Molecular characterization and aromatic potential of Debaryomyces hansenii strains isolated from naturally fermented sausages

Screening and evaluating microorganisms with broad-spectrum biogenic amine-degrading ability from naturally fermented dry sausage collected from Northeast China

This study aimed to screen autochthonous strains with broad-spectrum biogenic amine (BA) degradation ability from traditional dry sausages and to evaluate their BA-degrading ability in dry sausages. A total of 120 strains were isolated from dry sausages collected from various regions in Northeast China, and 35 of 120 isolates were identified as non-BA producing strains by the in vitro agar method. The random amplified polymorphic DNA polymerase chain reaction technique genotyped these 35 isolates into 18 biotypes. Moreover, high performance liquid chromatography (HPLC) quantification showed that six strains (Latilactobacillus sakei MDJ6; Lactiplantibacillus plantarum SH7; Weissella hellenica DQ9; Staphylococcus saprophyticus JX18 and SYS8; and Macrococcus caseolyticus SYS11) of the 18 biotypes exhibited broad-spectrum BA-degrading ability, all of which had various levels of amine oxidase activity with monoamine oxidase and diamine oxidase activities ranged of 6.60-619.04 and 26.32-352.81 U/mg protein, respectively. These six strains were subsequently inoculated into dry sausages and the results showed that they exhibited varying degrees of BA-degrading ability, of which strain Lat. sakei MDJ6 allowed to have less BA production on dry sausage with a final concentration of 61.33 mg/kg.

Bioprotective yeasts: Potential to limit postharvest spoilage and to extend shelf life or improve microbial safety of processed foods

Yeasts are a widespread group of microorganisms that are receiving increasing attention from scientists and industry. Their diverse biological activities and broad-spectrum antifungal activity make them promising candidates for application, especially in postharvest biocontrol of fruits and vegetables and food biopreservation. The present review focuses on recent knowledge of the mechanisms by which yeasts inhibit pathogenic fungi and/or spoilage fungi and bacteria. The main mechanisms of action of bioprotective yeasts include competition for nutrients and space, synthesis and secretion of antibacterial compounds, mycoparasitism and the secretion of lytic enzymes, biofilm formation, quorum sensing, induced systemic resistance of fruit host, as well as the production of reactive oxygen species. Preadaptation of yeasts to abiotic stresses such as cold acclimatization and sublethal oxidative stress can improve the effectiveness of antagonistic yeasts and thus more effectively play biocontrol roles under a wider range of environmental conditions, thereby reducing economic losses. Combined application with other antimicrobial substances can effectively improve the efficacy of yeasts as biocontrol agents. Yeasts show great potential as substitute for chemical additives in various food fields, but their commercialization is still limited. Hence, additional investigation is required to explore the prospective advancements of yeasts in the field of biopreservation for food.

Metabolic cross-feeding enhances branched-chain aldehydes production in a synthetic community of fermented sausages

Microbial interactions play an important role in regulating the metabolic function of fermented food communities, especially the production of key flavor compounds. However, little is known about specific molecular mechanisms that regulate the production of key flavor compounds through microbial interactions. Here, we designed a synthetic consortium containing Debaryomyces hansenii D1, Staphylococcus xylosus S1, and Pediococcus pentosaceus PP1 to explore the mechanism of the microbial interactions underlying the branched-chain aldehydes production. In this consortium, firstly, D. hansenii secreted amino acids that promoted the growth of P. pentosaceus and S. xylosus. Specifically, D. hansenii D1 secreted alanine, aspartate, glutamate, glutamine, glycine, phenylalanine, serine, and threonine, which were the primary nutrients for bacterial growth. P. pentosaceus PP1 utilized all these eight amino acids through cross-feeding, whereas S. xylosus S1 did not utilize aspartate and serine. Furthermore, D. hansenii D1 promoted the production of branched-chain aldehydes from S. xylosus and P. pentosaceus through cross-feeding of α-keto acids (intermediate metabolites). Thus, the accumulation of 2-methyl-butanal was promoted in all co-culture. Overall, this work revealed the mechanism by which D. hansenii and bacteria cross-feed to produce branched-chain aldehydes in fermented sausages.

Production of flavor compounds from rice bran by yeasts metabolisms of Kluyveromyces marxianus and Debaryomyces hansenii

The aim of this study was to evaluate the biosynthesis of flavor compounds from rice bran by fermentation facilitated by Kluyveromyces marxianus and Debaryomyces hansenii. The growth of both yeasts was assessed by specific growth rates and doubling time. The biosynthesis of flavor compounds was evaluated by gas chromatography-olfactometry (GC-O), gas chromatography-mass spectrometry (GC-MS), and Spectrum™ sensory analysis. The specific growth rate (µ) and doubling time (t_d) of K. marxianus was calculated as 0.16/h and 4.21h, respectively, whereas that of D. hansenii was determined as 0.13/h and 5.33h, respectively. K. marxianus and D. hansenii produced significant levels of higher alcohols and acetate esters from rice bran. Results showed that K. marxianus can produce 827.27 µg/kg of isoamyl alcohol, 169.77 µg/kg of phenyl ethyl alcohol, and 216.08 µg/kg of phenyl ethyl acetate after 24-h batch fermentation. A significant amount of isovaleric acid was also synthesized by K. marxianus (4013 µg/kg) after the batch fermentation of 96 h. 415.64 µg/kg of isoamyl alcohol and 135.77 µg/kg of phenyl ethyl acetate was determined in rice bran fermented by D. hansenii after 24-h fermentation. Fermented cereals and rose were the characteristic flavor descriptors of the fermented rice bran samples. Rose flavor in fermented rice bran samples was found to be associated with phenyl ethyl alcohol, phenyl ethyl acetate, isoamyl acetate, and guaiacol. Thus, the findings of this study demonstrate that the valorization of rice bran can be achieved with the production of natural flavor compounds by yeast metabolism.

Metagenomics reveals the formation mechanism of flavor metabolites during the spontaneous fermentation of potherb mustard (Brassica juncea var. multiceps)

Fermented vegetable flavors are closely associated with microbial metabolism. Here, shifts in flavor metabolites and their correlations to the structure and function of fermentative microbial communities were explored during the spontaneous fermentation process of potherb mustard (Brassica juncea var. multiceps), a traditionally fermented vegetable from China. Halophilic bacteria (HAB, i.e., Halomonas, Salinivibrio, and Vibrio) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) became highly abundant after potherb mustard fermentation. Further, HAB and LAB abundances exhibited significant, positive correlations with metabolites important in fermented potherb mustard flavoring (e.g., organic acids, amino acids, alcohols, aldehydes, and nitriles). Metagenomic analysis indicated that Halomonas, Salinivibrio, Weissella, and Lactobacillus-related genera were likely actively engaged in pyruvate metabolism (ko00620) and citrate cycle (TCA cycle, ko00020), leading to higher lactic and acetic acid concentrations, along with lower pH, which would affect levels of volatile isothiocyanates and nitriles that contribute to flavoring of fermented potherb mustard. Further, HAB and LAB were the primary populations inferred to be responsible for amino acid and fatty acid metabolism in addition to the biosynthesis of numerous volatile flavor compounds. This study highlights the predominance and importance of LAB and HAB during spontaneous fermentation of potherb mustard and provides new insights into their roles in this process.

Debaryomyces hansenii Is a Real Tool to Improve a Diversity of Characteristics in Sausages and Dry-Meat Products

Debaryomyces hansenii yeast represents a promising target for basic and applied biotechnological research It is known that D. hansenii is abundant in sausages and dry-meat products, but information regarding its contribution to their characteristics is blurry and contradictory. The main goal in this review was to define the biological contribution of D. hansenii to the final features of these products. Depending on multiple factors, D. hansenii may affect diverse physicochemical characteristics of meat products. However, there is general agreement about the significant generation of volatile and aromatic compounds caused by the metabolic activities of this yeast, which consequently provide a tendency for improved consumer acceptance. We also summarize current evidence highlighting that it is not possible to predict what the results would be after the inoculation of a meat product with a selected D. hansenii strain without a pivotal previous study. The use of D. hansenii as a biocontrol agent and to manufacture new meat products by decreasing preservatives are examples of exploring research lines that will complement current knowledge and contribute to prepare new and more ecological products.

Biochemical changes and microbial community dynamics during spontaneous fermentation of Zhacai, a traditional pickled mustard tuber from China

Zhacai is a traditional fermented vegetable that has been consumed in China for centuries. It is currently manufactured by spontaneous fermentation and therefore mostly relies on the activities of autochthonous microorganisms. Here, we characterized microbial community dynamics and associated biochemical changes in 12% salted Zhacai during a 90-day spontaneous fermentation process using high-throughput sequencing and chromatography-based approaches to identify associations between microorganisms and fermentation characteristics. Amplicon sequencing targeting bacterial 16S rRNA genes revealed that bacterial communities were dominated by halophilic bacteria (HAB, i.e., Halomonas and Idiomarina) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) after 30 days of fermentation. In addition, the relative abundances of the fungal genera Debaryomyces, Sterigmatomyces, and Sporidiobolus increased as fermentation progressed. Concomitantly, pH decreased while titratable acidity increased during fermentation, along with associated variation in biochemical profiles. Overall, the levels of organic acids (i.e., lactic and acetic acid), free amino acids (i.e., alanine, lysine, and glutamic acid), and volatiles (i.e., alcohols, esters, aldehydes, and ketones) increased in mature Zhacai. In addition, the abundances of Lactobacillus-related species, Halomonas spp., Idiomarina loihiensis, as well as that of the yeast Debaryomyces hansenii, were strongly correlated with increased concentrations of organic acids, amino acids, biogenic amines, and volatiles. This study provides new detailed insights into the succession of microbial communities and their potential roles in Zhacai fermentation.

The potential correlations between the fungal communities and volatile compounds of traditional dry sausages from Northeast China

The fungal communities and volatile compounds of traditional dry sausages collected from five different regions in Northeast China, including Harbin (HRB), Daqing (DQ), Suihua (SH), Hegang (HG) and Mudanjiang (MDJ) were investigated in this study. The results revealed clear differences among the fungal community structures of the sausages. Aspergillus pseudoglaucus, Debaryomyces hansenii, and Trichosporon asahii were found to be the predominant species in the sausages from HRB, HG, and MDJ, respectively. Candida zeylanoides was the predominant species in the sausage from DQ and SH. Additionally, 88 volatile compounds were identified in all sausages, of which 31 volatile compounds were the most important flavor contributors (odor activity value > 1). Potential correlation analysis revealed that 8 fungi (D. hansenii, C. zeylanoides, T. asahii, A. pseudoglaucus, Aspergillus sydowii, Penicillium expansum, A. alternata, and Alternaria tenuissima) showed significant positive correlations with ≥3 key volatile compounds. Among these fungi, D. hansenii was regarded as a core functional fungus responsible for the formation of the volatile compounds, given its strong connection with the highest number of key volatile compounds. These results provide detailed insight into the fungal communities of traditional dry sausages and a deeper understanding of the contribution of these fungi to sausage flavor.

Combination of Flos Sophorae and chili pepper as a nitrite alternative improves the antioxidant, microbial communities and quality traits in Chinese sausages

The main issue remains finding a nitrite alternative able to provide its multiple functions. Flos Sophorae exerts antioxidant and prebiotic actions, chili pepper has potent coloring capacity, thus this study investigated whether combination of Flos Sophorae and chili pepper could address the multiple activities of nitrite in Chinese sausages. Dry-fermented sausages were prepared: control and four treatments added with 150 mg/kg sodium nitrite (Nit), 0.2% Flos Sophorae (FS), 1% chili pepper (CP), and combination of 0.2% Flos Sophorae and 1% chili pepper (FS + CP). Results indicated that FS, CP and FS + CP had higher moisture, antioxidant activity and numbers of beneficial Staphylococcus and yeasts Candida, and lower numbers of Escherichia coli and harmful fungi, while FS had lower redness and harder texture than control. Their combination inhibited the declines of capsanthin and antioxidant capacity with ripening time, further improved microbiological communities compared with CP, and resulted in higher redness, similar color score and bacterial community, less lipid oxidation and softer texture compared with Nit. These results suggested that Flos Sophorae in combination with chili pepper could replace the nitrite's contribution to red curing color and microbiological communities, and effectively hinder lipid oxidation in Chinese sausages.

Yeast Microbiota during Sauerkraut Fermentation and Its Characteristics

Sauerkraut is the most important fermented vegetable obtained in Europe. It is produced traditionally by spontaneous fermentation of cabbage. The aim of this study was to determine biodiversity of yeasts present during fermentation of eight varieties of cabbages (Ambrosia, Avak, Cabton, Galaxy, Jaguar, Kamienna Głowa, Manama and Ramco), as well as characterize obtained yeast isolates. WL Nutrient Agar with Chloramphenicol was used to enumerate yeast. Isolates were differentiated using RAPD-PCR and identified by sequencing of the 5.8S-ITS rRNA gene region. The volatiles production was analyzed using SPME-GC-TOFMS. Our research confirmed that during sauerkraut fermentation there is an active growth of the yeasts, which begins in the first phases. The maximal number of yeast cells from 1.82 to 4.46 log CFU g⁻¹ occurred after 24 h of fermentation, then decrease in yeast counts was found in all samples. Among the isolates dominated the cultures Debaryomyces hansenii, Clavispora lusitaniae and Rhodotorula mucilaginosa. All isolates could grow at NaCl concentrations higher than 5%, were relatively resistant to low pH and the presence of lactic acid, and most of them were characterized by killer toxins activity. The highest concentration of volatiles (mainly esters and alcohols) were produced by Pichia fermentans and D. hansenii strains.

Autochthonous Yeast from Pork and Game Meat Fermented Sausages for Application in Meat Protection and Aroma Developing

Simple Summary

Yeasts are microorganisms presented naturally in meat products microbiota, which carry out an essential role in the maturation process of fermented sausages. The maturation of this type of product could be better controlled by the addition of a starter culture or a mix of strains that could standardize the process in diverse factories. Moreover, it would be favorable to find cultures that, not only conduct the curing process, but also present an added value such as the meat product protection (antioxidant capability and biocontrol activity). Yeasts also have an important role in the meat product aroma development. Therefore, it would be interesting to select a pleasant-aroma forming strain in order to elaborate a future starter culture for fermented sausage maturation.

Abstract

The wild yeast community was studied in fermented sausages from pork and game meat (deer and wild boar) during the maturation process from different curing rooms. Although the biotechnological importance of yeasts in the maturation process of pork sausages is known, there is a lack of information for sausage maturation involving game meat. A total of 123 yeasts were isolated and, by amplifying and sequencing of the ITS region, were classified in 14 species. Debaryomyces hansenii, Kazachstania servazzii, and Wickerhamomyces anomalus were isolated in both pork and game samples. The PCR-RAPD technique differentiated between 26 and 18 strains from pork and game meat sausages, respectively. The physicochemical parameters and their relationship with the yeast community were also studied. The antioxidant and anti-lipid peroxidation capability were analyzed and the 70% and 50% of the tested strains showed these abilities, respectively. Moreover, the biocontrol capability against mycotoxigenic molds was found in 19 strains, but better results were observed in game meat yeasts. On the other hand, almost 30% of strains produce a pleasant olfactory aroma, and volatile compounds associated with the yeast pathway metabolic during the maturation process have been characterized such as esters, aldehydes, fusel alcohols, etc. This study has allowed a better understanding of the biodiversity of this type of food, as well as selecting potential yeast strains for their future use as starters.

Characterization of yeast population from unstudied natural sources in La Mancha region

AIMS

This study aims to identify the yeast species and strains which entitled an unstudied area of Spain and evaluate the yeast species diversity richness and the genetic variety.

METHODS AND RESULTS

A total of 702 yeasts were isolated from different environments in a central Spanish region (La Mancha) with diverse sources of origin (food, animals, flowers and environmental sources) during spring season. Thanks to the analysis carried out by the PCR-RFLP technique and sequencing, 35 species were identified. A neighbour-joining phylogenetic tree was created based on D1/D2 sequences. Moreover 330 strains were determined by PCR-RAPD and their profiles were analysed using the bioinformatics programme BioNumerics 7·6. The Simpson's index (D) and the genetic diversity percentage were calculated with the aim of studying the richness of the species in each environment and the genetic variety in each species.

CONCLUSIONS

This study has permitted to know that the majority of the species found was Diutina rugosa while the most ubiquitous was Rhodotorula mucilaginosa which expose the dispersion capability of this species. The diversity parameters has revealed that the highest species richness was associated to environmental samples and the highest genetic variety was presented in those species with better dispersion capability or a smaller number of isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study permits to better understand the yeast communities in La Mancha region which gives a value the microbial potential of this region.

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury).IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.

Bacteriocinogenic LAB Strains for Fermented Meat Preservation: Perspectives, Challenges, and Limitations

Over the last decades, much research has focused on lactic acid bacteria (LAB) bacteriocins because of their potential as biopreservatives and their action against the growth of spoilage microbes. Meat and fermented meat products are prone to microbial contamination, causing health risks, as well as economic losses in the meat industry. The use of bacteriocin-producing LAB starter or protective cultures is suitable for fermented meats. However, although bacteriocins can be produced during meat processing, their levels are usually much lower than those achieved during in vitro fermentations under optimal environmental conditions. Thus, the direct addition of a bacteriocin food additive would be desirable. Moreover, safety and technological characteristics of the bacteriocinogenic LAB must be considered before their widespread applications. This review describes the perspectives and challenges toward the complete disclosure of new bacteriocins as effective preservatives in the production of safe and "healthy" fermented meat products.

Potential characterization of yeasts isolated from Kazak artisanal cheese to produce flavoring compounds

Cheese is a typical handcrafted fermented food in Kazak minority from the Uighur Autonomy Region in China and Central Asia. Among the microbial community that is responsible for Kazak cheese fermentation, yeasts play important role in flavor formation during ripening. To develop ripening cultures, we isolated 123 yeasts from 25 cheese products in Kazak, and identified 87 isolates by the D1/D2 domain of the large subunit rRNA gene sequence. Pichia kudriavzevii was the dominant yeast in Kazak cheese, followed by Kluyveromyces marxianus and Kluyveromyces lactis. Of these, the ability to exhibit enzyme of dominant isolates and contribution to the typical flavor of cheeses was assessed. Enzyme producing yeast strains were inoculated in Hazak cheese‐like medium and volatile compounds were identified by head space solid phase micro extraction coupled to gas chromatography and mass spectroscopy. Pichia kudriavzevii N‐X displayed the strongest extracellular proteolytic and activity on skim milk agar and produced a range of aroma compounds (ethanol, ethyl acetate, 3‐methylbutanol, and acetic acid) for Kazak cheese flavor, could be explored as ripening cultures in commercial production of Kazak cheeses.

Screening of Debaryomyces hansenii Strains for Flavor Production under a Reduced Concentration of Nitrifying Preservatives Used in Meat Products

A total of 15 Debaryomyces hansenii strains from different food origins were genetically characterized and tested on a culture medium resembling the composition of fermented sausages but different concentrations of nitrifying preservatives. Genetic typing of the D. hansenii strains revealed two levels of discrimination: isolation source or strain specific. Different abilities to proliferate on culture media containing different concentrations of nitrate and nitrite, as sole nitrogen sources and in the presence of amino acids, were observed within D. hansenii strains. Overall metabolism of amino acids and generation of aroma compounds were related to the strain origin of isolation. The best producers of branched aldehydes and ethyl ester compounds were strains isolated from pork sausages. Strains from cheese and llama sausages were good producers of ester compounds and branched alcohols, while vegetable strains produced mainly acid compounds. Nitrate and nitrite reduction affected in different ways the production of volatiles by D. hansenii.

Yeast inoculation as a strategy to improve the physico-chemical and sensory properties of reduced salt fermented sausages produced with entire male fat

Yeast inoculation of dry fermented sausages manufactured with entire male fat was evaluated as a strategy to improve sausage quality. Four different formulations with entire male/gilt back fat and inoculated/non-inoculated with Debaryomyces hansenii were manufactured. The use of entire male back fat produced the highest weight losses, hardness and chewiness in dry sausages. Consumers clearly distinguished samples according to drying time and D. hansenii inoculation while the use of entire/gilt back fat was not highly perceived. The presence of androstenone and skatole was close to their sensory thresholds. Androstenone was not degraded during the process but skatole was affected by yeast inoculation. D. hansenii growth on the surface regulated water release during ripening, reduced hardness and chewiness in entire male sausages and resulted with similar texture to gilt sausages. Yeast inoculation inhibited lipid oxidation providing fruity odours and less oxidized fatty sausages in the sensory analysis. The effectiveness of yeast to mask boar taint was demonstrated by sensory analysis.

Development of species-specific primers for rapid identification of Debaryomyces hansenii

In this work, we developed a specific PCR assay for Debaryomyces hansenii strains that uses a putative homologous PAD1 region (729 bp) present in this yeast species as a target. The amplification of this sequence with the D. hansenii specific primer pair (DhPADF/DhPADR) was found to be a rapid, specific and an affordable method enabling identification of D. hansenii from other yeast strains. Primers were tested in almost 100 strains, 49 strains from Type Culture Collection belonging to the genus Debaryomyces and to other yeast species commonly found in foods or related genera. These primers were able to discriminate between closely related species of Debaryomyces, such as Debaryomyces fabryi and Debaryomyces subglobosus, with a 100% detection rate for D. hansenii. Also, the method was tested in 45 strains from different foods. Results confirmed the specificity of the PCR method and detected two earlier misidentifications of D. hansenii strains obtained by RFLP analysis of the 5.8S ITS rDNA region. Subsequently we confirmed by sequencing the D1/D2 domain of 26S rDNA that these strains belonged to D. fabryi. We call attention in this work to the fact that the RFLPs of the 5.8S ITS rDNA profiles of D. hansenii, D. fabryi and D. subglobosus are the same and this technique will thus lead to incorrect identifications.

Application of ISSR-PCR for rapid strain typing of Debaryomyces hansenii isolated from dry-cured Iberian ham

Yeast populations of dry-cured Iberian ham isolated from seven industries in the province of Badajoz were characterized by ISSR-PCR using the (CAG)4 primer and PCR-RFLP of the ITS1-5.8S rRNA-ITS2 fragment, and identified by DNA sequencing. A total of 242 isolates were analyzed, indicating the primary species present was Debaryomyces hansenii at 80.9% of the isolates followed by Candida zeylanoides at 10.3% of the isolates. The remainders of isolates were identified as Yamadazyma triangularis, Sporobolomyces roseus, Meyerozyma guilliermondii, Rhodotorula slooffiae, and Cryptococcus victoriae. The ISSR-PCR method was a fast and reliable method which was able to discriminate species at a level comparable to restriction analyses of the ITS1-5.8S rRNA-ITS2 region. This method allowed for strain typing of D. hansenii, yielding 29 different PCR patterns within 196 isolates. Moreover, ISSR-PCR using the (CAG)4 primer indicated that this technique could be a promising tool for rapid discrimination of yeast starter cultures and spoilage species in dry-cured Iberian ham.