Nonconventional starter cultures of coagulase-negative staphylococci to produce animal-derived fermented foods, a SWOT analysis

Bioactive Specialized Metabolites from Staphylococcus: Diversity, Biosynthesis, and Biotechnological Potential

Staphylococci are a heterogeneous group of bacteria capable of colonizing diverse ecological niches and adopting a wide variety of lifestyles. While several strains are known as notorious, multidrug-resistant human pathogens, others are harmless inhabitants of soil, water, and food products, or beneficial members of the skin microbiota. To survive and remain competitive under challenging environmental conditions, staphylococci have evolved the ability to assemble and secrete a diverse range of ribosomally synthesized and posttranslationally modified peptides, nonribosomal peptides, terpenes, siderophores, and other specialized metabolites with antibiotic, immunomodulating and metal chelating activities. In this review, an overview of the bioactive metabolite arsenal of staphylococci is provided with a focus on their biosynthetic pathway, mode of action, and industrial application potential. Also, unexplored natural product biosynthetic pathways in staphylococci, along with strategies to access this hidden potential, are highlighted.

The role of coagulase-negative staphylococci on aroma generation of fermented sausage

Fermented sausages are popular meat products with many different varieties. The aroma of fermented sausages depends on the metabolic activities of microbiota, mainly involving lactic acid bacteria and catalase-positive cocci, the group of coagulase-negative staphylococci (CNS) in particular. Regarding staphylococci, this work elucidated their generation of aroma precursors from hydrolase, metabolic activities contributing to aroma development, antioxidant effects that improve aroma via preventing excessive lipid oxidation. The metabolic pathways of staphylococci that play a role in aroma formation involve carbohydrate fermentation, amino acid degradation, fatty acid β-oxidation, and esterase activities. Their antioxidant activities are associated with superoxidase dismutase and catalase activities, as well as the production of antioxidant peptides. Processing conditions may influence CNS communities and affect aroma characteristics of fermented sausages. Implementation of genome sequencing and editing to select and customize CNS with specific biosynthetic metabolic pathways was proposed forward, offering a great potential for enhancing aroma development during sausage fermentation.

Insights into the flavor contribution, mechanisms of action, and future trends of coagulase-negative staphylococci in fermented meat products: A review

During fermentation, meat is pre-treated and cured to cultivate a diverse microflora, resulting in fermented meat products with distinctive flavors. Coagulase-negative staphylococcus holds a crucial role in all fermented meat products, contributing to the breakdown of proteins, carbohydrates, and fats, and the creation of flavor compounds. Fermentation technology has important research value and significance in fermented meat products. The optimization and improvement of flavor by CNS can be achieved by regulating the fermentation environment, initial microflora and processing conditions. The review explores the ways in which coagulase-negative staphylococci contribute to the flavors in fermented meat products. The mechanism of flavor substance formation and means of regulation in coagulase-negative staphylococci were also investigated. The review concludes by summarizing future development trends and drawing conclusions.

Impact and correlation of fermentation temperature on the bacterial community, flavor characteristics, and proteolysis of Harbin dry sausages

Proteins undergo degradation to produce peptides and free amino acids, which in turn promote the production of volatile compounds with important contributions to the taste and aroma. This study investigated the effect of fermentation temperatures (8, 15, and 25 °C) on the bacterial community, flavor profile, and protein degradation of Harbin dry sausages. The physical and chemical properties were improved at 25 °C compared with 8 and 15 °C. Staphylococcus xylosus increased with the increase in fermentation temperature, whereas Latilactobacillus sakei decreased. The degree of protein degradation increased, and the content and proportion of taste peptides and free amino acids increased. Similarly, a higher fermentation temperature led to an increase in volatile compounds, such as aldehydes, alcohols, and esters. In conclusion, there is an inseparable relationship between proteolysis and microbial proteases. The fermentation temperature of 25 °C best contributed to the sensory quality and flavor characteristics of Harbin dry sausages.

Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites

BACKGROUND

Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated.

RESULTS

The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms.

CONCLUSIONS

Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.

Antibiotic Resistance/Susceptibility Profiles of Staphylococcus equorum Strains from Cheese, and Genome Analysis for Antibiotic Resistance Genes

In food, bacteria carrying antibiotic resistance genes could play a prominent role in the spread of resistance. Staphylococcus equorum populations can become large in a number of fermented foods, yet the antibiotic resistance properties of this species have been little studied. In this work, the resistance/susceptibility (R/S) profile of S. equorum strains (n = 30) from cheese to 16 antibiotics was determined by broth microdilution. The minimum inhibitory concentration (MIC) for all antibiotics was low in most strains, although higher MICs compatible with acquired genes were also noted. Genome analysis of 13 strains showed the S. equorum resistome to be composed of intrinsic mechanisms, acquired mutations, and acquired genes. As such, a plasmidic cat gene providing resistance to chloramphenicol was found in one strain; this was able to provide resistance to Staphylococcus aureus after electroporation. An msr(A) polymorphic gene was identified in five strains. The Mrs(A) variants were associated with variable resistance to erythromycin. However, the genetic data did not always correlate with the phenotype. As such, all strains harbored a polymorphic fosB/fosD gene, although only one acquired copy was associated with strong resistance to fosfomycin. Similarly, a plasmid-associated blaR1-blaZI operon encoding a penicillinase system was identified in five ampicillin- and penicillin G-susceptible strains. Identified genes not associated with phenotypic resistance further included mph(C) in two strains and norA in all strains. The antibiotic R/S status and gene content of S. equorum strains intended to be employed in food systems should be carefully determined.

Comprehensive Approaches for the Search and Characterization of Staphylococcins

Novel and sustainable approaches are required to curb the increasing threat of antimicrobial resistance (AMR). Within the last decades, antimicrobial peptides, especially bacteriocins, have received increased attention and are being explored as suitable alternatives to antibiotics. Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria as a self-preservation method against competitors. Bacteriocins produced by Staphylococcus, also referred to as staphylococcins, have steadily shown great antimicrobial potential and are currently being considered promising candidates to mitigate the AMR menace. Moreover, several bacteriocin-producing Staphylococcus isolates of different species, especially coagulase-negative staphylococci (CoNS), have been described and are being targeted as a good alternative. This revision aims to help researchers in the search and characterization of staphylococcins, so we provide an up-to-date list of bacteriocin produced by Staphylococcus. Moreover, a universal nucleotide and amino acid-based phylogeny system of the well-characterized staphylococcins is proposed that could be of interest in the classification and search for these promising antimicrobials. Finally, we discuss the state of art of the staphylococcin applications and an overview of the emerging concerns.

Role of Microorganisms in the Development of Quality during the Fermentation of Salted White Herring (Ilisha elongata)

Salted white herring (Ilisha elongata) is a popular fish product in the coastal region of China. The complex endogenous enzymes and microbial action determine the quality of a traditionally salted herring. In order to investigate the role of microorganisms in the quality formation of salted herring, three groups for different salting processes were established: traditional salted (TS), non-starter salted (NS), and starter culture salted (SS). The predominant microorganism in each processing group was Staphylococcus spp., as inferred by next-generation sequencing data. Different physicochemical parameters were obtained in each of the three processing groups (TCA-soluble peptide (trichloroacetic acid-soluble peptide), TVB-N (Total volatile basic nitrogen), and TBA values (thiobarbituric acid-reactive substance)). The TS group had the maximum level of total biogenic amines, while the SS group had the lowest. A strong positive correlation was found between Staphylococcus and 14 aromatic compounds, of which 5 were odor-active compounds that created fishy, grassy, fatty, and fruity flavors. Shewanella may produce trimethylamine, which is responsible for the salted herrings’ fishy, salty, and deteriorating flavor. The findings demonstrated that autochthonous strains of Staphylococcus saprophyticus M90−61 were useful in improving product quality because they adapted quickly to the high osmotic environment.

Combination of Solid State and Submerged Fermentation Strategies to Produce a New Jellyfish-Based Food

This study describes the set-up and optimization of a fermentation strategy applied to a composite raw material containing jellyfish biomass as the principal ingredient. New fermented food was developed by combining fresh jellyfish Rhizostoma pulmo and the sequential solid-state submerged liquid fermentation method used in Asian countries for processing a high-salt-containing raw material. Aspergillus oryzae was used to drive the first fermentation, conducted in solid-state conditions, of a jellyfish-based product, here named Jelly paste. The second fermentation was performed by inoculating the Jelly paste with different selected bacteria and yeasts, leading to a final product named fermented Jellyfish paste. For the first time, a set of safety parameters necessary for monitoring and describing a jellyfish-based fermented food was established. The new fermented products obtained by the use of Debaryomyces hansenii BC T3-23 yeast strain and the Bacillus amyloliquefaciens MS3 bacterial strain revealed desirable nutritional traits in terms of protein, lipids and total phenolic content, as well as valuable total antioxidant activity. The obtained final products also showed a complex enzyme profile rich in amylase, protease and lipase activities, thus making them characterized by unique composite sensory odor descriptors (umami, smoked, dried fruit, spices).

The Controlled Semi-Solid Fermentation of Seaweeds as a Strategy for Their Stabilization and New Food Applications

For centuries, macroalgae, or seaweeds, have been a significant part of East Asian diets. In Europe, seaweeds are not considered traditional foods, even though they are increasingly popular in Western diets in human food applications. In this study, a biological processing method based on semi-solid fermentation was optimized for the treatment of the seaweed Gracilaria gracilis. For the first time, selected lactic acid bacteria and non-conventional coagulase-negative staphylococci were used as starter preparations for driving a bio-processing and bio-stabilization of raw macroalga material to obtain new seaweed-based food prototypes for human consumption. Definite food safety and process hygiene criteria were identified and successfully applied. The obtained fermented products did not show any presence of pathogenic or spoilage microorganisms, thereby indicating safety and good shelf life. Lactobacillus acidophilus-treated seaweeds revealed higher α-amylase, protease, lipase, endo-cellulase, and endo-xylanase activity than in the untreated sample. This fermented sample showed a balanced n-6/n-3 fatty acid ratio. SBM-11 (Lactobacillus sakei, Staphylococcus carnosus and Staphylococcus xylosus) and PROMIX 1 (Staphylococcus xylosus) treated samples showed fatty acid compositions that were considered of good nutritional quality and contained relevant amounts of isoprenoids (vitamin E and A). All the starters improved the nutritional value of the seaweeds by significantly reducing the insoluble indigestible fractions. Preliminary data were obtained on the cytocompatibility of G. gracilis fermented products by in vitro tests. This approach served as a valid strategy for the easy bio-stabilization of this valuable but perishable food resource and could boost its employment for newly designed seaweed-based food products.

Characterization of coagulase-negative staphylococci and macrococci isolated from cheese in Germany

Cheese, especially ripened varieties, harbor a very complex and heterogeneous microbiota. In addition to the desired microorganisms (starter cultures) added during cheese production, potentially harmful bacteria may also enter the production chain. Regarding the latter, the focus of this study was on coagulase-negative staphylococci (CNS) and Macrococcus caseolyticus. Both are known to harbor a variety of genes coding for antibiotic resistance, including mecA, mecB, mecC, and mecD. Coagulase-negative staphylococci or macrococci carrying such genes or other virulence factors should not be present in cheese. Cheese samples (101 in total) were collected from retail sources. Coagulase-negative staphylococci and M. caseolyticus were isolated utilizing selective agars, and species were identified by phenotypical tests and partial sequencing of the sodA gene. The results allowed identification of 53 CNS strains and 19 M. caseolyticus strains. Among the CNS, 11 isolates of Staphylococcus saprophyticus and one Staphylococcus epidermidis isolate were obtained. Both species are potential human pathogens and may thus adversely affect the safety of these food products. Screening for antimicrobial resistance was performed by application of disc diffusion tests, a gradient strip-test, and 14 different PCR tests. Evidence for methicillin resistance (by either positive disc diffusion assay for cefoxitin or by mec PCR) was found in CNS isolates and M. caseolyticus (9 isolates each). Regarding other virulence factors, no genetic determinants for coagulase or the most common staphylococcal enterotoxins sea, seb, sec, sed, and see were detected in any of the CNS or M. caseolyticus isolates by PCR testing. In conclusion, the presence of facultatively pathogenic CNS and carriers of genes for antibiotic resistance in both groups of microorganisms, especially mec genes, and the respective food safety issues need further evaluation and surveillance.

Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation

Although the microbial diversity and structure in bean-based fermented foods have been widely studied, systematic studies on functional microbiota and mechanism of community forms in multi-microbial fermentation systems were still lacking. In this work, the metabolic pathway and functional potential of microbial community in broad bean paste (BBP) were investigated by metagenomics approach, and Staphylococcus, Bacillus, Weissella, Aspergillus and Zygosaccharomyces were found to be the potential predominant populations responsible for substrate alteration and flavor biosynthesis. Among them, Staphylococcus was the most abundant and widespread functional microbe, and closely related Staphylococcus species were diverse and ubiquitously distributed, with the opportunistic pathogen S. gallinarum being the most abundant Staphylococcus specie isolated from BBP. To explain the dominance status of S. gallinarum and species distributions of Staphylococcus genus, we tested the effects of abiotic and biotic factors on three Staphylococcus species using a tractable BBP model, demonstrating that adaptation to environmental conditions (environmental parameters and other functional microbes) led to the dominant position and species coexistence of Staphylococcus, and congeneric competition among Staphylococcus species further shaped ecological distributions of closely related Staphylococcus species. In general, this work revealed the metabolic potential of microbial community and distribution mechanism of Staphylococcus species during BBP fermentation, which could help traditional factories to more precisely control the safety and quality of bean-based fermented foods.

A comprehensive review of the role of microorganisms on texture change, flavor and biogenic amines formation in fermented meat with their action mechanisms and safety

Meat fermentation ensures its preservation, improved safety and quality. This prominently used traditional process has survived for ages, creating physical, biochemical, and microbial changes, and to significantly affect the functionality, organoleptic property, and nutrition of the fermented products. In some process, the growth of various pathogenic and spoilage microorganisms is inhibited. The production of fermented meat relies on naturally occurring enzymes (in the muscle or the intestinal tract) as well as microbial metabolic activities. In this review, fermented meat types and their health benefits were firstly introduced. This was followed by a description of fermentation conditions vis-à-vis starters, bacterial, yeast and mold cultures, and their role in meat. The review focuses on how microorganisms affect texture change, flavor formation, and biogenic amines (BA) accumulation in fermented meat. In addition, the production conditions and the major biochemical changes in fermented meat products were also introduced to present the best factors influencing the quality of fermented meat. Microorganisms and microbial enzymes in fermented meats were discussed as they could affect organoleptic characteristics of fermented meats. Moreover, safety concerns and prospects for further research of fermented meat were also discussed with emphasis on novel probiotic and starter cultures development; bioinformatics, omics technologies and data modeling to maximize the benefit from fermentation process in meat production.

Staphylococcins: an update on antimicrobial peptides produced by staphylococci and their diverse potential applications

Staphylococcins are antimicrobial peptides or proteins produced by staphylococci. They can be separated into different classes, depending on their amino acid composition, structural complexity, and steps involved in their production. In this review, an overview of the current knowledge on staphylococcins will be presented with emphasis on the information collected in the last decade, including a brief description of new peptides. Most staphylococcins characterized to date are either lantibiotics or linear class II bacteriocins. Recently, gene clusters coding for production of circular bacteriocins, sactipeptides, and thiopeptides have been mined from the genome of staphylococcal isolates. In contrast to class II bacteriocins, lantibiotics, sactipeptides, and thiopeptides undergo post-translational modifications that can be quite extensive, depending on the peptide. Few staphylococcins inhibit only some staphylococcal species, but most of them have proven to target pathogens belonging to different genera and involved in a variety of infectious diseases of clinical or agronomic importance. Therefore, these peptides exhibit potential application as anti-infective drugs in different areas. This review will also cover this diverse and remarkable potential. To be commercialized, however, staphylococcin production should be cost-effective and result in high bacteriocin yields, which are not generally achieved from the culture supernatant of their native producers. Such low yields make their production quite costly and not suitable at large industrial scale. Efforts already made to overcome this limitation, minimizing costs and time of production of some staphylococcins and employing either chemical synthesis or in vivo biosynthesis, will be addressed in this review as well. KEY POINTS: • Staphylococci produce a variety of antimicrobial peptides known as staphylococcins. • Most staphylococcins are post-translationally modified peptides. • Staphylococcins exhibit potential biotechnological applications. Graphical abstract.

Potential of Bacteria from Alternative Fermented Foods as Starter Cultures for the Production of Wheat Sourdoughs

Microbial strains for starter culture-initiated sourdough productions are commonly isolated from a fermenting flour-water mixture. Yet, starter culture strains isolated from matrices other than sourdoughs could provide the dough with interesting metabolic properties and hence change the organoleptic properties of the concomitant breads. Furthermore, the selection of sourdough starter cultures does not need to be limited to lactic acid bacteria (LAB), as other food-grade microorganisms are sometimes found in sourdoughs. Therefore, different strains belonging to LAB, acetic acid bacteria (AAB), and coagulase-negative staphylococci (CNS) that originated from different fermented food matrices (fermenting cocoa pulp-bean mass, fermented sausage, and water kefir), were examined as to their prevalence in a wheat sourdough ecosystem during 72-h fermentations. Limosilactobacillus fermentum IMDO 222 (fermented cocoa pulp-bean mass isolate) and Latilactobacillus sakei CTC 494 (fermented sausage isolate) seemed to be promising candidates as sourdough starter culture strains, as were the AAB strains Acetobacter pasteurianus IMDO 386B and Gluconobacter oxydans IMDO A845 (both isolated from fermented cocoa pulp-bean mass), due to their competitiveness in the wheat flour-water mixtures. Wheat breads made with G. oxydans IMDO A845 sourdoughs were significantly darker than reference wheat breads.

Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins

Insight into the microbial species diversity of fermented meats is not only paramount to gain control over quality development, but also to better understand the link with processing technology and geographical origin. To study the composition of the microbial communities, the use of culture-independent methods is increasingly popular but often still suffers from drawbacks, such as a limited taxonomic resolution. This study aimed to apply a previously developed high-throughput amplicon sequencing (HTS) method targeting the 16S rRNA and tuf genes to characterize the bacterial communities in European fermented meats in greater detail. The data obtained broadened the view on the microbial communities that were associated with the various products examined, revealing the presence of previously underreported subdominant species. Moreover, the composition of these communities could be linked to the specificities of individual products, in particular pH, salt content, and geographical origin. In contrast, no clear links were found between the volatile organic compound profiles of the different products and the country of origin, distinct processing conditions, or microbial communities. Future application of the HTS method offers the potential to further unravel complex microbial communities in fermented meats, as well as to assess the impact of different processing conditions on microbial consortia.

Exploring the Link Between the Geographical Origin of European Fermented Foods and the Diversity of Their Bacterial Communities: The Case of Fermented Meats

European fermented meat products are prepared according to a wide variety of different recipes and processing conditions, which can influence their fermentative microbiota. However, due to the diverse processing conditions applied across Europe, it remained unclear to which degree bacterial heterogeneity can be encountered in commercially available fermented meat products and whether this is linked to their geographical origin. Therefore, the bacterial species diversity of 80 fermented meat products available in the Belgian retail, coming from five different countries, was investigated. It was also assessed how this related to the country of origin and the key processing parameters pH and salt concentration. The samples originated from Belgium, France, Germany, Italy, and Spain. In general, Southern European fermented meat products commonly had a higher pH, with their lactic acid bacteria (LAB) communities being represented by Lactobacillus sakei and with mostly Staphylococcus xylosus and Staphylococcus equorum governing over the coagulase-negative staphylococci (CNS) communities. Among these products, the Spanish variants showed a higher prevalence of S. equorum, whereas S. xylosus was the prevailing CNS species in most French and Italian fermented meat products. In contrast, Northern European fermented meat products were generally more acidified and showed a higher prevalence of Pediococcus pentosaceus in their LAB communities, whereas Staphylococcus carnosus represented the CNS communities. Non-parametric statistical tests indicated the impact of the geographical origin on the prevalence of the LAB and CNS species. The latter was likely due to the combination of differences in process technology as well as starter culture use.

Role of Starter Cultures on the Safety of Fermented Meat Products

Starters are microbial cultures used to promote and conduct the fermentation of meat products. Bacteria, particularly lactic acid bacteria (LAB) and coagulase-negative staphylococci (CNS), as well as yeasts and molds, may be used as starters. They can increase the safety of fermented meat products by means of rapid matrix acidification or due to the production of antimicrobial substances, such as bacteriocins. Besides, starters may help to standardize product properties and shorten ripening times. Safety of fermented meat products may be jeopardized by microbiological, namely foodborne pathogens (Salmonella spp., Listeria spp., etc), and chemical hazards, particularly biogenic amines, nitrosamines, polycyclic aromatic hydrocarbons (PAH), and mycotoxins. Biogenic amines (BA) are potentially unsafe nitrogenous compounds that result from the decarboxylation of some amino acids. Some microorganisms may be responsible for their formation. Starters can cause a fast pH decrease, inhibiting the development of microorganisms with amino acid decarboxylative ability, thus preventing the accumulation of BA in fermented meat products. Besides, starters can compete with the autochthonous, non-starter microbiota throughout ripening and storage, thus reducing BA production. Some strains of Lactobacillus sakei and Lactobacillus plantarum have been shown to reduce the formation/accumulation of BA. On the other hand, Staphylococcus xylosus and Debaryomyces hansenii strains have been reported to degrade BA in food. PAH are organic compounds containing multiple aromatic rings and produced by the incomplete combustion of organic matter, such as the wood used for smoking meat. Mixed starters containing Lactobacillus spp., Gram-positive catalase-positive cocci and yeasts have been used in the manufacturing of traditional meat sausages. However, the effect of starters on reducing the accumulation of PAH is poorly understood. Starters may also be engaged in competitive exclusion, outcompeting the spoiling or deteriorating autochthonous microbiota. For example, Pediococcus acidilactici has been shown to inhibit Listeria monocytogenes in meat products. Additionally, the role of molds, such as Penicillium nalgiovense, in the competitive exclusion of undesired filamentous fungi, has also been demonstrated. Most of these undesired fungi produce mycotoxins, secondary metabolites capable of causing disease. The current review addresses the role of starters on the microbiological and chemical safety of fermented meat products.