 16S rDNA gene fragment allowed for 100% identification of two strains isolated from human samples as Staphylococus succinus subsp. casei. Sequencing of identified unique nucH gene fragment seems to be a promising diagnostic assay for the identification of Staphylococcus species. Based on our results, we can assume that probably other Staphylococcus species originated from different clinical samples could be identified using nucH gene sequencing method we developed. However, an extension of the genetic databases with a substantially bigger number of reference staphylococcal species for nucH gene is needed to make this method better than widely used standard 16S rDNA sequencing assay. To the best of our knowledge, it is the second published isolation of S. succinus subsp. casei from human clinical specimens. Moreover, possibility of decreasing the number of dimensions from multi-PCR-bands results using ribotyping analysis is also described.

The Use of Less Conventional Meats or Meat with High pH Can Lead to the Growth of Undesirable Microorganisms during Natural Meat Fermentation

The bacterial communities that are established during natural meat fermentation depend on the processing conditions and the type of meat substrate used. Six pork samples of variable quality (reflected in pH values) and six less conventional meats (beef, horse, hare, wild deer, wild duck, and wild boar) were naturally fermented under controlled conditions in model systems. The development of lactic acid bacteria (LAB), coagulase-negative staphylococci (CNS), and enterobacteria was followed using culture-dependent techniques and (GTG)₅-PCR fingerprinting of genomic DNA from the isolates obtained. Taken together, Latilactobacillus sakei was the most abundant LAB species, although Latilactobacillus curvatus was more manifest in high-pH pork. Within staphylococci, common species were encountered (i.e., Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus), although some atypical ones (i.e., Staphylococcus succinus) were also recovered. Within enterobacteria, Serratia spp. prevailed in more acidic pork batches and in beef, whereas Hafnia spp. prevailed in game meat fermentations. Enterobacterial counts were particularly high in fermentations with low acidity, namely for some pork batches, hare, wild duck, and wild boar. These findings should be considered when naturally fermented meat products are manufactured, as the use of game meat or meat with high pH can give rise to safety concerns.

Enterotoxigenic Potential of Coagulase-Negative Staphylococci from Ready-to-Eat Food

Although coagulase-positive staphylococci are considered to be the main factor responsible for food poisoning, an increasing role for the coagulase-negative staphylococci in the production of enterotoxins has been observed in recent years. This study was conducted to assess the occurrence of genes responsible for the production of staphylococcal enterotoxins (SE), enterotoxin-like toxins (SEI) and toxic shock syndrome toxin-1 (TSST-1) in coagulase-negative staphylococci (CoNS) isolated from ready-to-eat food from bars and restaurants. One hundred and eighteen CoNS strains were tested using polymerase chain reaction (PCR) to five superantigenic toxin genes, including five different types of classical enterotoxins (sea, seb, sec, sed and see) and the toxic shock syndrome toxin-1 (tsst-1) as well as to supertoxin-like genes. PCR-positive isolates were then tested using immunoenzymatic methods (SET-RPLA, Vidas SET 2) for toxin expression. Out of 118 CoNS strains, the presence of staphylococcal enterotoxins was confirmed in 72% of them. The most frequently found enterotoxin-like genotype was ser, selu. Two of the tested strains had up to ten different enterotoxin genes in the genome at the same time. Although no production of enterotoxins was detected in the CoNS, which means that their possible role in the epidemiology of food-borne diseases is minimal, the data demonstrated that the toxigenic capacity of the CoNS should not be ignored, and that this group of microorganisms should be continuously monitored in food.

Food-derived coagulase-negative Staphylococcus as starter cultures for fermented foods

Food safety is of significant concern to consumers and is a major issue for the food industry. As such, the industry is aware of the importance of safety assessments of starters used in the production of fermented foods. Coagulase-negative staphylococci (CNS) are the predominant bacteria found in fermented foods worldwide. Because of this, food-derived CNS are used as starters for cheese and meat fermentation, and have been investigated for use as starters in soybean fermentation. Although food-derived CNS are generally considered non-pathogenic, their safety remains uncertain following the isolation of CNS from skin infections in humans and animals, and because they belong to the same genus as the highly pathogenic species Staphylococcus aureus. This review explores what is known about the safety of food-derived CNS, focusing on antibiotic resistance, enterotoxin genes, and biogenic amine production, to aid in the selection of starter candidates.

Evolution of indigenous starter microorganisms and physicochemical parameters in spontaneously fermented beef, horse, wild boar and pork salamis produced under controlled conditions

The present work was carried out to evaluate the microbiological and physicochemical composition of salamis produced with the meat of beef, horse, wild boar and pork. Salami productions occurred under controlled laboratory conditions to exclude butchery environmental contaminations, without the addition of nitrate and nitrite. All trials were monitored during the ripening (13 °C and 90% relative humidity) extended until 45 d. The evolution of physicochemical parameters showed that beef and pork salamis were characterized by a higher content of branched chain fatty acids (FA) and rumenic acid than horse and wild boar salamis, whereas the last two productions showed higher values of secondary lipid oxidation. Plate counts showed that lactic acid bacteria (LAB), yeasts and coagulase-negative staphylococci (CNS) populations dominated the microbial community of all productions with Lactobacillus and Staphylococcus as most frequently isolated bacteria. The microbial diversity evaluated by MiSeq Illumina showed the presence of members of Gammaproteobacteria phylum, Moraxellaceae family, Acinetobacter, Pseudomonas, Carnobacterium and Enterococcus in all salamis. This study showed the natural evolution of indigenous fermented meat starter cultures and confirmed a higher suitability of horse and beef meat for nitrate/nitrite free salami production due to their hygienic quality at 30 d.

Effects of different starter culture combinations on microbial counts and physico-chemical properties in dry fermented mutton sausages

This study was conducted to evaluate the effects of inoculation with different mixed starter culture combinations on microbial counts, physico-chemical properties, and proteolytic and lipolytic properties of dry fermented mutton sausages during fermentation and ripening. Four different batches of mutton sausages were manufactured: CO batch, no starter cultures, used as control; LB batch with Lactobacillus sakei; LS batch with L. sakei + Staphylococcus xylosus; and LSS batch with L. sakei + S. xylosus + Staphylococcus carnosus. The results showed that adding starter culture caused Lactobacillus and Staphylococcus to become dominant bacteria and reduced the Enterobacteriaceae count in the inoculated sausages. The mixed starter cultures (LS & LSS) accelerated acidification and reduced water activity and lipid oxidation. Statistical analysis revealed that the use of mixed starter cultures, especially the combination L. sakei + S. xylosus + S. carnosus, contributed to proteolysis and lipolysis, increasing total free amino acids and polyunsaturated fatty acids. The above results demonstrate that the use of mixed starter cultures contributes to improving the composition of free amino acids and free fatty acids as well as the hygienic quality of dry fermented mutton sausages.

Species Pervasiveness Within the Group of Coagulase-Negative Staphylococci Associated With Meat Fermentation Is Modulated by pH

During spontaneous meat fermentations, Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus are generally the most prevailing species within the communities of coagulase-negative staphylococci (CNS). There is an interest to introduce CNS isolates from artisan-style spontaneous meat fermentations as starter cultures in more industrialized processes, as to confer additional quality benefits. However, staphylococcal competitiveness within the meat matrix is affected by the processing conditions, which vary considerably among product types. A major factor of variability relates to the intensity of acidification, driven by the concentration of added carbohydrates. The effect of pH on CNS prevalence was studied in both a mince-based meat fermentation model and in fermented sausages produced on pilot scale. Roughly, from all experiments combined, it appeared that a pH of 5.3 corresponded with a breakpoint for CNS selection. Above this value, a general prevalence by S. xylosus was found, even overruling the addition of starter cultures consisting of S. equorum and S. saprophyticus strains. At pH values below 5.3, S. xylosus was also accompanied by S. equorum (following a mild pH drop) and S. saprophyticus (following a stronger pH drop). Still, addition of starter cultures affected the volatile profile compared to the control batch, even if those starter cultures were not able to dominate during the ripening process. This study nonetheless provides a warning for an overly confident use of specific CNS species as starter cultures, especially when in a given processing context the prevailing conditions do not allow superior growth compared to the CNS from the background microbiota.

Nitric oxide synthase: What is its potential role in the physiology of staphylococci in meat products?

Coagulase-negative staphylococci are frequently isolated from meat products and two species are used as starter cultures in dry fermented sausages. In these products, they face various environmental conditions such as variation of redox potential and oxygen levels that can lead to oxidative stress. Furthermore, when nitrate and nitrite are added as curing salts, staphylococci also experience nitrosative stress. A nos gene encoding a nitric oxide synthase (NOS) is present in the genome of all staphylococci. NOS produces nitric oxide (NO) and citrulline from arginine, but its activity is still poorly characterized, particularly in coagulase-negative staphylococci. NO is highly reactive with a broad spectrum of activity resulting from targeting metal centres (heme and non-heme) and protein thiols. At low concentration, NO acts as a signalling molecule, while at higher concentration it generates stress. Thus, it was initially suggested that staphylococcal NOS counteract oxidative stress in relation to PerR and Fur regulators. In the physiology of staphylococci, it has recently been highlighted that NO controls the rate of aerobic respiration and regulates the transition from aerobic to nitrate respiration and also helps maintain the membrane potential in relation to the two-component systems SrrAB and AirRS. As NO interacts with heme centres, it binds the heme iron atom of myoglobin to form nitrosomyglobin, which is the typical red pigment of cured meat. However, the contribution of NOS to this reaction in meat products has yet to be evaluated.

Effect of temperature and pH on the community dynamics of coagulase-negative staphylococci during spontaneous meat fermentation in a model system

Coagulase-negative staphylococci (CNS) contribute to the product quality of fermented meats. In spontaneously fermented meats, CNS communities are variable and difficult to predict, as their compositions depend on a superposed combination of different processing factors. To partially disentangle this superposition, a meat model system was used to study the influence of temperature and pH on the CNS community dynamics. Therefore, cured pork mince was prepared that was divided into three batches of different initial acidity levels, namely pH 5.7, pH 5.5, and pH 5.3. These three batches were incubated at three different temperatures, namely 23 °C, 30 °C, and 37 °C. Hence, the experimental set-up resulted in nine combinations of different temperature and initial pH values. Samples were analysed after 3 and 14 days to monitor pH, colony counts, and species diversity of the CNS communities, based on mannitol-salt-phenol-red agar (MSA) medium. At conditions of mild acidity (pH 5.7) and low temperature (23 °C), as often encountered during artisan-type meat fermentations, a co-prevalence of Staphylococcus xylosus, Staphylococcus equorum, and Staphylococcus saprophyticus occurred. At the same initial pH but higher incubation temperatures (30 °C and 37 °C), Staphylococcus lugdunensis became the prevailing CNS species, besides S. saprophyticus (30 °C) and the coagulase-positive species Staphylococcus aureus (37 °C). When the initial pH was set at 5.5, S. saprophyticus was the prevailing CNS species at both 23 °C and 30 °C, but it was replaced by Staphylococcus epidermidis and Staphylococcus simulans at 37 °C after 3 and 14 days, respectively. At the most acidic conditions (pH 5.3), CNS counts declined and many of the MSA isolates were of non-staphylococcal nature. Among others, Staphylococcus carnosus (23 °C), Staphylococcus warneri (30 °C), and S. epidermidis (37 °C) were found. Overall, the results of the present study indicated that the processing factors temperature and pH had a clear impact on the shaping of staphylococcal communities during meat fermentation.

The narrowing down of inoculated communities of coagulase-negative staphylococci in fermented meat models is modulated by temperature and pH

Coagulase-negative staphylococci (CNS) are involved in colour and flavour formation of fermented meats. Their communities are established either spontaneously, as in some artisan-type products, or using a starter culture. The latter usually consists of Staphylococcus carnosus and/or Staphylococcus xylosus strains, although strains from other CNS species also have potential for application. However, it is not entirely clear how the fitness of alternative starter cultures within a fermented meat matrix compares to conventional ones and how this may be affected by processing conditions. Therefore, the aim of this study was to assess the influence of two key processing conditions, namely temperature and acidity, on the competitiveness of a cocktail of five different strains of CNS belonging to species that are potentially important for meat fermentation (Staphylococcus xylosus 2S7-2, S. carnosus 833, Staphylococcus epidermidis ATCC 12228, Staphylococcus equorum DFL-S19, and Staphylococcus saprophyticus FPS1). To this end, fermented meat models consisting of cured meat batters with initial pH values of 5.3, 5.5, or 5.7 were inoculated with these strains, stuffed in containers, and incubated at 23, 30, or 37 °C. Both the pH level and the temperature influenced the composition of the CNS communities, giving a competitive advantage to the best adapted species. Staphylococcus xylosus preferred low temperature and mild acidity, whereas an elevated temperature selected for S. epidermidis and a low pH for S. carnosus. Under the conditions tested, S. saprophyticus and S. equorum were outcompeted by the three other CNS species. Hence, CNS communities in fermented meats are not only established based on the initial presence of specific species in the meat batter but also by their subsequent adaptation to the processing conditions during fermentation, potentially overruling the use of starter cultures.

Genomic insights into Staphylococcus equorum KS1039 as a potential starter culture for the fermentation of high-salt foods

BACKGROUND

Our previous comparative genomic analysis of Staphylococcus equorum KS1039 with five S. equorum strains illuminated the genomic basis of its safety and salt tolerance. However, a comprehensive picture of the cellular components and metabolic pathways involved in the degradation of macromolecules and development of sensory properties has not been obtained for S. equorum. Therefore, in this study, we examined the general metabolism of S. equorum based on information obtained from published complete genome sequences of six S. equorum strains isolated from different niches. Additionally, the utility of strain KS1039 as a starter culture for high-salt food fermentations was examined.

RESULTS

All six S. equorum strains contained genes involved in glycolysis, the tricarboxylic acid cycle, and amino acid metabolic pathways, as well as color development. Moreover, the strains had the potential to produce acetoin, butanediol, and branched chain fatty acids, all of which are important flavor compounds. None of the strains contained decarboxylase genes, which are required for histamine and tyramine production. Strain KS1039 contained bacteriocin and CRISPR/Cas gene clusters, and experimental results suggested that these genes were functional in vitro.

CONCLUSIONS

The comparative genomic analysis carried out herein provides important information on the usefulness of S. equorum KS1039 as a starter culture for the fermentation of high-salt foods in terms of safety, salt tolerance, bacteriocin production, and foreign plasmid restriction.

Contribution of nitric oxide synthase from coagulase-negative staphylococci to the development of red myoglobin derivatives

As part of the microbial community of meat or as starter cultures, coagulase-negative staphylococci (CNS) serve several essential technological purposes in meat products, such as color development through the reduction of nitrate to nitrite. As the safety of nitrite as an additive has been questioned, we explored the potential of CNS to develop red myoglobin derivatives such as oxymyoglobin and nitrosomyoglobin. Nitrosoheme was extracted to evaluate NO production. This production could be due to a nitric oxide synthase (NOS) activity. In all CNS strains, a nos gene was identified. The NOS sequences deduced were highly conserved within CNS. A phylogenetic tree based on the NOS sequences revealed that the strains within species were clustered. Ninety-one percent of the strains, whatever the species, were able to form red myoglobin derivatives in aerobic conditions, but a high variability was observed between strains within species. However, NO production was low as nitrosomyoglobin represented 8% to 16% of the red pigments according to the species. Formation of oxymyoglobin, especially under aerobic conditions, was substantial, but varied greatly within species. The mechanism involved in the formation of oxymyoglobin could rely on staphylococcal reductases and remains to be explored.

Genomic insights into the virulence and salt tolerance of Staphylococcus equorum

To shed light on the genetic background behind the virulence and salt tolerance of Staphylococcus equorum, we performed comparative genome analysis of six S. equorum strains. Data on four previously published genome sequences were obtained from the NCBI database, while those on strain KM1031 displaying resistance to multiple antibiotics and strain C2014 causing haemolysis were determined in this study. Examination of the pan-genome of five of the six S. equorum strains showed that the conserved core genome retained the genes for general physiological processes and survival of the species. In this comparative genomic analysis, the factors that distinguish the strains from each other, including acquired genomic factors in mobile elements, were identified. Additionally, the high salt tolerance of strains enabling growth at a NaCl concentration of 25% (w/v) was attributed to the genes encoding potassium voltage-gated channels. Among the six strains, KS1039 does not possess any of the functional virulence determinants expressed in the other strains.

Quality determination of vegetable oils used as an addition to fermented meat products with different starter cultures

There were developed samples of fermented meat products of „Mettwurst" with an addition of a starter culture pentosacceus AS-3/100 or probiotic culture Lactobacillus casei Lc-01 and its combinations for this thesis. A part of animal fat was replaced with vegetable oils - sunflower oil and rapeseed oil. For comparison, there was also used a sample without an addition of vegetable oil. There were determined the characteristics of fats in samples: saponification value, acidity value, esteric, iodine and peroxide value. The samples were determined on the day of production and always once a week in a period of three following weeks. Every single sample was hereby determined 3 times. According to the results, it is more advantageous to use the samples with sunflower oil with an addition of specific cultures Lactobacillus casei Lc-01 and Pediococcus pentosaceus AS-3/100. The saponification value when adding sunflower oil detects that the quality of fat remains stable till the 14th day of storage (p <0.05). The comparison of acid value detects that a sample with sunflower oil and culture Pediococcus pentosaceus AS-3/100 is more advantageous due to fast acidification in the first half of storage period. Good results of iodine and peroxide value had the variation of a sample with sunflower oil and a combination of both cultures. The variation of peroxide value maintained the lowest values. By using the samples with sunflower oil and unispecific cultures L. casei Lc-01 and P. pentosaceus AS-3/100, the culture P. pentosaceus AS-3/100, which remained stable till the 14th day of production, reached the best values of peroxide value. The sunflower oil is in spite of high content of PUFA more stable to which also contributes the increased content of vitamin E that works as an antioxidant here. The disadvantage of rapeseed oil is its higher susceptibility to oxidation. For reasons of faster decomposition of vegetable oils would be essential to cut down on the minimum durability. From the 14th day of storage, the content of free FA increases and the fat is still considerably quickly oxidized. The content of unsaturated FA, of which the vegetable fat is a source, quickly decreases. The sensory quality simultaneously decreases, too. 

Characterization and Technological Features of Autochthonous Coagulase-Negative Staphylococci as Potential Starters for Portuguese Dry Fermented Sausages

The manufacture of dry fermented sausages is an important part of the meat industry in Southern European countries. These products are usually produced in small shops from a mixture of pork, fat, salt, and condiments and are stuffed into natural casings. Meat sausages are slowly cured through spontaneous fermentation by autochthonous microbiota present in the raw materials or introduced during manufacturing. The aim of this work was to evaluate the technological and safety features of coagulase-negative staphylococci (CNS) isolated from Portuguese dry fermented meat sausages in order to select autochthonous starters. Isolates (n = 104) obtained from 2 small manufacturers were identified as Staphylococcus xylosus, Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus carnosus. Genomically diverse isolates (n = 82) were selected for further analysis to determine the ability to produce enzymes (for example, nitrate-reductases, proteases, lipases) and antibiotic susceptibility. Autochthonous CNS producing a wide range of enzymes and showing low antibioresistance were selected as potential starters for future use in the production of dry fermented meat sausages.

Ferritin, an iron source in meat for Staphylococcus xylosus?

Staphylococcus xylosus is frequently isolated from food of animal origin. Moreover, this species is one of the major starter cultures used for meat fermentation. Iron is a key element for growth and survival of bacteria. Meat is particularly rich in haemic (myoglobin and haemoglobin) and non-haemic (ferritin and transferrin) iron sources. Ferritin is a storage protein able to capture large quantities of iron. It is highly resistant to microbial attack and few microorganisms can use it as an iron source. Surprisingly, we found that the S. xylosus C2a strain grows in the presence of ferritin as a sole iron source. A three-cistron operon was highly overexpressed under ferritin iron growth conditions. We generated a deletion-insertion in the first gene of the operon and evaluated the phenotype of the mutant. The mutant showed decreased growth because it was less able to acquire iron from ferritin. Transcriptional analysis of the mutant revealed downregulation of several genes involved in the response to oxidative stress. This study characterized for the first time the capacity of a Staphylococcus to use iron from ferritin and revealed that a potential reductive pathway was involved in this acquisition. We hypothesize that this ability could give an advantage to S. xylosus in meat products.

Genomic investigation reveals evolution and lifestyle adaptation of endophytic Staphylococcus epidermidis

Staphylococcus epidermidis is a major human associated bacterium and also an emerging nosocomial pathogen. There are reports of its association to rodents, sheep and plants. However, comparative and evolutionary studies of ecologically diverse strains of S. epidermidis are lacking. Here, we report the whole genome sequences of four S. epidermidis strains isolated from surface sterilized rice seeds along with genome sequence of type strain. Phylogenomic analysis of rice endophytic S. epidermidis (RESE) with “type strain” unequivocally established their species identity. Whole genome based tree of 93 strains of S. epidermidis revealed RESE as distinct sub-lineage which is more related to rodent sub-lineage than to majority of human lineage strains. Furthermore, comparative genomics revealed 20% variable gene-pool in S. epidermidis, suggesting that genomes of ecologically diverse strains are under flux. Interestingly, we were also able to map several genomic regions that are under flux and gave rise to RESE strains. The largest of these genomic regions encodes a cluster of genes unique to RESE that are known to be required for survival and stress tolerance, apart from those required for adaptation to plant habitat. The genomes and genes of RESE represent distinct ecological resource/sequences and provided first evolutionary insights into adaptation of S. epidermidis to plants.

Metabolic characterization of Bacillus subtilis and Bacillus amyloliquefaciens strains isolated from traditional dry-cured sausages

The aim of this study was to investigate the effect of pH, temperature, and NaCl on growth, proteolytic and lipolytic activities, and the ability to produce biogenic amines of 19 strains of Bacillus isolated from Androlla and Botillo (two Spanish traditional sausages) to elucidate the role of these bacteria in sausage manufacture. All strains grew in the presence of 10% salt and at pH values of 5.0 and 5.5, whereas only 9 strains grew at 10°C. Proteolytic activity was assessed by the agar plate method, which revealed that 100 and 94.7% of the strains were able to hydrolyze sarcoplasmic and myofibrillar proteins, respectively. These results were confirmed by electrophoretic assays. The titration method revealed that only two strains hydrolyzed pork fat to any extent, and the profiles of the fatty acids freed were different. Most strains produced biogenic amines, but the quantities were generally low.

Genetic diversity of Staphylococcus equorum isolates from Saeu-jeotgal evaluated by multilocus sequence typing

Staphylococcus equorum, the predominant bacterial species detected in Saeu-jeotgal, a Korean high-salt fermented seafood, is a candidate starter bacterium for Saeu-jeotgal fermentation. A multilocus sequence typing (MLST) scheme was developed to evaluate the genetic diversity and background of S. equorum strains isolated from Saeu-jeotgal. A total of 135 strains, including 117 isolates from Saeu-jeotgal, and others from Myeolchi-jeotgal, sausage, cheese and horse skin, were subjected to MLST, and the internal fragments of seven housekeeping genes, aroE, dnaJ, glpF, gmk, hsp60, mutS, and pta, were compared. This MLST scheme produced 45 sequence types (STs) and the eBURST algorithm clustered the STs into nine clonal groups and seven singletons. Clonal group 1, the major group, consisted of 30 isolates from cheese, Saeu-jeotgal and sausages, which were classified into 12 STs. The predominant ST, ST26, comprised 25 isolates and presented as a singleton. Most of the isolates from Myeolchi-jeotgal and sausages clustered on two different branches of a phylogenetic tree generated with a cluster analysis using the maximum likelihood algorithm. This MLST scheme established the genetic backgrounds of S. equorum strains isolated from different types of food. Among the housekeeping genes used for MLST, gmk had the fewest allele types and fairly low sequence identities (74.0-90.0%) within the Staphylococcus species. Therefore, sequence analyses of the gmk gene and 16S rRNA gene can be used for the accurate and rapid identification of S. equorum.

Isolation of methicillin-resistant Staphylococcus spp. from ready-to-eat fish products

A hundred samples from ready-to-eat (RTE) fish products were examined for the presence and antimicrobial susceptibility of Staphylococcus spp. Staphylococci were isolated from 43% of these samples (n = 100). The identified species in the samples were Staphylococcus aureus (7%), Staphylococcus epidermidis (13%), Staphylococcus xylosus (12%), Staphylococcus sciuri (4%), Staphylococcus warneri (3%), Staphylococcus saprophyticus (2%), Staphylococcus schleiferi (1%) and Staphylococcus auricularis (1%). Two Staph. aureus (MRSA) isolates, three Staph. epidermidis (MRSE), five Staph. xylosus, four Staph. sciuri, one Staph. schleiferi and one Staph. saprophyticus isolates were resistant to oxacillin and all of them carried the mecA gene. The two MRSA isolates belonged to the spa types t316 (ST359) and t548 (ST5) and none of them was able to produce enterotoxins. Pulsed field gel electrophoresis for Staph. aureus and Staph. epidermidis isolates revealed 6 and 11 distinct PFGE types, respectively, reflecting diversity. The presence of methicillin-resistant staphylococci, especially MRSA and MRSE, in RTE fish products may constitute a potential health risk for consumers.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides the first data on the occurrence of methicillin-resistant Staphylococcus aureus and methicillin-resistant coagulase-negative staphylococci in salted and smoked fish products in Greece. These results are important and useful for Staphylococcus spp. risk assessment and management programmes for ready-to-eat fish products.

High prevalence of Cfr-producing Staphylococcus species in retail meat in Guangzhou, China

Background

The emergence and wide distribution of the transferable gene for linezolid resistance, cfr, in staphylococci of human and animal origins is of great concern as it poses a serious threat to the public health. In the present study, we investigated the emergence and presence of the multiresistance gene, cfr, in retail meat sourced from supermarkets and free markets of Guangzhou, China.

Results

A total of 118 pork and chicken samples, collected from Guangzhou markets, were screened by PCR for cfr. Twenty-two Staphylococcus isolates obtained from 12 pork and 10 chicken samples harbored cfr. The 22 cfr-positive staphylococci isolates, including Staphylococcus equorum (n = 8), Staphylococcus simulans (n = 7), Staphylococcus cohnii (n = 4), and Staphylococcus sciuri (n = 3), exhibited 17 major SmaI pulsed-field gel electrophoresis (PFGE) patterns. In 14 isolates, cfr was located on the plasmids. Sequence analysis revealed that the genetic structures (including ΔtnpA of Tn558, IS21-558, ΔtnpB, and tnpC of Tn558, orf138, fexA) of cfr in plasmid pHNTLD18 of a S. sciuri strain and in the plasmid pHNLKJC2 (including rep, Δpre/mob, cfr, pre/mob and partial ermC) of a S. equorum strain were identical or similar to the corresponding regions of some plasmids in staphylococcal species of animal and human origins.

Conclusions

To the best of our knowledge, this is the first study to report the presence of the multiresistance gene, cfr, in animal meat. A high occurrence of cfr was observed in the tested retail meat samples. Thus, it is important to monitor the presence of cfr in animal foods in China.

Barcoded pyrosequencing analysis of the bacterial community of Daqu for light-flavour Chinese liquor

The bacterial community of Daqu affects its characteristics and functions by their metabolic products, such as amylase, protease, esterase. In this study, barcoded pyrosequencing was used to analyse the bacterial communities of three kinds of Daqu for light-flavour Chinese liquor brewing. A total of 13672 sequences were identified as bacterial sequences. The Shannon index of QC, HX and GT for clusters sharing 97% homology was 5·0, 4·2 and 4·2, respectively, indicating that QC had the highest biodiversity. The Good's coverage index of QC, HX and GT was 88·2, 93·4 and 93%, respectively, indicating that the vast majority of phylotypes have been detected. Among the three kinds of Daqu, the majority of annotated reads were assigned to two phyla (Firmicutes and Actinobacteria). The phylum Firmicutes was the most abundant group in QC (74·2%), HX (81·4%) and GT (98·6%), and the phylum Actinobacteria was the second in QC (23·9%), HX (17·9%) and GT (1·1%). There were many lactic acid bacteria in all three kinds of Daqu QC (45·8%), HX (46·3%) and GT (24·7%). In addition, the most abundant family in GT was Bacillus, accounting for 65·0%, while in HX, the families Thermoactinomycetaceae and Streptomycetaceae accounted for 19·5 and 14·1%, respectively, and in QC, 13·1% were Streptomycetaceae, 12·2% were heterofermentative Leuconostocaceae.

SIGNIFICANCE AND IMPACT OF THE STUDY

There are three kinds of Daqu (starter material) used for famous Chinese light-flavour liquor brewing, that is Qingcha, Hongxin and Houhuo. Since Daqu was fermented in an open environment, the microbiology communities were different with different kind of Daqu. Objective bacterial communities determined by barcoded pyrosequencing help to speculate possible metabolic productions, even to guess the function of many kind of Daqu in light-flavour liquor brewing.

Comparative genomic and transcriptomic analyses of NaCl-tolerant Staphylococcus sp. OJ82 isolated from fermented seafood

Bacteria belonging to the Staphylococcus genus reside in various natural environments; however, only disease-associated Staphylococcus strains have received attention while ecological function and physiologies of non-pathogenic strains were often neglected. Because high level of tolerance against NaCl is a common trait of Staphylococcus, we investigated the characteristics of halotolerance in Staphylococcus sp. OJ82 isolated from fermented seafood containing a high concentration of NaCl. Among the 292 isolates screened, OJ82 showed the highest β-galactosidase and extracellular protease activities under high-salt conditions. Comparative genomic analysis with other Staphylococcus strains showed that (a) replication origins are highly conserved, (b) the OJ82 strain has a high number of amino acid transport- and metabolism-related genes, and (c) OJ82 has many unique proteins (15 %) and 12 prophage-related genomic islands. RNA-seq analysis under high-salt conditions showed that genes involved in cell membranes, transport, osmotic stress, ATP synthesis, and translation are highly expressed. OJ82 may use the ribulose monophosphate pathway to detoxify some toxic intermediates under high-salt conditions. Six new and three known non-coding small RNAs of the OJ82 strain were also found in the RNA-seq analysis. Genomic and transcriptomic analyses identified target β-galactosidase and extracellular protease. Interestingly, the OJ82 strain became resistant to bacteriocin produced by the Bacillus strain only under high-salt conditions. Our data showed that the OJ82 strain adapted to high-salt conditions by expressing core cellular processes (translation, ATP production) and defense genes (membrane synthesis, compatible solute transports, ribulose monophosphate pathway) could survive bacteriocin exposure under high-salt conditions.

Vancomycin-resistant gram-positive cocci isolated from the saliva of wild songbirds

We analyzed highly vancomycin-resistant Gram-positive bacteria isolated from the saliva of migratory songbirds captured, sampled, and released from a bird-banding station in western Kansas. Individual bacterial isolates were identified by partial 16S rRNA sequencing. Most of the bacteria in this study were shown to be Staphylococcus succinus with the majority being isolated from the American Robin. Some of these bacteria were shown to carry vanA, vanB, and vanC vancomycin-resistance genes and have the ability to form biofilms. One of the van gene-carrying isolates is also coagulase positive, which is normally considered a virulence factor. Other organisms isolated included Staphylococcus saprophyticus as well as Enterococcus gallinarum. Given the wide range of the American Robin and ease of horizontal gene transfer between Gram-positive cocci, we postulate that these organisms could serve as a reservoir of vancomycin-resistance genes capable of transferring to human pathogens.