The microbial ecology of a typical Italian salami during its natural fermentation

Effect of the Addition of Dandelion (Taraxacum officinale) on the Protein Profile, Antiradical Activity, and Microbiological Status of Raw-Ripening Pork Sausage

The study evaluated the effect of adding dandelion extract on the characteristics of raw-ripening pork sausages while reducing the nitrite addition from 150 to 80 mg/kg. The sausages were made primarily from pork ham (80%) and pork jowl (20%). The process involved curing, preparing the meat stuffing, forming the links, and then subjecting the sausages to a 21-day ripening period. Physicochemical parameters such as pH, water activity, and oxidation-reduction potential were compared at the beginning of production and after the ripening process. The study also examined the impact of ripening on protein metabolism in pork sausages and compared the protein profiles of different sausage variants. The obtained research results indicate that dandelion-leaf extract (Taraxacum officinale) were rich in phenolic acids, flavonoids, coumarins, and their derivatives (LC-QTOF-MS method). Antiradical activity test against the ABTS+* and DPPH radical, and the TBARS index, demonstrated that addition of dandelion (0.5-1%) significantly improved the oxidative stability of raw-ripening sausages with nitrite content reduction to 80 mg/kg. A microbiological evaluation of the sausages was also carried out to assess the correctness of the ripening process. The total number of viable bacteria, lactic acid bacteria, and coliforms were evaluated and subsequently identified by mass spectrometry.

Effect of probiotic Bacillus cereus DM423 on the flavor formation of fermented sausage

Insufficient protein and fat hydrolysis capacity of lactic acid bacteria (LAB) limit the flavor formation of fermented sausage. Bacillus is known for its substantial expression of proteases and lipases. However, its application in meat fermentation remains underexplored. In this study, a strain of probiotic Bacillus cereus (B. cereus DM423) was employed as a co-starter to improve the quality of Lactiplantibacillus plantarum (L. plantarum HH-LP56) fermented sausage. The addition of DM423 did not interfere with regular fermentation, but it significantly improved the flavor, as measured by electronic tongue and electronic nose. Further analyses using SDS-PAGE and thin-layer chromatography observed enhanced hydrolysis of protein and fat in sausages in which DM423 was involved in fermentation. GC-IMS identified DM423 mediated upregulation of various flavor compounds, including esters, ketones, furans, and branched-chain fatty acids. In addition, genomic de novo sequencing revealed that DM423 carried an abundance of genes associated with proteolysis, lipolysis, and the production of flavor substances, whereas HH-LP56 lacked these genes. Overall, this study finds that B. cereus DM423 can promote flavor formation in fermented sausages. It may illuminate a promising direction for the development of sausage co-starters from a wider microbial pool.

Isolation of Debaryomyces hansenii and selection of an optimal strain to improve the quality of low-grade beef rump (middle gluteal) during dry aging

OBJECTIVE

The objective of this study was to evaluate the effect of Debaryomyces hansenii isolated from dry-aged beef on the tenderness and flavor attributes of low-grade beef during dry aging.

METHODS

Five D. hansenii strains were isolated from dry-aged beef samples. The rump of low-grade beef was inoculated with individual D. hansenii isolates and subjected to dry aging for 4 weeks at 5°C and 75% relative humidity. Microbial contamination levels, meat quality attributes, and flavor attributes in the dry-aged beef were measured.

RESULTS

Of the five isolates, the shear force of dry-aged beef inoculated with SMFM201812-3 and SMFM201905-5 was lower than that of control samples. Meanwhile, all five isolates increased the total free amino acid, glutamic acid, serine, glycine, alanine, and leucine contents in dry-aged beef. In particular, the total fatty acid, palmitic acid, and oleic acid contents in samples inoculated with D. hansenii SMFM201905-5 were higher than those in control samples.

CONCLUSION

These results indicate that D. hansenii SMFM201905-5 might be used to improve the quality of beef during dry aging.

Perspectives on the Probiotic Potential of Indigenous Moulds and Yeasts in Dry-Fermented Sausages

The role of indigenous fungi in the appropriate development of sensory properties and the safety of dry-fermented sausages has been widely established. Nonetheless, their applications as probiotic agents have not been elucidated in such products yet, despite their promising functional features. Thus, it should be interesting to evaluate the probiotic potential of native Debaryomyces hansenii isolates from dry-fermented sausages and their application in the meat industry, because it is the most frequently isolated yeast species from these foodstuffs and its probiotic effects for animals as well as its possible probiotic activity for human beings have been demonstrated. Within the functional ability of foodborne yeasts, anti-inflammatory, antioxidant, antimicrobial, antigenotoxic, and immunomodulatory properties have been reported. Similarly, the use of dry-fermented sausages as vehicles for probiotic moulds remains a challenge because the survival and development of moulds in the gastrointestinal tract are still unknown. Nevertheless, some moulds have been isolated from faeces possibly from their spores as a form of resistance. Additionally, their beneficial effects on animals and humans, such as the decrease in lipid content and the anti-inflammatory activity, have been reported, although they seem to be more related to their postbiotic capacity due to the generated bioactive compounds with profunctional attributes than to their role as probiotics. Therefore, further studies providing knowledge useful for generating dry-fermented sausages with improved functionality are fully necessary.

Changes in N-nitrosamines, residual nitrites, lipid oxidation, biogenic amines, and microbiota in Chinese sausages following treatment with tea polyphenols and their palmitic acid–modified derivatives

This study aimed to investigate the effects of tea polyphenol (TP), epigallocatechin gallate (EGCG), and their palmitic acid-modified derivatives palmitoyl-TP (pTP) and palmitoyl-EGCG (pEGCG) on the accumulation of N-nitrosamine and biogenic amines (BAs), residual nitrites, and lipid oxidation in Chinese sausages. The microorganisms, color, and texture properties of sausages were evaluated. TP, EGCG, pTP, or pEGCG significantly inhibited the accumulation of N-nitrosodimethylamine (NDMA) and BAs, residual nitrites, and lipid oxidation, but enhanced the redness, hardness, and chewiness of sausages. The concentration of NDMA in sausages was reduced by 58.11%, 63.51%, 36.49%, and 44.59%, respectively, after treatment with TP, EGCG, pTP, and pEGCG. Both EGCG and pEGCG exhibited excellent inhibitory effects on the predominant BAs, including putrescine, tyramine, cadaverine, histamine, and 2-phenylethylamine. Palmitoyl-EGCG was found to be the strongest inhibitor of lipid oxidation. Besides, the four antioxidants weakly affected the population of total aerobic bacteria and lactic acid bacteria but totally suppressed the growth of undesirable Enterobacteriaceae. The principal component and correlation analyses proved that BAs, nitrites, lipid oxidation, and microbiota were responsible for the formation of NDMA. The results indicated that palmitic acid-modified TPs and similar derivatives might serve as potential preservatives to improve the safety and quality of fermented meat 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.

Freeze-Dried Powder of Fermented Chili Paste-New Approach to Cured Salami Production

Fermented chili powders were obtained through the freeze-drying of fermented chili pastes and used as a condiment, acidifier, antioxidant, colorant, and microbial starter carrier in fermented salami production. Fermented chili powders were examined regarding carbohydrates, organic acids, vitamin C, phenolic compounds, carotenoids, and aroma profile. High concentrations of lactic (10.57-12.20%) and acetic acids (3.39-4.10%) were recorded. Vitamin C content was identified in the range of 398-1107 mg/100 g, with maximum values for C. annuum cv. Cayenne chili powder. Phenolic compounds showed values between 302-771 mg/100 g. Total carotenoid content was identified between 544-2462 µg/g, with high concentrations of capsanthin esters. Aroma profile analysis evidenced specific compounds (1-hexanol, 2-hexanol, hexenal, E-2-hexenal) with sensory importance and a more complex spectrum for Capsicum chinense cultivar. Plant-specific lactic acid bacteria showed dominance both in fermented chili paste, chili powder, and salami. Lactic and acetic acids from the fermented chili powder reduced the pH of the filling immediately, having a stabilizing effect on the meat. Nor molds or pathogens were identified in outer limits. Based on these results, fermented chili powders could be used as starter carriers in the production of fermented meat products for exceptional sensory properties and food safety management.

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

Interaction and Application of Molds and Yeasts in Chinese Fermented Foods

Fermentation is an ancient food preservation and processing technology with a long history of thousands of years, that is still practiced all over the world. Fermented foods are usually defined as foods or beverages made by controlling the growth of microorganisms and the transformation of raw and auxiliary food components, which provide the human body with many beneficial nutrients or health factors. As fungus widely used in traditional Chinese fermented foods, molds and yeasts play an irreplaceable role in the formation of flavor substances and the production of functional components in fermented foods. The research progress of molds and yeasts in traditional Chinese fermented foods from traditional to modern is reviewed, including the research on the diversity, and population structure of molds and yeasts in fermented foods. The interaction between fermenting mold and yeast and the latest research results and application development prospects of related industries were discussed.

Inactivation of Listeria monocytogenes and Salmonella spp. in Milano-Type Salami Made with Alternative Formulations to the Use of Synthetic Nitrates/Nitrites

During the manufacture of Italian salami, a traditional meat product, a sequence of hurdles like meat fermentation, air-drying, and long ripening processes are generally sufficient to inhibit the growth of most pathogens. Furthermore, Italian salami are traditionally produced by adding synthetic nitrates/nitrites to raw meat with safety and technological aims, even if controversial opinions about their use still remain, particularly in relation to the consumer demand for natural food products. In this context, the aim of the study was to investigate the inactivation of Listeria monocytogenes and Salmonella spp. during the manufacturing process of Milano-type salami made with different formulations to evaluate the contribution of the hurdles and the vegetable or synthetic additives on the inactivation of pathogens. Thus, a challenge study was performed dividing ca. 400 kg of Milano-type salami batter into three batches: Batch (A) without nitrates/nitrites; Batch (B) with vegetable nitrates, and Batch (C) with synthetic nitrates/nitrites. The batches were separately inoculated with L. monocytogenes and Salmonella spp. and the pathogens’ survival was evaluated during the fermentation, draining, and 70-day ripening of the Milano-type salami. The pathogen counts decreased in all tested conditions, even though the highest inactivation of L. monocytogenes and Salmonella spp. (p < 0.05) was observed when nitrates or nitrites were added to the batter. This study shows how the safety of these products cannot exclude the aspect of the hurdle technology during the process, which plays a major role in the reduction of pathogens, but additives like nitrates and nitrites allow for a greater margin of safety. Thus, further studies are needed to validate the use of natural compounds as alternatives to conventional preservatives in meat products. These results may provide new information to support food business operators in producing traditional foods with alternative preservatives and competent authorities in verifying the safety of the products made with natural compounds, and to control the process parameters responsible for the synergistic effect against pathogens such as L. monocytogenes and Salmonella spp.

The Carbohydrate Metabolism of Lactiplantibacillus plantarum

Lactiplantibacillus plantarum has a strong carbohydrate utilization ability. This characteristic plays an important role in its gastrointestinal tract colonization and probiotic effects. L. plantarum LP-F1 presents a high carbohydrate utilization capacity. The genome analysis of 165 L. plantarum strains indicated the species has a plenty of carbohydrate metabolism genes, presenting a strain specificity. Furthermore, two-component systems (TCSs) analysis revealed that the species has more TCSs than other lactic acid bacteria, and the distribution of TCS also shows the strain specificity. In order to clarify the sugar metabolism mechanism under different carbohydrate fermentation conditions, the expressions of 27 carbohydrate metabolism genes, catabolite control protein A (CcpA) gene ccpA, and TCSs genes were analyzed by quantitative real-time PCR technology. The correlation analysis between the expressions of regulatory genes and sugar metabolism genes showed that some regulatory genes were correlated with most of the sugar metabolism genes, suggesting that some TCSs might be involved in the regulation of sugar metabolism.

Autochthonous fungi are central components in microbial community structure in raw fermented sausages

Raw meat sausage represents a unique ecological niche rich in nutrients for microbial consumption, making it particularly vulnerable to microbial spoilage. Starter cultures are applied to improve product stability and safety as well as flavour characteristics. However, the influence of starter cultures on microbial community assembly and succession throughout the fermentation process is largely unknown. In particular the effect on the fungal community has not yet been explored. We evaluate the microbiological status of four different raw meat sausages using high‐throughput 16S rRNA gene and ITS2 gene sequencing. The objective was to study temporal changes of microbial composition during the fermentation process and to identify potential keystone species that play an important role within the microbial community. Our results suggest that fungi assigned to the species Debaryomyces hansenii and Alternaria alternata play a key role in microbial community dynamics during fermentation. In addition, bacteria related to the starter culture Lactobacillus sakei and the spoilage‐associated genera Acinetobacter, Pseudomonas and Psychrobacter are central components of the microbial ecosystem in raw fermented sausages. Elucidating the exact role and interactions of these microorganisms has the potential to have direct impacts on the quality and safety of fermented foods.

Mediterranean Spontaneously Fermented Sausages: Spotlight on Microbiological and Quality Features to Exploit Their Bacterial Biodiversity

The wide array of spontaneously fermented sausages of the Mediterranean area can represent a reservoir of microbial biodiversity and can be an important source of new technological and functional strains able to preserve product properties, counteracting the impoverishment of their organoleptic typical features due to the introduction of commercial starter cultures. We analysed 15 artisanal salamis from Italy, Spain, Croatia and Slovenia to evaluate the microbiota composition, through culture-dependent and culture-independent techniques (i.e., metagenomic analysis), chemical-physical features, biogenic amines and aroma profile. The final pH varied according to origin and procedures (e.g., higher pH in Italian samples due to long ripening and mold growth). Lactic acid bacteria (LAB) and coagulase-negative cocci (CNC) were the dominant population, with highest LAB counts in Croatian and Italian samples. Metagenomic analysis showed high variability in qualitative and quantitative microbial composition: among LAB, Latilactobacillus sakei was the dominant species, but Companilactobacillus spp. was present in high amounts (45-55% of the total ASVs) in some Spanish sausages. Among staphylococci, S. epidermidis, S. equorum, S. saprophyticus, S. succinus and S. xylosus were detected. As far as biogenic amines, tyramine was always present, while histamine was found only in two Spanish samples. These results can valorize the bacterial genetic heritage present in Mediterranean products, to find new candidates of autochthonous starter cultures or bioprotective agents.

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.

Strain diversity of plant-associated Lactiplantibacillus plantarum

Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is a lactic acid bacteria species found on plants that is essential for many plant food fermentations. In this study, we investigated the intraspecific phenotypic and genetic diversity of 13 L. plantarum strains isolated from different plant foods, including fermented olives and tomatoes, cactus fruit, teff injera, wheat boza and wheat sourdough starter. We found that strains from the same or similar plant food types frequently exhibited similar carbohydrate metabolism and stress tolerance responses. The isolates from acidic, brine‐containing ferments (olives and tomatoes) were more resistant to MRS adjusted to pH 3.5 or containing 4% w/v NaCl, than those recovered from grain fermentations. Strains from fermented olives grew robustly on raffinose as the sole carbon source and were better able to grow in the presence of ethanol (8% v/v or sequential exposure of 8% (v/v) and then 12% (v/v) ethanol) than most isolates from other plant types and the reference strain NCIMB8826R. Cell free culture supernatants from the olive‐associated strains were also more effective at inhibiting growth of an olive spoilage strain of Saccharomyces cerevisiae. Multi‐locus sequence typing and comparative genomics indicated that isolates from the same source tended to be genetically related. However, despite these similarities, other traits were highly variable between strains from the same plant source, including the capacity for biofilm formation and survival at pH 2 or 50°C. Genomic comparisons were unable to resolve strain differences, with the exception of the most phenotypically impaired and robust isolates, highlighting the importance of utilizing phenotypic studies to investigate differences between strains of L. plantarum. The findings show that L. plantarum is adapted for growth on specific plants or plant food types, but that intraspecific variation may be important for ecological fitness and strain coexistence within individual habitats.

Microbial communities and volatile profile of Queijo de Azeitão PDO cheese, a traditional Mediterranean thistle-curdled cheese from Portugal

The production of ovine or caprine milk cheeses with thistle rennet is a common practice in the Mediterranean basin. The aim of the present study was to obtain information on bacteria and yeast communities harboured by Queijo de Azeitão PDO cheese through viable counting and, for the first time, via metataxonomic analysis. Moreover, solid phase microextraction (SPME) technique was applied to characterize Queijo de Azeitão PDO cheese volatile compounds. Nine cheese samples were collected from three different artisan producers located in Portugal. The results of physico-chemical analyses showed significant differences between producers, with mean values ranging from 5.40 ± 0.25 (Producer 1) to 6.00 ± 0.22 (Producer 2). As for TTA, Producer 1 showed the highest mean value attesting at 18.04 ± 6.57 mL of 0.1 M NaOH used to reach pH 8.3. Regarding lactic acid concentration, Producer 1 showed the highest mean value attesting at 0.488 ± 0.106 g 100 g^-1, whereas, for acetic acid, no significant differences were evidenced among producers with values comprised between 0.141 ± 0.021 g 100 g^-1 and 0.245 ± 0.016 g 100 g^-1. No significant differences were observed between overall mean values of the three producers for viable counts of presumptive lactococci, thermophilic cocci, presumptive lactobacilli, thermophilic lactobacilli and total mesophilic aerobes with values in the order of 7-8 log cfu g^-1. Moreover, no significant differences were evidenced for viable counts of coagulase-negative cocci, enterococci, Enterobacteriaceae and Pseudomonadaceae. As for eumycetes, cheeses from Producer 1 showed the lowest mean value (2.78 ± 2.42 log cfu g^-1) in respect with values detected in cheeses from Producer 2 and 3. Concerning microbiota and mycobiota of the analyzed cheeses, the alpha diversity index did not show any significant difference between the three producers in terms of composition and complexity of the microbial population. A simple composition was apparently shared by the three producers, whose cheese manufactures were dominated by the presence of Leuconostoc mesenteroides (37% of the relative frequency in average), Lactococcus lactis (29%), Lacticaseibacillus zeae (4.7%), Lentilactobacillus kefiri (4.4%), Serratia spp. (3.5%), Lactiplantibacillus plantarum (2.7%), and Latilactobacillus sakei (2.5%). The mycobiota composition showed the neat dominance of Yarrowia lipolytica (46.7% of the relative frequency in average), followed by Candida ethanolica (13.6%), Kurtzmaniella zeylanoides (9.4%), Geotrichum candidum (8.8%), Galactomyces geotrichum (8.7%), Kluyveromyces lactis (3.5%), and Geotrichum silvicola (2.7%). The volatile profile analysis allowed 24 different compounds to be identified: 7 acids, 7 esters, 4 alcohols, 3 ketones, 2 aromatic hydrocarbons, and 1 aldehyde. The most represented volatile organic compounds (VOCs) were 2-butanone, butanoic acid and hexanoic acid. A positive correlation between Len. kefiri and hexanoic acid and isopentyl isobutyrate was observed (P < 0.05), whereas Y. lipolytica displayed the highest number of positive correlations with 3-methyl-butanal, 2-pentanone and 2-pentanol (P < 0.05). To the authors' knowledge, this is the very first detection of Len. kefiri in a raw ewe's milk cheese coagulated with vegetable rennet.

Mycobiota dynamics and mycotoxin detection in PGI Salame Piemonte

AIMS

The complex mycobiota that colonizes traditional fermented sausages plays an important role in the organoleptic properties of such products. The aim of the present study was to investigate fungal diversity and mycotoxin production during maturation of PGI Salame Piemonte.

METHODS AND RESULTS

Casing and meat samples were collected at five sampling times from three different batches produced in the same factory and analysed using culture-dependent and independent approaches. Penicillium nalgiovense, which was deliberately inoculated, and Debaryomyces hansenii were the most dominant taxa in casings. Several other fungi mainly belonging to Penicillium crustosum, Penicillium glabrum, Penicillium nordicum, Cladosporium spp., Candida sake, Candida zeylanoides and Yarrowia divulgata were also identified. The casing mycobiota was compared to that of the meat using a metataxonomic approach and a higher fungal diversity was observed in meat as compared to casings. Mycotoxins and penicillin G were monitored using QTOF LC-MS and only trace amounts of roquefortine C were detected in two batches.

CONCLUSIONS

The present study highlighted the diversity of Salame Piemonte mycobiota and the important contribution of autochthonous fungi to its diversity. The absence of mycotoxins and penicillin G confirmed the high hygienic quality of the studied product regarding fungal and mycotoxin contamination.

SIGNIFICANCE AND IMPACT OF THE STUDY

For the first time, this study provides insights about Salame Piemonte mycobiota, which together with the bacterial microbiota and Salame Piemonte process specifications, are responsible for the product organoleptic properties.

Fungal community succession and volatile compound dynamics in Harbin dry sausage during fermentation

This study investigated the fungal community succession and volatile compound dynamics of Harbin dry sausage during a twelve-day fermentation using high-throughput internal transcribed spacer amplicon sequencing and headspace solid-phase microextraction gas chromatography-mass spectrometry. Aspergillus pseudoglaucus was found to be the primary species in the sausages during fermentation, whereas Lasiodiplodia theobromae, Alternaria alternata, Aspergillus caesiellus, and Trichosporon asahii were also prevalent. Additionally, a total of 72 volatile compounds were identified in the dry sausages, of which 24 key compounds (odor activity value > 1) dominated flavor development, including 3 aldehydes, 1 ketone, 4 alcohols, 9 esters, 4 alkenes, and 3 other compounds. Furthermore, correlation analysis suggested that most of the core fungi were positively correlated with the key volatile compounds, particularly A. pseudoglaucus, Aspergillus gracilis, Trichosporon caseorum, Debaryomyces hansenii, and T. asahii. Our findings provide novel insights into the fungal ecology and flavor development of Harbin dry sausages.

Shifts in autochthonous microbial diversity and volatile metabolites during the fermentation of chili pepper (Capsicum frutescens L.)

To reveal the potential of core bacterial and fungal communities for aroma formation in the fermentation of chili pepper, shifts in microbial diversity and volatile metabolites during the 32-day fermentation process were measured using high-throughput sequencing and gas chromatography-mass spectrometry. Rosenbergiella and Staphylococcus were the dominant bacterial genera, where Hyphopichia and Kodamaea were the most abundant fungi, in fermented chili pepper. Sixteen differential volatile metabolites were detected in fermented and unfermented samples using differential metabolomics analysis. Nine strains from the genera Hyphopichia, Staphylococcus, Rosenbergiella, and Bacillus were isolated from fermented chili pepper. The correlation of dominant microorganisms with key odorants by Spearman correlation and two-way orthogonal partial least squares analysis indicated that Hyphopichia exhibited a significant positive correlation with the formation of 11 key odorants. These findings enhance our understanding of the core functional bacterial and fungal genera involved in the production of desirable flavors in fermented chili pepper.

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.

The life and times of yeasts in traditional food fermentations

Yeasts are eukaryotic microorganisms which have a long history in the biotechnology of food production, as they have been used since centuries in bread-making or in the production of alcoholic beverages such as wines or beers. Relative to this importance, a lot of research has been devoted to the study of yeasts involved in making these important products. The role of yeasts in other fermentations in association with other microorganisms - mainly lactic acid bacteria - has been relatively less studied, and often it is not clear if yeasts occurring in such fermentations are contaminants with no role in the fermentation, spoilage microorganisms or whether they actually serve a technological or functional purpose. Some knowledge is available for yeasts used as starter cultures in fermented raw sausages or in the production of acid curd cheeses. This review aimed to summarize the current knowledge on the taxonomy, the presence and potential functional or technological roles of yeasts in traditional fermented plant, dairy, fish and meat fermentations.

Unveiling hákarl: A study of the microbiota of the traditional Icelandic fermented fish

Hákarl is produced by curing of the Greenland shark (Somniosus microcephalus) flesh, which before fermentation is toxic due to the high content of trimethylamine (TMA) or trimethylamine N-oxide (TMAO). Despite its long history of consumption, little knowledge is available on the microbial consortia involved in the fermentation of this fish. In the present study, a polyphasic approach based on both culturing and DNA-based techniques was adopted to gain insight into the microbial species present in ready-to-eat hákarl. To this aim, samples of ready-to-eat hákarl were subjected to viable counting on different selective growth media. The DNA directly extracted from the samples was further subjected to Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and 16S amplicon-based sequencing. Moreover, the presence of Shiga toxin-producing Escherichia coli (STEC) and Pseudomonas aeruginosa was assessed via qualitative real-time PCR assays. pH values measured in the analyzed samples ranged from between 8.07 ± 0.06 and 8.76 ± 0.00. Viable counts revealed the presence of total mesophilic aerobes, lactic acid bacteria and Pseudomonadaceae. Regarding bacteria, PCR-DGGE analysis highlighted the dominance of close relatives of Tissierella creatinophila. For amplicon sequencing, the main operational taxonomic units (OTUs) shared among the data set were Tissierella, Pseudomonas, Oceanobacillus, Abyssivirga and Lactococcus. The presence of Pseudomonas in the analyzed samples supports the hypothesis of a possible role of this microorganism on the detoxification of shark meat from TMAO or TMA during fermentation. Several minor OTUs (<1%) were also detected, including Alkalibacterium, Staphylococcus, Proteiniclasticum, Acinetobacter, Erysipelothrix, Anaerobacillus, Ochrobactrum, Listeria and Photobacterium. Analysis of the yeast and filamentous fungi community composition by PCR-DGGE revealed the presence of close relatives of Candida tropicalis, Candida glabrata, Candida parapsilosis, Candida zeylanoides, Saccharomyces cerevisiae, Debaryomyces, Torulaspora, Yamadazyma, Sporobolomyces, Alternaria, Cladosporium tenuissimum, Moristroma quercinum and Phoma/Epicoccum, and some of these species probably play key roles in the development of the sensory qualities of the end product. Finally, qualitative real-time PCR assays revealed the absence of STEC and Pseudomonas aeruginosa in all of the analyzed samples.

Biocontrol of aflatoxigenic Aspergillus parasiticus by native Debaryomyces hansenii in dry-cured meat products

Dry-cured meat products, such as dry-cured ham or dry-fermented sausages, are characterized by their particular ripening process, where a mould population grows on their surface. Some of these moulds are hazardous to the consumers because of their ability to produce mycotoxins including aflatoxins (AFs). The use of native yeasts could be considered a potential strategy for controlling the presence of AFs in dry-cured meat products. The aim of this work was to evaluate the antagonistic activity of two native Debaryomyces hansenii strains on the relative growth rate and the AFs production in Aspergillus parasiticus. Both D. hansenii strains significantly reduced the growth rates of A. parasiticus when grown in a meat-model system at different water activity (a_w) conditions. The presence of D. hansenii strains caused a stimulation of AFs production by A. parasiticus at 0.99 a_w. However, at 0.92 a_w the yeasts significantly reduced the AFs concentration in the meat-model system. The relative expression levels of the aflR and aflS genes involved in the AFs biosynthetic pathway were also repressed at 0.92 a_w in the presence of both D. hansenii strains. These satisfactory results were confirmed in dry-cured ham and dry-fermented sausage slices inoculated with A. parasiticus, since both D. hansenii strains significantly reduced AFs amounts in these matrices. Therefore, both tested D. hansenii strains could be proposed as biocontrol agents within a HACCP framework to minimize the hazard associated with the presence of AFs in dry-cured meat products.

Effect of Ground Chopi (Zanthoxylum piperitum) on Physicochemical Traits and Microbial Community of Chicken Summer Sausage during Manufacture

Changes in microbial community and physicochemical traits of chicken summer sausage made from spent layer thigh added with different level (0%, 0.1%, 0.3%, and 0.5% w/w) of ground chopi (Zanthoxylum piperitum) during manufacture were analyzed. The microbial community was profiled and analyzed by sequencing 16S rRNA gene using Illumina MiSeq. Samples were taken from raw sausage batter, after 15 h of fermentation, 8 h of cooking including cooling down, and 7 d of drying. The final pH of the sausage was reduced by the addition of ground chopi. However, no clear effect on water activity was observed. Ground chopi inhibited the development of red curing color after fermentation as it exhibited antimicrobial effect. However, the effect on species richness and microbial composition after cooking was unclear. Ground chopi delayed lipid oxidation during manufacture and the effect was dependent on the addition level. Fermentation reduced the species richness with a dominancy of lactic acid bacteria. The profile of microbiota in the raw batter was different from other stages, while the closest relationship was observed after cooking and drying. Proteobacteria was predominant, followed by Firmicutes and Bacteroidetes in raw samples. Firmicutes became dominating after fermentation and so forth, whereas other predominant phylum decreased. At genus level, unclassified Lactobacillales was the most abundant group found after fermentation and so forth. Therefore, the overall microbial composition aspects were mainly controlled during fermentation by the abundance of lactic acid bacteria, while bacterial counts and lipid oxidation were controlled by cooking and the addition of ground chopi.

Metagenomic analysis and the functional profiles of traditional fermented pork fat 'sa-um' of Northeast India

Fermented pork fat (sa-um) is traditionally and extensively consumed in Northeast Indian region for several decades. However, no scientific reports are available regarding its nutritional value as well as its potential health risks. The objective of this work was essentially the characterization of sa-um using a polyphasic approach, viz., physicochemical, electrospray ionization-mass spectrometry (ESI+-MS) and metagenomic analysis in order to gain an understanding of the nutrient contents and microbial population diversity. On a dry weight basis, about 91% fat, 2% carbohydrate and 0.70% protein were present. ESI+-MS analysis of sa-um revealed the presence of various polar and neutral lipids corresponding to monoacylglyceride, diacylglyceride and triacylglyceride species. The dominant bacterial phyla were Firmicutes, Proteobacteria and Bacteroidetes. A total of 72 bacterial genera were identified, largely abundant with Clostridium species including C. butyricum, C. citroniae, C. methylpentosum, C. perfringens, C. saccharogumia and C. tetani. The imputed functional profiles of bacterial communities were predominantly involved in energy, carbohydrate and amino acid metabolisms. Furthermore, this study deduces the presence of pro-inflammatory molecules as well as antibiotic resistance genes associated with the bacterial families such as Bacillaceae, Bacteroidaceae, Clostridiaceae, Corynebacteriaceae and Enterobacteriaceae which might be a major health concern for the sa-um consuming population.

Fermented Foods as a Dietary Source of Live Organisms

The popularity of fermented foods and beverages is due to their enhanced shelf-life, safety, functionality, sensory, and nutritional properties. The latter includes the presence of bioactive molecules, vitamins, and other constituents with increased availability due to the process of fermentation. Many fermented foods also contain live microorganisms that may improve gastrointestinal health and provide other health benefits, including lowering the risk of type two diabetes and cardiovascular diseases. The number of organisms in fermented foods can vary significantly, depending on how products were manufactured and processed, as well as conditions and duration of storage. In this review, we surveyed published studies in which lactic acid and other relevant bacteria were enumerated from the most commonly consumed fermented foods, including cultured dairy products, cheese, fermented sausage, fermented vegetables, soy-fermented foods, and fermented cereal products. Most of the reported data were based on retail food samples, rather than experimentally produced products made on a laboratory scale. Results indicated that many of these fermented foods contained 105-7 lactic acid bacteria per mL or gram, although there was considerable variation based on geographical region and sampling time. In general, cultured dairy products consistently contained higher levels, up to 109/mL or g. Although few specific recommendations and claim legislations for what constitutes a relevant dose exist, the findings from this survey revealed that many fermented foods are a good source of live lactic acid bacteria, including species that reportedly provide human health benefits.

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.

Lactobacillus plantarum with Functional Properties: An Approach to Increase Safety and Shelf-Life of Fermented Foods

Lactobacillus plantarum (widespread member of the genus Lactobacillus) is one of the most studied species extensively used in food industry as probiotic microorganism and/or microbial starter. The exploitation of Lb. plantarum strains with their long history in food fermentation forms an emerging field and design of added-value foods. Lb. plantarum strains were also used to produce new functional (traditional/novel) foods and beverages with improved nutritional and technological features. Lb. plantarum strains were identified from many traditional foods and characterized for their systematics and molecular taxonomy, enzyme systems (α-amylase, esterase, lipase, α-glucosidase, β-glucosidase, enolase, phosphoketolase, lactase dehydrogenase, etc.), and bioactive compounds (bacteriocin, dipeptides, and other preservative compounds). This review emphasizes that the Lb. plantarum strains with their probiotic properties can have great effects against harmful microflora (foodborne pathogens) to increase safety and shelf-life of fermented foods.

RNA-Based Amplicon Sequencing Reveals Microbiota Development during Ripening of Artisanal versus Industrial Lard d'Arnad

Valle d'Aosta Lard d'Arnad is a protected designation of origin (PDO) product produced from fat of the shoulder and back of heavy pigs. Its manufacturing process can be very diverse, especially regarding the maturation temperature and the NaCl concentration used for the brine; thereby, the main goal of this study was to investigate the impact of those parameters on the microbiota developed during curing and ripening. Three farms producing Lard d'Arnad were selected. Two plants, reflecting the industrial process characterized either by low maturation temperature (plant A [10% NaCl, 2°C]) or by using a low NaCl concentration (plant B [2.5% NaCl, 4°C]), were selected, while the third was characterized by an artisanal process (plant C [30% NaCl, 8°C]). Lard samples were obtained at time 0 and after 7, 15, 30, 60, and 90 days of maturation. From each plant, 3 independent lots were analyzed. The diversity of live microbiota was evaluated by using classical plate counts and amplicon target sequencing of small subunit (SSU) rRNA. The main taxa identified by sequencing were Acinetobacter johnsonii, Psychrobacter, Staphylococcus equorum, Staphylococcus sciuri, Pseudomonas fragi, Brochothrix, Halomonas, and Vibrio, and differences in their relative abundances distinguished samples from the individual plants. The composition of the microbiota was more similar among plants A and B, and it was characterized by the higher presence of taxa recognized as undesired bacteria in food-processing environments. Oligotype analysis of Halomonas and Acinetobacter revealed the presence of several characteristic oligotypes associated with A and B samples.IMPORTANCE Changes in the food production process can drastically affect the microbial community structure, with a possible impact on the final characteristics of the products. The industrial processes of Lard d'Arnad production are characterized by a reduction in the salt concentration in the brines to address a consumer demand for less salty products; this can negatively affect the dynamics and development of the live microbiota and, as a consequence, can negatively impact the quality of the final product due to the higher abundance of spoilage bacteria. This study is an overview of the live microbiota that develop during lard manufacturing, and it highlights the importance of the use of traditional process to produce PDO from a spoilage perspective.

Complete genome sequence of bacteriocin-producing Lactobacillus plantarum KLDS1.0391, a probiotic strain with gastrointestinal tract resistance and adhesion to the intestinal epithelial cells

Lactobacillus plantarum KLDS1.0391 is a probiotic strain isolated from the traditional fermented dairy products and identified to produce bacteriocin against Gram-positive and Gram-negative bacteria. Previous studies showed that the strain has a high resistance to gastrointestinal stress and has a high adhesion ability to the intestinal epithelial cells (Caco-2). We reported the entire genome sequence of this strain, which contains a circular 2,886,607-bp chromosome and three circular plasmids. Genes, which are related to the biosynthesis of bacteriocins, the stress resistance to gastrointestinal tract environment and adhesive performance, were identified. Whole genome sequence of Lactobacillus plantarum KLDS1.0391 will be helpful for its applications in food industry.

Adding Value to Goat Meat: Biochemical and Technological Characterization of Autochthonous Lactic Acid Bacteria to Achieve High-Quality Fermented Sausages

Quality and safety are important challenges in traditional fermented sausage technology. Consequently, the development of a tailored starter culture based on indigenous microbiota constitutes an interesting alternative. In the present study, spontaneously fermented goat meat sausages were created and analyzed using a physicochemical and microbiological approach. Thereafter 170 lactic acid bacteria (LAB) strains were isolated and preliminary characterized by phenotypic assays. The hygienic and technological properties, and growth and fermentative potential of isolates using a goat-meat-based culture medium were evaluated. All strains proved to have bioprotective features due to their acidogenic metabolism. Almost all grew optimally in meat environments. LAB isolates presented proteolytic activity against meat proteins and enriched amino acid contents of the goat-meat-based model. The most efficient strains were four different Lactobacillus sakei isolates, as identified by genotyping and RAPD analysis. L. sakei strains are proposed as optimal candidates to improve the production of fermented goat meat sausages, creating a new added-value fermented product.

Molecular analysis of bacterial community dynamics during the fermentation of soy-daddawa condiment

Bacterial community dynamics during soy-daddawa fermentation was investigated using culture-dependent and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) molecular methods. The total titratable acidity (TTA), pH, and bacterial counts (BCs) were monitored daily during a 72-h fermentation period. Bacteria were characterized based on 16S rRNA gene sequencing. TTA ranged from 0.08 to 0.26 mg lactic acid/g, whereas pH ranged from 7.01 to 8.19. BCs increased from 3.9 to 10.61 log CFU/g. Fifty-eight isolates were obtained by culture method and clustered into seven operational taxonomic units (OTUs) at 97% sequence similarity, whereas four OTUs were obtained from the PCR-DGGE method. Taxonomic identification revealed that bacteria belonged to the genera Bacillus, Enterobacter, Enterococcus, and Staphylococcus with B. subtilis being present throughout fermentation. Medically significant isolates, including B. anthracis, Enterococcus casseliflavus, and Enterobacter hormaechei were detected. These results emphasize the need for starter culture utilization and offer a platform for starter culture screening and selection.

Complete genome sequence and description of Lactococcus garvieae M14 isolated from Algerian fermented milk

We describe using a polyphasic approach that combines proteomic by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) analysis, genomic data and phenotypic characterization the features of Lactococcus garvieae strain M14 newly isolated from the fermented milk (known as raib) of an Algerian cow. The 2 188 835 bp containing genome sequence displays a metabolic capacity to form acid fermentation that is very useful for industrial applications and encodes for two bacteriocins responsible for its eventual bioprotective properties.

Effect of Selected Starter Cultures on Physical, Chemical and Microbiological Characteristics and Biogenic Amine Content in Protected Geographical Indication Ciauscolo Salami

The aim of the study was to evaluate the biogenic amine (BA) content of Ciauscolo salami made with and without the use of a selected started culture. Two batches of salami were made following the guidelines of the Protected Geographical Indications: with and without adding a commercial starter culture made of Lactobacillus plantarum and Staphylococcus xylosus. Six samples of salami per batch were collected at different ripening times (0, 15, 30, 45 and 60 days) for physical, chemical and microbiological analyses and for the determination of BA content. No differences were recorded for physical, chemical and microbiological analyses except for Staphylococcus spp. count at the time of casing (T0) and total volatile basic nitrogen (TVBN) from 30 days (T2) to the end of the ripening time (60 days, T4). After 60 days of ripening, the use of selected starter culture significantly affected the amount of putrescine (195.15 vs 164.43 mg/100 g in salami without and with starters, respectively), cadaverine (96.95 vs 104.40 mg/100 g in salami without and with starters, respectively), histamine (81.94 vs 69.89 mg/100 g in salami without and with starters, respectively), and spermine (36.88 vs 33.57 mg/100 g in salami without and with starters, respectively). Despite significantly higher values of TVBN, the use of selected starter culture determined no significant effects on the BA content of the products.