Biodiversity and dynamics of meat fermentations: the contribution of molecular methods for a better comprehension of a complex ecosystem

New insights into the dominance of mixed fermentation of Staphylococcus cohnii and Staphylococcus saprophyticus in Chinese bacon: Complete genomic and comparative genomic perspectives

Previous studies have demonstrated that Staphylococcus cohnii WX_M8 and S. saprophyticus MY_A10 significantly enhanced the flavor of Chinese bacon in a mixed fermentation. However, due to the complexity of the processing, the contribution of the bacteria is deceptive when investigating only the phenotypic changes at the time of fermentation. In order to clarify the metabolic mechanisms of mixed fermentation, a technological characterization, whole genome and comparative genomics analysis, and metabolites were approached in this study. Results showed that differences in tolerance characteristics existed between WX_M8 and MY_A10. And the genomes of both the two strains consisted of one chromosome and four circular plasmids. Their genome sizes were 2.74 Mp and 2.62 Mp, the GC contents were 32.45% and 33.18%, and the predicted coding genes (CDS) were 2564 and 2541, respectively. Based on the annotation of gene functions and assessment of metabolic pathways in the KEGG database, WX_M8 and MY_A10 strains were found to harbor complete protein degradation and amino acid metabolic pathways, pyruvate and butanol metabolic pathways, and isoleucine metabolic pathways, and their diverse enzyme-encoding genes superimposed the metabolic functions, whereas the alcohol dehydrogenase genes, adh and frmA, achieved complementary functions in the production of esters. Comparative genomics analysis revealed a diversity of encoding genes of aminotransferases and a greater metabolism for sulfur-containing amino acids, aromatic amino acids, and branched-chain amino acids in the mixed fermentation of strains WX_M8 and MY_A10. Metabolites analysis showed that MY_A10 focused on the production of soluble peptides and free amino acids (FAAs), while WX_M8 focused on volatile organic compounds (VOCs), resulting in a significant enhancement of the flavor of Chinese bacon when the two were mixed fermented. This result may provide direction for strains WX_M8 and MY_A10 to be used as starter cultures and targeted to regulate flavor.

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.

Exopolysaccharides of lactic acid bacteria: Structure, biological activity, structure-activity relationship, and application in the food industry: A review

Over the past few decades, researchers have discovered that probiotics play an important role in our daily lives. With the further deepening of research, more and more evidence show that bacterial metabolites have an important role in food and human health, which opens up a new direction for the research of lactic acid bacteria (LAB) in the food and pharmaceutical industry. Many LAB have been widely studied because of the ability of exopolysaccharides (EPS). Lactic acid bacteria exopolysaccharides (LAB EPS) not only have great potential in the treatment of human diseases but also can become natural ingredients in the food industry to provide special qualitative structure and flavor. This paper has organized and summarized the biosynthesis, strain selection, production process parameters, structure, and biological activity of LAB EPS, filling in the monotony and incompleteness of previous articles' descriptions of LAB EPS. Therefore, this paper focuses on the general biosynthetic pathway, structural characterization, structure-activity relationship, biological activity of LAB EPS, and their application in the food industry, which will help to deepen people's understanding of LAB EPS and develop new active drugs from LAB EPS. Although the research results are relatively affluent, the low yield, complex structure, and few clinical trials of EPS are still the reasons that hinder its development. Therefore, future knowledge expansion should focus on the regulation of structure, physicochemical properties, function, higher production of EPS, and clinical trial applications, which can further increase the commercial significance and value of EPS. Furthermore, better understanding the structure-function relationship of EPS in food remains a challenge to date.

Role of microbiota and its ecological succession on flavor formation in traditional dry-cured ham: a review

Traditional dry cured ham (DCH) is favored by consumers for its distinctive flavor, derived from an array of volatile organic compounds (VOCs). Microbiota play a pivotal role in the formation of VOCs. To fully comprehend the pathway by which the microbiota enhance the flavor quality of DCH, it is imperative to elucidate the flavor profile of DCH, the structural and metabolic activities of the microbiota, and the intricate relationship between microbial and VOCs. Thus far, the impact of microbiota on the flavor profile of DCH has not been comprehensively discussed or reviewed, and the succession of bacteria, especially at distinct phases of processing, has not been adequately summarized. This article aims to encapsulate the considerable potential of ferments in shaping the flavor characteristics of DCH, while elucidating the underlying mechanisms through which VOCs are generated in hams via microbial metabolism. Throughout the various stages of DCH processing, the composition of microbiota undergoes dynamic changes. Furthermore, they directly participate in the formation of VOCs in DCH through the catabolism of amino acids, metabolism of fatty acids, and the breakdown of carbohydrates. Several microorganisms, including Lactobacillus, Penicillium, Debaryomyces, Pediococcus, and Staphylococcus, exhibit considerable potential as fermenters in ham production.

Strong ethanol- and frequency-dependent ecological interactions in a community of wine-fermenting yeasts

Natural wine fermentation depends on a complex consortium of native microorganisms rather than inoculation of industrial yeast strains. While this diversity of yeasts can result in an increased repertoire of wine flavors and aromas, it can also result in the inhibition of Saccharomyces cerevisiae, which is uniquely able to complete fermentation. Understanding how yeast species interact with each other within the wine-fermenting community and disentangling ecological interactions from environmental impacts on growth rates, is key to developing synthetic communities that can provide the sensory benefits of natural fermentation while lowering the risk of stuck ferments. Here, we co-culture all pairwise combinations of five commonly isolated wine-fermenting yeasts and show that competitive outcomes are a strong function of ethanol concentration, with frequency-dependent bistable interactions common at low alcohol and an increasingly transitive competitive hierarchy developing as alcohol increases. We also show that pairwise outcomes are predictive of five-species community outcomes, and that frequency dependence in pairwise interactions propagates to alternative states in the full community, highlighting the importance of species abundance as well as composition. We also observe that monoculture growth rates are only weakly predictive of competitive success, highlighting the need to incorporate ecological interactions when designing synthetic fermenting communities.

Microbial Dynamics of a Specialty Italian Raw Ewe's Milk Cheese Curdled with Extracts from Spontaneous and Cultivated Onopordum tauricum Willd

Milk coagulants prepared by maceration of flowers harvested from both spontaneous and cultivated Onopordum tauricum Willd. and a commercially available coagulant obtained from Cynara cardunculus L. (control) were assayed for small-scale manufacturing of Caciofiore, an Italian specialty raw ewe's milk cheese produced in a family run dairy farm located in the Marche region (Central Italy). The microbiota of the three thistle-based milk coagulants and their effect on the microbial dynamics of raw milk cheeses during fermentation and maturation (from day 0 up until day 60) were investigated through a combined approach based on viable counting and Illumina DNA sequencing. In both the control and experimental cheeses, despite the slight differences emerged depending on the coagulant used, Lactococcus lactis and Debaryomyces hansenii were the prevalent species among bacteria and fungi, respectively. Moreover, raw ewe's milk was the main factor affecting the evolution of both the bacterial and fungal microbiota in all cheeses. The overall similarities between control and experimental cheeses herein analyzed supports the exploitation of Onopordum tauricum Willd. as an alternative milk coagulating agent for production of Caciofiore and, more in general, raw ewe's milk cheeses.

Isolation of the high polyamine-producing bacterium Staphylococcus epidermidis FB146 from fermented foods and identification of polyamine-related genes

It has been reported that the intake of polyamines contributes to the extension of healthy life span in animals. Fermented foods contain high concentrations of polyamines thought to be derived from fermentation bacteria. This suggests that bacteria that produce high levels of polyamines could be isolated from fermented foods and utilized as a source of polyamines for human nutrition. In this study, Staphylococcus epidermidis FB146 was isolated from miso, a Japanese fermented bean paste, and found to have a high concentration of putrescine in its culture supernatant (452 μM). We analyzed the presence of polyamines in the culture supernatants and cells of the type strains of 21 representative Staphylococcus species in addition to S. epidermidis FB146, and only S. epidermidis FB146 showed high putrescine productivity. Furthermore, whole-genome sequencing of S. epidermidis FB146 was performed, and the ornithine decarboxylase gene (odc), which is involved in putrescine synthesis, and the putrescine:ornithine antiporter gene (potE), which is thought to contribute to the release of putrescine into the culture supernatant, were present on plasmid DNA harbored by S. epidermidis FB146.

Dynamic change of bacterial diversity, metabolic pathways, and flavor during ripening of the Chinese fermented sausage

Chinese fermented sausage is a famous fermented meat product with a complex microbiota that has a potential impact on flavor and quality. In this study, Lactobacillus plantarum MSZ2 and Staphylococcus xylosus YCC3 were used as starter cultures to investigate the change in bacterial diversity, metabolic pathways, and flavor compounds during the ripening process of fermented sausages. High-throughput sequencing technology and headspace solid-phase microextraction-gas chromatography–mass spectrometry (HS-SPME-GC/MS) were applied for characterizing the profiles of bacterial diversity, metabolic pathways, and flavor compounds in sausage samples on days 0, 6, and 12 during ripening. Results showed that Lactobacillus, Staphylococcus, Lactococcus, Leuconostoc, and Weissella were the most abundant bacterial genera found in the sausage samples during all stages of fermentation. Functional prediction reveals the abundance of 12 different metabolic pathways, the most important pathways are carbohydrate metabolism, nucleotide metabolism, lipid metabolism, and amino acid metabolism. A total of 63 volatile compounds were successfully identified in fermented sausage samples. Correlational analysis demonstrated that Staphylococcus and Leuconostoc were closely related to the formation of flavor compounds. Therefore, the present study may provide guidance for future use of microbiota to improve flavor, quality, and preservation of fermented sausages.

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.

Further culture-independent characterization of the lactic microbiota of Serro artisanal cheese

This study aimed to provide a further characterization of the lactic microbiota present in Minas artisanal cheese (MAC) from the Serro region by using culture-independent methods, as a complementary analysis of a previous study. The total DNA extracted from MAC samples (n = 55) was subjected to repetitive extragenic palindromic-PCR (rep-PCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Rep-PCR analysis showed that core microbiota of Serro MAC was closely related, independent of the production town, farm size, or time of production. The sequencing of PCR-DGGE bands identified the prevalence of Lactococcus lactis in all samples, and Streptococcus salivarius was also identified. Thus, we conclude that when more accurate methods are unavailable, rep-PCR can be used as a culture-independent method to demonstrate if the microbiota is closely related or not among the samples. PCR-DGGE results also matched to the main findings of high-throughput sequencing, previously presented, confirming its confidence to detect the main microbial groups present in the raw milk cheeses.

Development of Healthier and Functional Dry Fermented Sausages: Present and Future

In recent years, consumer perception about the healthiness of meat products has changed. In this scenario, the meat industry and the scientific and technological areas have put their efforts into improving meat products and achieving healthier and functional formulations that meet the demands of today’s market and consumers. This article aims to review the current functional fermented meat products, especially on sausage development. Firstly, an emphasis is given to reducing and replacing traditional ingredients associated with increased risk to consumer’s health (sodium, fat, and nitrites), adding functional components (prebiotics, probiotics, symbiotics, and polyphenols), and inducing health benefits. Secondly, a look at future fermented sausages is provided by mentioning emerging strategies to produce innovative healthier and functional meat products. Additional recommendations were also included to assist researchers in further development of healthier and functional sausages.

Recent developments in off-odor formation mechanism and the potential regulation by starter cultures in dry-cured ham

Foul-smelling odors are main quality defects of dry-cured ham, which are connected with the excessive degradation of the structural proteins and excessive oxidation of lipids caused by the abnormal growth of spoilage microorganisms, threatening the development of dry-cured ham industry. Characterizing the key microorganisms and metabolites resulted in the spoilage of dry-cured ham, and discussing the relationship between spoilage microorganisms and metabolites are the key aspects to deeply understand the formation mechanism of off-odor in dry-cured ham. Until now, there is no detailed discussion or critical review on the role of spoilage microorganisms in developing the off-odor of dry-cured ham, and the regulation of off-odor and spoilage microorganisms by starter cultures has been not discussed. This review shows the recent achievement in the off-odor formation mechanism of dry-cured ham, and outlines the potential regulation of off-odor defects in dry-cured ham by starter cultures. Results from current research show that the abnormal growth of Lactic acid bacteria, Micrococcaceae, Enterobacteriaceae, Yeasts and Molds plays a key role in developing the off-odor defects of dry-cured ham, while the key spoilage microorganisms of different type hams are discrepant. High profile of aldehydes, acids, sulfur compounds and biogenic amines are responsible for off-odor development in spoiled dry-cured ham. Several starter cultures derived from these species of Staphylococcus, Penicillium, Debaryomyces, Pediococcus and Lactobacillus show a great potential to prevent microbiological hazards and improve flavor quality of dry-cured ham, whereas, the ecology, function and compatibility of these starter cultures with the processing parameters of dry-cured ham need to be further evaluated in the future.

Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment

Humans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such as Pseudomonadaceae and Staphylococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.

Microbial community shifts association with physicochemical parameters: Visualizing enset bacterial wilt from different states of enset health

Bacterial wilt of enset caused by Xanthomonas campestris is a devastating disease in Ethiopia, where enset is domesticated and served as a staple food for about 20 million people in the country. While enset is infected by bacteria, it shows different wilting stages. However, the microbial community shifts at the different stages of enset infection and associated physicochemical parameter changes remain poorly understood. This study was aimed to visualize the proportion of enset wilt bacterium from other microbial community and its association with physicochemical parameter at different states of enset health. Soil and enset (zero, first, second and third stages) samples were collected from three districts in Gamo Highlands for physicochemical and biological (culture dependent and16S rRNA gene sequence) analysis. The results of culture dependent analysis which has been complemented by 16S rRNA gene sequence confirmed that increasing trends were observed for Xanthomonadaceae, Pseudomonadaceae, Lactobacillaceae and Flavobacteriaceae, while Bacillaceae and Enterobacteriaceae showed progressive decrease from zero to the third stage. Particularly, the 16S rRNA data showed that Xanthomonadaceae increased significantly from zero to different (2.5 × 10² times at the onset of disease and 1.0-2.0 × 10⁴ times at the second and third) stages of enset infection. Most physicochemical results showed that a decreasing trends from zero to third stage, while few parameters are showing an increasing trend. Moisture content (R² ≥ 0.951, P ≤ 0.049) of the soil and plant samples positively influenced Xanthomonas abundance, while this bacterium showed a strongly negative significant correlation with pH (R² ≥ -0.962, P ≤ 0.038), temperature (R² ≥ -0.958, P ≤ 0.042), OM (R² ≥ -0.952, P ≤ 0.048), and TN (R² ≥ -0.951, P ≤ 0.049). A strongly negative significant correlation (R² ≥ -0.948, P ≤ 0.050) was also observed between Xanthomonas and nutrients (K, Mg, Ca, and Cu). Overall, this study implies that different environmental factors found a key driving force of Xanthomonas proportional increment from low abundance at zero stage to higher abundance at the last stage of enset infection suggesting that considering these factors help to design an effective enset disease management strategy, for which further studies will be needed.

Effect of probiotic Lactiplantibacillus plantarum and chestnut flour (Castanea sativa mill) on microbiological and physicochemical characteristics of dry-cured sausages during storage

The effect of chestnut flour (Castanea sativa Mill) on L. plantarum viability and physicochemical characteristics in a dry-cured sausage (Longaniza de Pascua) during storage is discussed. Four batches were prepared: CL with 3% chestnut flour added; CPL with 3% chestnut flour and 8.5 log CFU/g L. plantarum added; PL with 8.5 log CFU/g L. plantarum added and L, the batch control. The sausages were stored at 4 °C and 20 °C, and vacuum packed for 43 d. L. plantarum viability was affected by storage time (P < 0.001). However, higher L. plantarum counts at the final of storage were reached due to chestnut flour addition (P < 0.001). At room storage, chestnut flour caused a higher increase in TBARS values (P = 0.022). Nevertheless, all lipid oxidation treatments were in the range of accepted values at the sensory detection level. In conclusion, Longaniza de Pascua can be kept at 4 °C or 20 °C for 43 d without causing any rancidity problems.

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.

Microbiota and volatilome of dry-cured pork loins manufactured with paprika and reduced concentration of nitrite and nitrate

Dry-cured pork loin is a very popular meat product in Mediterranean countries. Pork-loin is manufactured rubbing curing salts, nitrite and nitrate, and spices on the surface of the loin which is then dry-cured or smoked for several months. Although nitrite-derived compounds are crucial for the microbiological safety and development of a distinct flavour, there have been recent concerns about the adverse health effects of nitrite-derived compounds driving to the reduction of curing agents in meat products. In this study, we have evaluated the differences in microbiota and aroma of dry-cured pork loins manufactured with or without paprika and reduced ingoing amounts of nitrate and nitrite. Staphylococcus dominated the microbiota of pork loins without paprika, regardless of the nitrite and nitrate reduction. On the contrary, the reduction of nitrite and nitrate in loins with paprika had an important effect on the microbiota. In these loins a codominance of Staphylococcus and Bacillus together by Enterobacteriaceae occurred. Moreover, paprika addition and reduction of nitrite and nitrate seemed to promote proliferation of lactic acid bacteria. Occurrence of these genera was correlated with the generation of free amino acids and their derived volatile compounds setting clear differences in the aroma profile of dry-cured loins.

Characterisation of flavour profile of beef jerky inoculated with different autochthonous lactic acid bacteria using electronic nose and gas chromatography-ion mobility spectrometry

The flavour profiles of beef jerky separately inoculated with different autochthonous lactic acid bacteria (LAB) strains (Lactobacillus sakei BL6, Pediococcus acidilactici BP2, and Lactobacillus fermentum BL11) and a non-inoculated control were analysed using electronic nose (E-nose) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-IMS results revealed a total of 42 volatile compounds in beef jerky. Inoculation of the three LAB strains decreased the levels of lipid autoxidation-derived aldehydes (e.g., hexanal, heptanal, octanal, and nonanal). In addition, inoculation of P. acidilactici BP2 increased the levels of esters. Principal component analysis of the E-nose and GC-IMS results could effectively differentiate non-inoculated beef jerky and beef jerky separately inoculated with different LAB strains. Furthermore, there was a high correlation between the E-nose and GC-IMS results, providing a theoretical basis for the identification of different beef jerky formulations and selection of autochthonous starter cultures for beef jerky fermentation.

Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing

Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based taxonomic classification of DNA sequences revealed 53 bacterial genera. However, the amplicon sequencing variant (ASV)-based clustering revealed 43 classifiable bacterial genera. Taxonomic classifications revealed that the abundance of Sphingomonas, which was the predominant genus in the majority of tested samples, was more than 85–90% among the total identified bacterial community in most samples. Among these identified genera, 13 low abundance genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, and Streptococcus. Of these 13 genera, 13 major opportunistic pathogenic species were validated using polymerase chain reaction. The pathogens were not detected in the samples of different stages and the final products of fermentation, except in one sample from the first stage of fermentation in which S. aureus was detected. This finding was consistent with that of ASV-based taxonomic classification according to which S. aureus was detected only in the sample from the first stage of fermentation. However, S. aureus was not significantly correlated with the human disease pathways. These results indicated that fermentation is a reliable and safe process as pathogenic bacteria were not detected in the fermentation products. The hybrid method reported in this study can be used simultaneously to evaluate the bacterial diversity, their functional predictions and safety assessment of novel fermentation products. Additionally, this hybrid method does not involve the random detection of pathogens, which can markedly decrease the time of detection and food safety verification. Furthermore, this hybrid method can be used for the quality control of products and the identification of external contamination.

Gut Microbiota and Gynecological Cancers: A Summary of Pathogenetic Mechanisms and Future Directions

Over the past 20 years, important relationships between the microbiota and human health have emerged. A link between alterations of microbiota composition (dysbiosis) and cancer development has been recently demonstrated. In particular, the composition and the oncogenic role of intestinal bacterial flora has been extensively investigated in preclinical and clinical studies focusing on gastrointestinal tumors. Overall, the development of gastrointestinal tumors is favored by dysbiosis as it leads to depletion of antitumor substances (e.g., short-chain fatty acids) produced by healthy microbiota. Moreover, dysbiosis leads to alterations of the gut barrier, promotes a chronic inflammatory status through activation of toll-like receptors, and causes metabolic and hormonal dysregulations. However, the effects of these imbalances are not limited to the gastrointestinal tract and they can influence gynecological tumor carcinogenesis as well. The purpose of this Review is to provide a synthetic update about the mechanisms of interaction between gut microbiota and the female reproductive tract favoring the development of neoplasms. Furthermore, novel therapeutic approaches based on the modulation of microbiota and their role in gynecological oncology are discussed.

Influence of fermentation temperature on in situ heteropolysaccharide formation (Lactobacillus plantarum TMW 1.1478) and texture properties of raw sausages

This study puts a focus on the influence of microbial in situ heteropolysaccharide (HePS) formation on the quality of raw fermented sausages (salami). Since exopolysaccharide-production is often triggered by sub-optimal growth conditions, the influence of different fermentation temperatures was also investigated. For this reason, the sausage batter was inoculated with (Lactobacillus plantarum TMW 1.1478) or without (L. sakei TMW 1.2037; control) a HePS-producing starter culture (inoculation concentration ~108 CFU/g), and the sausages fermented at either 10, 16, or 24°C (7 days), followed by a drying period at 14°C until the final weight loss of 31% was reached. Microbial growth, pH, and weight loss development were monitored and the products further characterized using texture profile analysis and a sensory test. HePS in the salami matrix were determined using confocal laser scanning microscopy and a semi-quantitative data interpretation approach. Sausages containing L. plantarum were found to be significantly (p < .05) softer compared with control samples, which was also confirmed in the sensory analysis. The different fermentation temperatures had an influence on the drying speed. Here, sausages produced with L. plantarum needed more time to reach the final weight loss of 31% as compared to control samples, which could be attributed to the presence of exopolysaccharides in the matrix (p < .05). Using HePS-forming starter cultures in raw fermented sausage manufacturing can lead to products with a softer texture (undesired in Europe) depending on the strain and processing conditions used, highlighting the importance of a suitable starter culture selection in food processing.

Influence of microbial in-situ heteropolysaccharide production on textural properties of raw fermented sausages (salami)

The purpose of the study was to investigate the influence of a heteropolysacchride (HePS)-forming lactic acid bacteria (LAB) on the quality attributes of raw fermented sausages. Therefore, salamis with the HePS-producing strain Lactobacillus plantarum TMW 1.1478 or the non-EPS-producing strain Lactobacillus sakei TMW 1.2037 (control) were manufactured using two different inoculation concentrations: more precisely, 10⁷ CFU/g (typical starter culture concentration) or 10⁹ CFU/g. Growth behavior, a_w and pH development were recorded until a weight loss of 31% was reached and in-situ-formed EPS detected using confocal laser scanning microscopy. Moreover, the influence of the HePS formed on texture (texture profile analysis; TPA) and sensory attributes (26 panelists, ranking test) was investigated. The final products containing L. plantarum TMW 1.1478 were found to be significantly softer (p < 0.05) than the respective control samples, an effect that was even more pronounced at the higher inoculation level of 10⁹ CFU/g. The semi-quantitative data interpretation of the CLSM pictures revealed that the EPS were predominantly formed during the first 72 h of fermentation at 24 °C until the final pH of 4.95 ± 0.05 was reached (stationary phase). The sensory evaluation (consistency) was in accordance with the TPA results and taste was not negatively influenced by the HePS-forming strain. Results clearly indicate that EPS-producing LAB can have a negative influence on the quality of raw fermented sausages. However, these strains (in the present case L. plantarum TMW 1.1478) might be interesting for application in the field of spreadable raw sausage manufacturing.

Functional Characteristics of Lactobacillus and Yeast Single Starter Cultures in the Ripening Process of Dry Fermented Sausage

Dry fermented sausage is popular among the world because of its rich nutrition and unique flavor. Starter cultures play an important role in the quality of dry fermented sausage. In this study, probiotics lactic acid bacteria Lactobacillus delbrueckii N102, Latilactobacillus sakei H1-5, Debaryomyces hansenii Y4-1, and Wickerhamomyces anomalus Y12-3 were isolated from food-borne materials. The physicochemical properties, microbial populations, TBARS, lipolysis, proteolysis, and volatile flavor compounds of dry fermented sausages with different starter cultures were evaluated comparatively during the ripening process. The results showed that both L. delbrueckii N102 and L. sakei H1-5 grow well and could rapidly reduce the pH value of the products. At the same time, they could significantly reduce the number of Enterobacter putrefaciens, so as to ensure the safety of the products. In addition, the strains N102 promoted the formation of flavor compounds 2,3-butanedione, 3-hydroxy-2-butanone, and carnosine, whereas taurine content of batch H1-5 was significantly increased, while yeast y4-1 and y12-3 could also grow faster in sausage and promoted the esters and alcohols formation such as ethyl acetate and linalool, with the formation of γ-aminobutyric acid by y4-1. Compared with lactic acid bacteria, yeasts showed to contribute more in flavor formation and effective inhibition of lipid oxidation. The starter cultures played different roles in flavor contribution and had obvious differentiation in the ripening process of dry fermented sausage.

Usage of in situ exopolysaccharide-forming lactic acid bacteria in food production: Meat products-A new field of application?

In the meat industry, hydrocolloids and phosphates are used to improve the quality attributes of meat products. However, latest research results revealed that the usage of exopolysaccharide (EPS)-forming lactic acid bacteria (LAB), which are able to produce EPS in situ during processing could be an interesting alternative. The current review aims to give a better understanding of bacterial EPS production in food matrices with a special focus on meat products. This includes an introduction to microbial EPS production (homopolysaccharides as well as heteropolysaccharides) and an overview of parameters affecting EPS formation and yield depending on LAB used. This is followed by a summary of methods to detect and characterize EPS to facilitate a rational selection of starter cultures and fermentation conditions based on desired structure-function relationships in different food matrices. The mechanism of action of in situ generated EPS is then highlighted with an emphasis on different meat products. In the process, this review also highlights food additives currently used in meat production that could in the future be replaced by in situ EPS-forming LAB.

Microbial communities and gene contributions in smokeless tobacco products

Smokeless tobacco products (STP) contain bacteria, mold, and fungi due to exposure from surrounding environments and tobacco processing. This has been a cause for concern since the presence of microorganisms has been linked to the formation of highly carcinogenic tobacco-specific nitrosamines. These communities have also been reported to produce toxins and other pro-inflammatory molecules that can cause mouth lesions and elicit inflammatory responses in STP users. Moreover, microbial species in these products could transfer to the mouth and gastrointestinal tract, potentially altering the established respective microbiotas of the consumer. Here, we present the first metagenomic analysis of select smokeless tobacco products, specifically US domestic moist and dry snuff. Bacterial, eukaryotic, and viral species were found in all tobacco products where 68% of the total species was comprised of Bacteria with 3 dominant phyla but also included 32% Eukarya and 1% share abundance for Archaea and Viruses. Furthermore, 693,318 genes were found to be present and included nitrate and nitrite reduction and transport enzymes, antibiotic resistance genes associated with resistance to vancomycin, β-lactamases, their derivatives, and other antibiotics, as well as genes encoding multi-drug transporters and efflux pumps. Additional analyses showed the presence of endo- and exotoxin genes in addition to other molecules associated with inflammatory responses. Our results present a novel aspect of the smokeless tobacco microbiome and provide a better understanding of these products' microbiology. KEY POINTS: • The findings presented will help understand microbial contributions to overall STP chemistries. • Gene function categorization reveals harmful constituents outside canonical forms. • Pathway genes for TSNA precursor activity may occur at early stages of production. • Bacteria in STPs carry antibiotic resistance genes and gene transfer mechanisms.

High-throughput sequencing approach to reveal the bacterial diversity of traditional yak jerky from the Tibetan regions

A high-throughput sequencing approach was used to investigate the bacterial community diversity of traditional Tibetan yak jerky, which was collected from three different regions in Tibet and with different natural drying times. Tibetan yak jerky from different regions had different bacterial communities, which was mainly reflected in the relative abundance levels of unclassified Cyanobacteria, Psychrobacter and Acinetobacter. The unclassified Cyanobacteria was the dominant genus of Qamdo yak jerky, Acinetobacter was the dominant genus of Shigatse yak jerky, and Psychrobacteria was the dominant genus of Nyingchi yak jerky. With increasing natural drying time, the diversity of bacterial communities in yak jerky decreased, and unclassified Cyanobacteria become the dominant genus. Spearman's correlation analysis and canonical correspondence analysis revealed that physicochemical factors (moisture content, water activity, shear force and pH) were significantly correlated with bacterial community. Our results will be beneficial to improve and standardize the safety and quality of traditional Tibetan yak jerky.

Detection of Biogenic Amines and Tyramine-Producing Bacteria in Fermented Sausages from Switzerland

ABSTRACT

Fermented foods can cause human illness because of the unhealthy effect of biogenic amines (BAs) that accumulate by decarboxylation of free amino acids. Salami-type fermented sausages can contain BAs, but which bacteria and environmental factors contribute to BA production is not clear. Sixty-two sausages purchased from Swiss markets were evaluated for decarboxylating bacterial strains and concentrations of the BAs cadaverine, histamine, putrescine, and tyramine. Based on the size and number of employees of the meat processing plants, sausages were separated into two groups: artisanal and industrial. Concentrations of all four BAs were higher in industrial sausages than in artisanal sausages. Tyramine was the major BA detected in 46 of 62 sausages, at a maximum concentration of 785.22 mg/kg. Enterococci and coagulase-negative staphylococci (mainly the meat starter culture Staphylococcus xylosus) were the main tyramine producers. Putrescine was found in 20 of 62 samples, at a maximum concentration of 707.77 mg/kg. Concentrations of these two BAs were significantly correlated (P = 0.0407). Cadaverine and histamine were detected in nine and eight samples, respectively, and both were found in significantly higher concentrations (P = 0.019 and 0.036, respectively) in industrial sausages. Based on the tyramine concentration, five groups of fermented sausages were identified: group 1, very high concentrations (>700 mg/kg); group 2, high concentrations (400 to 700 mg/kg); group 3, moderate concentrations (200 to 400 mg/kg); group 4, low concentrations (<200 mg/kg); group 5, concentrations below the detection limit (0.05 mg/kg). Product samples with tyramine concentrations >200 mg/kg were considered of lower quality because consumption of such samples could be unhealthy for sensitive consumers.

HIGHLIGHTS

Sensory Changes and Listeria monocytogenes Behavior in Sliced Cured Pork Loins during Extended Storage

Cured pork loins are sausages with a production tradition in several regions worldwide. They are made from one of the noblest cuts of pork, and for this reason cured loins are one of the most expensive pork meat products. Establishing the correct shelf life allows products to be accepted by the consumer, and to avoid the costs associated with shorter shelf lives. The aim of this study is: (1) to establish proper shelf life by evaluating the willingness of participants to consume and the sensory modifications that occur during prolonged storage via Check All That Apply (CATA) questions; and (2) to study the behavior of Listeria monocytogenes through a microbial challenge test. Sliced cured pork loins can be stored at 6 ± 1 °C for 105 days while maintaining a consumer acceptance of more than 75%. The freshness loss was associated mainly with a decrease in aromatic notes (particularly the smoke and cured aroma), and with the appearance of spoiled characteristics, specifically a sour/vinegar aroma and acidic taste that were detected by a reduced proportion of participants. The freshness evaluation was positively influenced by the typical characteristics of cured products, such as color and a garlic and wine aroma. Sour/vinegar aroma and acidic taste were the attributes most associated with higher freshness penalization. During the period of the test, Listeria monocytogenes inoculated onto the cured loin slices did not grow.

Technological Characterisation of Probiotic Lactic Acid Bacteria as Starter Cultures for Dry Fermented Sausages

The objective of this study was to investigate probiotic microorganisms for use as starter cultures in dry fermented sausages production. A total of eight strains were studied evaluating technological and safety characteristics including the ability to grow, lactic acid production, gas formation, catalase activity, nitrate reductase activity, proteolytic activity, lipolytic activity, hydrogen peroxide production, salt tolerance, performance at low temperatures, decarboxylation of amino acids and antimicrobial activity against pathogens associated with the product. Lactobacillus rhamnosus R0011, L. rhamnosus Lr-32, Lactobacillus paracasei Lpc-37, Lactobacillus casei Shirota and Enterococcus faecium MXVK29 were good candidates for use as fermented sausages starters cultures because they showed the best technological and safety properties since they did not demonstrate amino acid decarboxylation but showed antimicrobial activity against Listeria monocytogenes, Escherichia coli, Salmonella Dublin and Staphylococcus aureus. L. rhamnosus Lr-32 was the strain best tolerating the levels of salt, nitrate and low pH during the simulated stages of fermentation and ripening of sausage. The strain was thus the most promising of the tested probiotics as sausage starter culture. The findings warrant studies in a meat matrix, such as that of raw-cured sausage, to evaluate the effects of L. rhamnosus Lr-32 under actual conditions.

In vitro probiotic properties of Pediococcus pentosaceus L1 and its effects on enterotoxigenic Escherichia coli-induced inflammatory responses in porcine intestinal epithelial cells

This study aimed to evaluate in vitro probiotic characteristics of Pediococcus pentosaceus strain L1 from pickled radish and investigate its impacts on inflammatory responses in porcine intestinal epithelial cells (IEC) to enterotoxigenic Escherichia coli (ETEC) F4⁺. The abilities of P. pentosaceus L1 to tolerate gastrointestinal conditions and to antagonize ETEC F4⁺ growth were determined. Adhesion of P. pentosaceus L1 and its effect on ETEC F4⁺ adhesion to porcine IPEC-J2 IEC were evaluated. Furthermore, the effects of this strain on proinflammatory gene expression and cytokines/chemokine production in porcine IPEC-J2 IEC induced by ETEC F4⁺ were determined. P. pentosaceus L1 showed good tolerance to the medium adjusted at pH 2.5 and consequently supplemented with 0.3% oxgall. Reduction of ETEC F4⁺ growth in co-culture with L1 was found. Effective adhesion of L1 to porcine. IPEC-J2 IEC was observed under these conditions. P. pentosaceus L1 decreased the adhesion of ETEC F4⁺ to IPEC-J2 IEC and the extent of inhibition of ETEC F4⁺ adhesion depended on the timing of L1 addition. Further analysis revealed down-regulation of expression of ETEC F4⁺-induced proinflammatory genes encoding interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and interleukin-8 (IL-8) in IPEC-J2 IEC. Expression of the genes involved in NF-κB pathway, including RELA and NFKB1, were also repressed, as was production of IL-6, TNF-α, and IL-8. These results indicate that P. pentosaceus L1 may have potential as a probiotic for control of ETEC infection in pigs.

Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans

The microbial ecology in the fermentation of Australian coffee beans was investigated in this study. Pulped coffee beans were kept underwater for 36 h before air dried. Samples were collected periodically, and the microbial communities were analyzed by culture-dependent and independent methods. Changes in sugars, organic acids and microbial metabolites in the mucilage and endosperm of the coffee beans during fermentation were monitored by HPLC. Culture-dependent methods identified 6 yeast and 17 bacterial species, while the culture-independent methods, multiple-step total direct DNA extraction and high throughput sequencing, identified 212 fungal and 40 bacterial species. Most of the microbial species in the community have been reported for wet fermentation of coffee beans in other parts of the world, but the yeast Pichia kudriavzevii was isolated for the first time in wet coffee bean fermentation. The bacterial community was dominated by aerobic mesophilic bacteria (AMB) with Citrobacter being the predominant genus. Hanseniaspora uvarum and Pichia kudriavzevii were the predominant yeasts while Leuconostoc mesenteroides and Lactococcus lactis were the predominant LAB. The yeasts and bacteria grew significantly during fermentation, utilizing sugars in the mucilage and produced mannitol, glycerol, and lactic acid, leading to a significant decrease in pH. The results of this study provided a preliminary understanding of the microbial ecology of wet coffee fermentation under Australian conditions. Further studies are needed to explore the impact of microbial growth and metabolism on coffee quality, especially flavour.

Industrial Validation of a Promising Functional Strain of Lactobacillus plantarum to Improve the Quality of Italian Sausages

This paper proposes the industrial validation of a functional strain of Lactobacillus plantarum (strain 178). First, acidification in a meat model medium and bioactivity towards Staphylococcus aureus, Salmonella sp., Listeria monocytogenes, and Escherichia coli were assessed; the performances of Lb. plantarum 178 were compared to those of a commercial Lb. sakei and a probiotic Lb. casei. Lb. plantarum 178 inhibited the pathogens and experienced a higher acidification at 15 °C. Lb. casei and Lb. plantarum were used for an industrial fermentation of traditional Italian sausages. The strains assured the correct course of fermentation and inhibited pathogens and enterobacteria. This study represents the scaling up and the validation of a promising strain at industrial level and shows the possibility of performing the fermentation of traditional Italian sausage through functional starter cultures, combining the benefit of a controlled fermentation and possible health benefits.

Fermented foods in a global age: East meets West

Fermented foods and alcoholic beverages have long been an important part of the human diet in nearly every culture on every continent. These foods are often well-preserved and serve as stable and significant sources of proteins, vitamins, minerals, and other nutrients. Despite these common features, however, many differences exist with respect to substrates and products and the types of microbes involved in the manufacture of fermented foods and beverages produced globally. In this review, we describe these differences and consider the influence of geography and industrialization on fermented foods manufacture. Whereas fermented foods produced in Europe, North America, Australia, and New Zealand usually depend on defined starter cultures, those made in Asia and Africa often rely on spontaneous fermentation. Likewise, in developing countries, fermented foods are not often commercially produced on an industrial scale. Although many fermented products rely on autochthonous microbes present in the raw material, for other products, the introduction of starter culture technology has led to greater consistency, safety, and quality. The diversity and function of microbes present in a wide range of fermented foods can now be examined in detail using molecular and other omic approaches. The nutritional value of fermented foods is now well-appreciated, especially in resource-poor regions where yoghurt and other fermented foods can improve public health and provide opportunities for economic development. Manufacturers of fermented foods, whether small or large, should follow Good Manufacturing Practices and have sustainable development goals. Ultimately, preferences for fermented foods and beverages depend on dietary habits of consumers, as well as regional agricultural conditions and availability of resources.

High-Hydrostatic-Pressure (HHP) Processing Technology as a Novel Control Method for Listeria monocytogenes Occurrence in Mediterranean-Style Dry-Fermented Sausages

Although conventional microbial control techniques are currently employed and largely successful, their major drawbacks are related to their effects on quality of processed food. In recent years, there has been a growing demand for high-quality foods that are microbially safe and retain most of their natural freshness. Therefore, several modern and innovative methods of microbial control in food processing have been developed. High-hydrostatic-pressure (HHP) processing technology has been mainly used to enhance the food safety of ready-to-eat (RTE) products as a new pre-/post-packaging, non-thermal purification method in the meat industry. Listeria monocytogenes is a pertinent target for microbiological safety and shelf-life; due to its capacity to multiply in a broad range of food environments, is extremely complicated to prevent in fermented-sausage-producing plants. The frequent detection of L. monocytogenes in final products emphasizes the necessity for the producers of fermented sausages to correctly overcome the hurdles of the technological process and to prevent the presence of L. monocytogenes by applying novel control techniques. This review discusses a collection of recent studies describing pressure-induced elimination of L. monocytogenes in fermented sausages produced in the Mediterranean area.

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.

Physicochemical, sensory and microbiological characterization of Asturian Chorizo, a traditional fermented sausage manufactured in Northern Spain

Industrial standardization of fermented meat products requires starter culturesto avoid random variations in the initial microbiota of food matrix. This allows to homogenize production batches regarding sensory and physicochemical characteristics. Also, starters contribute to assure safety, as they compete with pathogens or spoilage species, facilitating pH reduction and secretion of inhibitors. Asturian Chorizo is a traditional fermented sausage from Northern Spain, still produced in a traditional way, without starters. This work describes its characterization at the sensory, physicochemical and microbiological levels. In contrast to other fermented sausages, Asturian Chorizo microbiota is represented mainly by Lactobacillus plantarum, with secondary contributions from Lb. sakei and Lb. futsai. This results may path the way towards development of specific starter cultures for this product, avoiding the loss of the original characteristics of the fermented product in a traditional way, as it would happen in the case of using industrial processes with conventional starters.

Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment

The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.

Impact of Lactobacillus curvatus 54M16 on microbiota composition and growth of Listeria monocytogenes in fermented sausages

Lactobacillus curvatus 54M16 produced bacteriocins sak X, sak T_α, sak T_β and sak P. The aim of this study was to investigate the anti-listerial activity of the bacteriocins-producing strain against Listeria monocytogenes in vitro co-culture experiments and during the manufacture of fermented sausages. In MRS broth, Lb. curvatus 54M16 was able to inhibit L. monocytogenes to undetectable levels after 48 h at 20 °C or 5 days at 15 °C. Anti-listerial activity was lower during the production of fermented sausages with pathogen inoculation at levels of approximately 4 Log CFU g^-1. However, total inhibition of L. monocytogenes native to the raw ingredients was achieved over the course of the fermentation. Moreover, 16S rRNA-based analysis revealed the ability of Lb. curvatus 54M16 to dominate and affect the bacterial ecosystem, whereas spoilage-associated bacterial genera, such as Brochothrix, Psychrobacter, Pseudomonas and some Enterobacteriaceae, were found until the end of ripening in sausages without Lb. curvatus 54M16. The use of the bacteriocins-producing Lb. curvatus 54M16 in fermented sausages could be an important contribution to product safety, provided that eco-physiological factors and other preservation methods are maintained at levels required for the inhibition of pathogens in controlled conditions.

Complete Genome Sequences of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311, Isolated from Fermented Meat Products

The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311 were sequenced and assembled using PacBio single-molecule real-time (SMRT) technology. The strains were isolated from Swiss fermented meat products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95 Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.

Foodomics and Food Safety: Where We Are

The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods

Artisanal Minas cheese is produced in Minas Gerais state, Brazil and its varieties are named according to their geographical origin (Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes). The cheese is produced with raw cow's milk and the whey from the previous cheese production ("pingo"). The high economic and cultural importance of artisanal cheese in Brazil justifies the efforts to ensure its safety, quality and provenance. This study aimed to characterize the microbial diversity composition, and geographical distribution of artisanal Minas cheese, focusing on the characterization of its autochthonous lactic acid bacteria (LAB) microbiota. Artisanal Minas cheese varieties from Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes were analyzed by culture-dependent (culturing and LAB sequencing) and -independent (repetitive extragenic palindromic-PCR (rep-PCR) and length heterogeneity-PCR, LH-PCR) methods to characterize the microbiota. The microbial counts were variable between cheese samples, and some samples presented high number of coagulase positive bacteria and coliforms that may be associated with hygienic issues. In all samples was observed a prevalence of LAB. 16S rRNA sequencing and rep-PCR of the LAB strains identified four genus (Lactobacillus, Lactococcus, Enterococcus and Weissella), ten species and more than one strain per species. Lactobacillus was the most prevalent genera in all the cheeses. LH-PCR revealed a further six genera and ten species that were not identified by culturing, highlighting the importance of combining both culture-dependent and -independent methods to fully characterize microbiota diversity. Principal component analysis of the LH-PCR data and cluster analysis of rep-PCR data revealed that the artisanal Minas cheese microbiota was influenced not only by their geographical origin but also by the cheese farm. The lack of standardization in the milking and cheese manufacturing procedures between artisanal cheese farms could explain the microbial diversity.