Amino acid conversions by coagulase-negative staphylococci in a rich medium: Assessment of inter- and intraspecies heterogeneity

Characterization of indigenous coagulase-negative staphylococci isolated from Chinese spontaneously fermented meat products

Technological, safety-related and volatile properties were analyzed in coagulase-negative staphylococci (CNS) isolates from Chinese spontaneously fermented meat products. A total of 107 CNS isolates were identified via 16 S rRNA sequencing, and the most recovered species were S. saprophyticus (53.3 %), S. edaphicus (12.1 %), and S. epidermidis (10.3 %). Among them, 58 CNS isolates belonging to 9 species were selected with higher activities of catalase, nitrate reductase, proteolysis, and lipolysis, as well as higher tolerance to stressful environmental conditions. Then, 7 CNS isolates belonging to 4 species were further selected based upon excellent technological characteristics, lack of hemolysis and antibiotic resistance, and a low production of biogenic amines. The volatile profiles of these 7 strains cultivated in pork broth was determined. S. casei No. 1 produced significant amounts of phenethyl alcohol, geraniol, and 3-methyl-butanol. S. xylosus No. 120 produced the highest amount of methyl ketones with the potential to provide dry-cured odor of fermented meats. The volatile profile was highly strain dependent. Several CNS identified in this study have the potential to be used as the starter cultures for fermented meat products.

Competition between Starter Cultures and Wild Microbial Population in Sausage Fermentation: A Case Study Regarding a Typical Italian Salami (Ventricina)

The work reports a case study describing how the competition wild microflora vs. starter cultures affects the final product characteristics. This study regards an industrial lot of Ventricina, an Italian long-ripened traditional fermented sausages, produced using starter cultures. After ripening, some relevant organoleptic defects (off-odour, crust formation) were observed. Therefore, analyses were carried out in the inner and outer sausage section to explain this phenomenon. Microbiological analyses indicated a high meat batter contamination and metagenomic analyses evidenced the inability of LAB starter cultures to lead the fermentation process. The results of this not controlled fermentation were the accumulation of high levels of biogenic amines (including histamine) and the formation of a volatile profile different if compared with similar products. Indeed, the volatilome analysis revealed unusually high amounts of molecules such as isovaleric acid, propanoic acid, 1-propanol, which can be responsible for off-odours. This study demonstrated that starter culture use needs to be modulated in relation to production parameters to avoid safety and organoleptic concerns.

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.

Exploring the Ambiguous Status of Coagulase-Negative Staphylococci in the Biosafety of Fermented Meats: The Case of Antibacterial Activity Versus Biogenic Amine Formation

A total of 332 staphylococcal strains, mainly isolated from meat, were screened for antibacterial activity. Eighteen strains exhibited antibacterial activity towards species within the same genus. These antibacterial strains were further screened against Clostridium botulinum, to assess their potential as anticlostridial starter cultures for the development of fermented meat products without added nitrate or nitrite. Only Staphylococcus sciuri IMDO-S72 had the ability to inhibit all clostridial strains tested, whilst displaying additional activity against Bacillus cereus, Listeria monocytogenes and Staphylococcus aureus. Apart from their potential as bioprotective cultures, the staphylococcal collection was also screened for biogenic amine production, as these compounds may compromise food quality. To this end, ultra-high-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) was applied. A low incidence of biogenic amine production was found, with tyramine and β-phenylethylamine being the most prevalent ones. Concentrations remained relatively low (< 52 mg/L) after a prolonged incubation period, posing no or little threat towards food safety. Taken together, S. sciuri IMDO-S72 could serve as an interesting candidate for the bioprotection of fermented meats as it showed promising antibacterial activity as well as absence of biogenic amine production.

SadA-Expressing Staphylococci in the Human Gut Show Increased Cell Adherence and Internalization

A subgroup of biogenic amines, the so-called trace amines (TAs), are produced by mammals and bacteria and can act as neuromodulators. In the genus Staphylococcus, certain species are capable of producing TAs through the activity of staphylococcal aromatic amino acid decarboxylase (SadA). SadA decarboxylates aromatic amino acids to produce TAs, as well as dihydroxy phenylalanine and 5-hydroxytryptophan to thus produce the neurotransmitters dopamine and serotonin. SadA-expressing staphylococci were prevalent in the gut of most probands, where they are part of the human intestinal microflora. Furthermore, sadA-expressing staphylococci showed increased adherence to HT-29 cells and 2- to 3-fold increased internalization. Internalization and adherence was also increased in a sadA mutant in the presence of tryptamine. The α2-adrenergic receptor is required for enhanced adherence and internalization. Thus, staphylococci in the gut might contribute to gut activity and intestinal colonization.

A comprehensive look into the volatile exometabolome of enteroxic and non-enterotoxic Staphylococcus aureus strains

Staphylococcal food poisoning is a disease that originates significant health and economic losses and is caused by Staphylococcus aureus strains able to produce enterotoxins. The aim of this work is to go further on the study of the volatile exometabolome of S. aureus using an advanced gas chromatographic technique. Enterotoxic and non-enterotoxic strains were assessed. The volatile exometabolome profile comprised 240 volatiles belonging to ten chemical families. This volatiles were mainly by-products of branched-chain amino acids and methionine degradation, pyruvate metabolism, diacetyl pathway, oxidative stress and carotenoid cleavage. Metabolites released by the first two pathways were produced in higher contents by the enterotoxic strains. This study add further insights to S. aureus volatile exometabolome, and also shows that by applying it, it is possible to distinguish strains of S. aureus by the number of produced enterotoxins, which is especially important from the food safety point of view.

Effect of Fermentation with Different Lactic Acid Bacteria Starter Cultures on Biogenic Amine Content and Ripening Patterns in Dry Fermented Sausages

In the present study, two different diameter (small and large) Milano-type dry fermented sausages were industrially produced to evaluate the effect of two different LAB starter cultures (Lactobacillus sakei and Pediococcus pentosaceus) on biogenic amines (BAs) content, proteolysis, and lipolysis taking place during both fermentation and ripening. With regard to BAs, putrescine and tyramine were mostly found in fermented sausages having large diameter and those inoculated with P. pentosaceus/S. xylosus exhibited significantly higher accumulation of these compounds. Overall, the small size sausages showed a more pronounced proteolysis taking place during processing. In addition, aside from the distinctive electrophoretic bands detected with both starter cultures, a more pronounced proteolysis and a faster protein hydrolysis was observed in salami inoculated with P. pentosaceus/S. xylosus. As for lipolysis, a significantly higher amount of diacylglycerols was observed at the end of ripening in the sausages inoculated with L. sakei/S. xylosus, which concurrently exhibited an increased D32, D34, and D36 series. The results of the present study confirms profound differences in BAs concentration, proteolysis, and lipolysis. These findings are strictly dependent on the starter cultures, which demonstrates that the choice of an appropriate starter optimized for peculiar products and processes should be the key factor to improve safety and quality features of traditional fermented 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.

Assessment of Coagulase-Negative Staphylococci and Lactic Acid Bacteria Isolated from Portuguese Dry Fermented Sausages as Potential Starters Based on Their Biogenic Amine Profile

The aim of this study was to evaluate the decarboxylase activity of coagulase-negative staphylococci (CNS) and lactic acid bacteria (LAB) involved in meat products fermentation, in order to characterize and select the strains most suitable to be used as safe starter cultures. Isolates were obtained from traditional Portuguese dry fermented meat sausages, identified by PCR and characterized according to their technological properties. Lactobacilli and enterococci were assessed for their bacteriocinogenic potential. Biogenic amines (BA) were screened by culture method and analyzed by RP-HPLC/UV. The screening method, compared with chromatographic analysis, was not reliable for CNS and LAB strains selection. Tyramine decarboxylase activity was present in CNS strains, with a slight production of amines. No other hazardous BA were produced. Among lactobacilli, moderate production of tyramine was related only to Lactobacillus curvatus, with some strains producing putrescine or 2-phenylethylamine. Enterococci were high and moderate producers of tyramine and 2-phenylethylamine, respectively. Staphylococcus xylosus, Staphylococcus equorum, and Staphylococcus carnosus, independent of their genetic and technological profiles and BA production, were adequate for use in meat products, according to the data. Lactobacillus plantarum and Lactobacillus sakei strains could also be selected for starters.

PRACTICAL APPLICATION

The selection of coagulase-negative staphylococci and lactic acid bacteria (LAB) isolates were based on their production of biogenic amines in order to avoid this potential hazard production in meat products. The most suitable isolates could be used as safe starter cultures in meat products industry. The staphylococci and LAB selected will achieve particular organoleptic characteristics in meat products and bioprotection from pathogens.

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

Coagulase-negative staphylococci (CNS) are ubiquitous micro-organisms that are commonly present on animal skin and animal-derived foods. They are members of the beneficial microbial consortia of several fermented food products where they contribute to quality. Currently, only a few CNS species are included in commercial starter cultures, although many other ones with promising properties have been isolated from diverse food ecosystems. In the present study, a Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis of the potential use of unconventional CNS starter cultures for the fermentation of animal-derived foods is carried out. An overview of both their desirable and worrisome metabolic traits is given. In general, the application of innovative CNS-based starter cultures offers opportunities to modulate flavour, improve the safety and health aspects and develop novel colour development strategies for clean label products. Yet, their implementation is often not straightforward as nontrivial obstacles or threats are encountered, which relate to technological, food safety and legal concerns. As most of the desirable and undesirable characteristics of CNS species are strain dependent, a case-by-case evaluation is needed when evaluating specific strains for their potential use as novel starter cultures.

Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria

Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, their microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice fermentations were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that Enterobacteriaceae were outcompeted by lactic acid bacteria (LAB) between 3 and 13 days of fermentation. Metabolite-target analysis showed that lactic acid and mannitol were highly produced, as well as the biogenic amine cadaverine. High-throughput 16S rRNA gene sequencing revealed that mainly species of Leuconostoc and Lactobacillus (as identified by 8 and 20 amplicon sequence variants [ASVs], respectively) mediated the fermentations in subsequent order. The analyses at the DNA level still detected a high number of Enterobacteriaceae, but their relative abundance was low when RNA-based sequencing was performed to detect presumptive metabolically active bacterial cells. In addition, this method greatly reduced host read contamination. Phylogenetic placement indicated a high LAB diversity, with ASVs from nine different phylogenetic groups of the Lactobacillus genus complex. However, fermentation experiments with isolates showed that only strains belonging to the most prevalent phylogenetic groups preserved the fermentation dynamics. The carrot juice fermentation thus forms a robust man-made microbial ecosystem suitable for studies on LAB diversity and niche specificity.

IMPORTANCE The usage of fermented food products by professional chefs is steadily growing worldwide. Meanwhile, this interest has also increased at the household level. However, many of these artisanal food products remain understudied. Here, an extensive microbial analysis was performed of spontaneous fermented carrot juices which are used as nonalcoholic alternatives for wine in a Belgian Michelin star restaurant. Samples were collected through an active citizen science approach with 38 participants, in addition to three laboratory fermentations. Identification of the main microbial players revealed that mainly species of Leuconostoc and Lactobacillus mediated the fermentations in subsequent order. In addition, a high diversity of lactic acid bacteria was found; however, fermentation experiments with isolates showed that only strains belonging to the most prevalent lactic acid bacteria preserved the fermentation dynamics. Finally, this study showed that the usage of RNA-based 16S rRNA amplicon sequencing greatly reduces host read contamination.

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.

Detection of Sepsis in Preterm Infants by Fecal Volatile Organic Compounds Analysis: A Proof of Principle Study

OBJECTIVES

Several studies associated altered gut microbiota composition in preterm infants with late-onset sepsis (LOS), up to days before clinical onset of sepsis. Microbiota analysis as early diagnostic biomarker is, however, in clinical practice currently not feasible because of logistic aspects and high costs. Therefore, we hypothesized that analysis of fecal volatile organic compounds (VOCs) may serve as noninvasive biomarker to predict LOS at a preclinical stage, because VOC reflect the composition and activity of intestinal microbial communities.

METHODS

In a prospective multicenter study, fecal samples were collected daily from infants with a gestational age of <30 weeks. VOC signatures of fecal samples from infants with LOS, collected up to 5 days before diagnosis, were analyzed by means of an electronic nose technology (Cyranose 320) and compared to matched controls.

RESULTS

Fecal VOC profiles of infants with LOS (n = 36) could be discriminated from controls (n = 40) at 3 days (area under the curve [±95% confidence interval], P value, sensitivity, specificity; 70.2 [52.2-88.3], 0.033, 57.1%, 61.5%), 2 days (77.7 [62.7-92.7], 0.050, 75.0%, 70.8%), and 1 day (70.4 [49.6-91.3], 0.037, 64.3%, 64.3%) before the onset of LOS.

CONCLUSIONS

Fecal VOC profiles of preterm infants with LOS could be discriminated from matched controls, up to 3 days before clinical onset of the disease, underlining the hypothesis that intestinal microbiota may play an etiological role in LOS. Notably, VOC profiling is clinically feasible and the potential of this technique in the early detection of LOS needs to be confirmed in future studies.

Insight into the Genome of Staphylococcus xylosus, a Ubiquitous Species Well Adapted to Meat Products

Staphylococcus xylosus belongs to the vast group of coagulase-negative staphylococci. It is frequently isolated from meat products, either fermented or salted and dried, and is commonly used as starter cultures in sausage manufacturing. Analysis of the S. xylosus genome together with expression in situ in a meat model revealed that this bacterium is well adapted to meat substrates, being able to use diverse substrates as sources of carbon and energy and different sources of nitrogen. It is well-equipped with genes involved in osmotic, oxidative/nitrosative, and acidic stress responses. It is responsible for the development of the typical colour of cured meat products via its nitrate reductase activity. It contributes to sensorial properties, mainly by the the catabolism of pyruvate and amino acids resulting in odorous compounds and by the limiting of the oxidation of fatty acids, thereby avoiding rancidity.

Effects of glucose and oxygen on arginine metabolism by coagulase-negative staphylococci

Coagulase-negative staphylococci (CNS) are not only part of the desirable microbiota of fermented meat products but also commonly inhabit skin and flesh wounds. Their proliferation depends on the versatility to use energy sources and the adaptation to fluctuating environmental parameters. In this study, the conversion of the amino acid arginine by two strains with arginine deiminase (ADI) activity (Staphylococcus carnosus 833 and S. pasteuri αs3-13) and a strain with nitric oxide synthase (NOS) activity (S. haemolyticus G110) was modelled as a function of glucose and oxygen availability. Both factors moderately inhibited the ADI-based conversion kinetics, never leading to full repression. However, for NOS-driven conversion of arginine by S. haemolyticus G110, oxygen was an absolute requirement. When changing from microaerobic conditions to aerobiosis, a switch from homolactic fermentation to a combined formation of lactic acid, acetic acid, and acetoin was found in all cases, after which lactic acid and acetic acid were used as substrates. The kinetic model proposed provided a suitable description of the data of glucose and arginine co-metabolism as a function of oxygen levels and may serve as a tool to further analyse the behaviour of staphylococci in different ecosystems or when applying specific food processing conditions.