New insights into Lactococcus lactis diacetyl- and acetoin-producing strains isolated from diverse origins

Combined Non-Thermal Microbial Inactivation Techniques to Enhance the Effectiveness of Starter Cultures for Kimchi Fermentation

For quality standardization, the application of functional lactic acid bacteria (LAB) as starter cultures for food fermentation is a well-known method in the fermented food industry. This study assessed the effect of adding a non-thermally microbial inactivated starter culture to kimchi, a traditional Korean food, in standardizing its quality. In this study, pretreatment based on sterilization processes, namely, slightly acidic electrolyzed water (SAEW) disinfection and ultraviolet C light-emitting diode (UVC-LED) of raw and subsidiary kimchi materials were used to reduce the initial microorganisms in them, thereby increasing the efficiency and value of the kimchi LAB starter during fermentation. Pretreatment sterilization effectively suppressed microorganisms that threatened the sanitary value and quality of kimchi. In addition, pretreatment based on sterilization effectively reduced the number of initial microbial colonies in kimchi, creating an environment in which kimchi LAB starters could settle or dominate, compared to non-sterilized kimchi. These differences in the initial microbial composition following the sterilization process and the addition of kimchi LAB starters led to differences in the metabolites that positively affect the taste and flavor of kimchi. The combined processing technology used in our study, that is, pre-sterilization and LAB addition, may be a powerful approach for kimchi quality standardization.

Improving acetoin production through construction of a genome-scale metabolic model

Acetoin was widely used in food, medicine, and other industries, because of its unique fragrance. Bacillus amyloliquefaciens was recognized as a safe strain and a promising acetoin producer in fermentation. However, due to the complexity of its metabolic network, it had not been fully utilized. Therefore, a genome-scale metabolic network model (iJYQ746) of B. amyloliquefaciens was constructed in this study, containing 746 genes, 1736 reactions, and 1611 metabolites. The results showed that Mg²⁺, Mn²⁺, and Fe²⁺ have inhibitory effects on acetoin. When the stirring speed was 400 rpm, the maximum titer was 49.8 g L^-1. Minimization of metabolic adjustments (MOMA) was used to identify potential metabolic modification targets 2-oxoglutarate aminotransferase (serC, EC 2.6.1.52) and glucose-6-phosphate isomerase (pgi, EC 5.3.1.9). These targets could effectively accumulate acetoin by increasing pyruvate content, and the acetoin synthesis rate was increased by 610% and 10%, respectively. This provides a theoretical basis for metabolic engineering to reasonably transform B. amyloliquefaciens and produce acetoin.

Application of Commercial Biopreservation Starter in Combination with MAP for Shelf-Life Extension of Burrata Cheese

Burrata is a fresh pasta filata cheese manufactured in Italy. Its demand on the worldwide market is constantly growing, and prolonging its shelf-life is an important challenge for the Italian dairy industry. In the present study, combining a commercial bio-protective starter and modified atmosphere packaging (MAP) was evaluated as a strategy to delay the spoilage of product quality. Three experimental samples of burrata were produced by experimental trials at the industrial level and stored for 28 days under refrigerated conditions. Two samples contained the protective starter but were packaged differently (under MAP and immersed in water), and one did not contain the starter and was packaged under MAP. A sample of burrata without a starter and immersed in water was also prepared and used as a control. The combination of MAP and bio-protective starter delayed the degradation of lactose and citric acid, used as indices of microbial activity. In fact, lower counts of Enterobacteriaceae and Pseudomonas were observed in this sample. In contrast, control burrata had the highest level of total Volatile Organic Compounds (VOC) at the end of the storage period, because of higher microbial activity. Even though all samples were judged to be unacceptable after 28 days from the sensory point of view, the sample with bio-protective starter under MAP had the best score after 21 days, obtaining a shelf-life extension of about 7 days with respect to control. In conclusion, the combination of MAP and protective starter culture could be an easy way to extend the shelf-life of burrata stored under correct refrigerated conditions.

Effect of different organic acid additives on the fermentation quality and bacterial community of paper mulberry (Broussonetia papyrifera) silage

To investigate the effects of different organic acid additives and their concentrations on the fermentation quality and bacterial community of paper mulberry silage, paper mulberry was left untreated (control) or was treated with ethylenediaminetetraacetic acid (EDTA), propionic acid (PA) or citric acid (CA), the amount of each additive was 2 g.kg^-1 FM, 5 g.kg^-1 FM and g.kg^-1 FM. All groups were ensiled for 3, 7, 15, 30 and 60 days. Compared to the control, adding EDTA reduced protein breakdown, preserved more water-soluble carbohydrates of the silages (WSCs, 24.74 g.kg^-1 DM), and high concentrations of EDTA inhibited the activity of undesirable microorganisms. Adding PA increased the abundance of Lactiplantibacillus and decreased the abundance of Enterococcus, and it caused a rapid decrease in the pH of the silage at an early stage (from 6.50 to 5.31) while altering the microbiota, and low concentrations of PA resulted in high LA (66.22 g.kg^-1 DM) concentration and low PA (9.92 g.kg^-1 DM) concentration at 60 days of ensiling. Different concentrations of additives altered the microbial community of paper mulberry to different degrees. High concentrations of PA and CA can increase the abundance of Lactiplantibacillus. High concentrations of CA resulted in a rapid decrease in silage pH at an early stage and higher WSC concentration. These results suggest that EDTA, PA and CA can be used as additives to improve the quality of paper mulberry silage.

Phenotype testing, genome analysis, and metabolic interactions of three lactic acid bacteria strains existing as a consortium in a naturally fermented milk

This work reports the characterization of three lactic acid bacteria (LAB) strains -Lactococcus lactis LA1, Lactococcus cremoris LA10, and Lactiplantibacillus plantarum LA30- existing as a stable consortium in a backslopping-inoculated, naturally fermented milk (NFM). This study aimed at uncovering the biochemical and genetic basis of the stability of the consortium and the cooperativity among the strains during milk fermentation. All three strains were subjected to phenotyping, covering the utilization of carbohydrates, enzyme activity, and antibiotic resistance. The strains were grown in milk individually, as well as in all possible combinations, and the resulting fermented product was analyzed for sugars, organic acids, and volatile compounds. Finally, the genomes of the three strains were sequenced and analyzed for genes associated with technological and safety properties. As expected, wide phenotypic diversity was seen between the strains. Lactococcus cremoris LA10 was the only strain to reach high cell densities and coagulate milk alone after incubation at 22°C for 24 h; congruently, it possessed a gene coding for a PrtP type II caseinolytic protease. Compared to any other fermentation, acetaldehyde concentrations were greater by a factor of six when all three strains grew together in milk, suggesting that its production might be the result of an interaction between them. Lactococcus lactis LA1, which carried a plasmid-encoded citQRP operon, was able to utilize milk citrate producing diacetyl and acetoin. No genes encoding virulence traits or pathogenicity factors were identified in any of the strains, and none produced biogenic amines from amino acid precursors, suggesting them to be safe. Lactiplantibacillus plantarum LA30 was susceptible to tetracycline, although it harbors a disrupted antibiotic resistance gene belonging to the tetM/tetW/tetO/tetS family. All three strains contained large numbers of pseudogenes, suggesting that they are well adapted ("domesticated") to the milk environment. The consortium as a whole or its individual strains might have a use as a starter or as starter components for dairy fermentations. The study of simple consortia, such as that existing in this NFM, can help reveal how microorganisms interact with one another, and what influence they may have on the sensorial properties of fermented products.

Genomic and Transcriptional Characteristics of Strain Rum-meliibacillus sp. TYF-LIM-RU47 with an Aptitude of Directly Producing Acetoin from Lignocellulose

Rummeliibacillus sp. TYF-LIM-RU47, isolated from the fermentation substrate of grain vinegar, could produce acetoin using a variety of carbon sources, including pentose, hexose and lignocellulose. The draft genome of TYF-LIM-RU47 was constructed and the genomic information revealed that TYF-LIM-RU47 contains genes related to starch and sucrose metabolism, pyruvate metabolism, the oxidative phosphorylation metabolic pathway and lignocellulosic metabolism. The acetoin anabolic pathway of TYF-LIM-RU47 has been deduced from the sequencing results, and acetoin is produced from α-acetolactate via decarboxylation and diacetyl reductase catalytic steps. The results of quantitative real-time PCR tests showed that the synthesis and degradation of acetoin had a dynamic balance in acetoin metabolism, and the transcription of the α-acetolactate synthase gene might exist to the extent of feedback regulation. This study can help researchers to better understand the bioinformation of thermophilic-lignocellulosic bacteria and the mechanisms of the acetoin biosynthesis pathway.

Harnessing diversity of Lactococcus lactis from raw goat milk: Design of an indigenous starter for the production of Rocamadour, a French PDO cheese

Twenty-four strains of Lactococcus lactis isolated from raw goat milk collected in the Rocamadour PDO area were analysed by MLST typing and phenotypic characterisation. The strains were combined to design an indigenous starter for the production of Rocamadour PDO cheese. The strains were divided into three classes based on their technological properties: acidifying and proteolytic strains in class I (12/24 strains), slightly acidifying and non-proteolytic strains in class II (2/24 strains), and non-acidifying and non-proteolytic strains in class III (10/24 strains). Interestingly, all but three strains (21/24) produced diacetyl/acetoin despite not having citrate metabolism genes, as would classically be expected for the production of these aroma compounds. Three strains (EIP07A, EIP13D, and EIP20B) were selected for the indigenous starter based on the following inclusion/exclusion criteria: (i) no negative interactions between included strains, (ii) ability to metabolize lactose and at least one strain with the prtP gene and/or capable of producing diacetyl/acetoin, and (iii) selected strains derived from different farms to maximise genetic and phenotypic diversity. Despite consisting exclusively of L. lactis strains, the designed indigenous starter allowed reproducible cheese production with performances similar to those obtained with an industrial starter and with the sensory qualities expected of Rocamadour PDO cheese.

Impact of lactic acid bacteria and their metabolites on the techno-functional properties and health benefits of fermented dairy products

After conversion of lactose to lactic acid, several biochemical changes occur such as enhanced protein digestibility, fatty acids release, and production of bioactive compounds etc. during the fermentation process that brings nutritional and quality improvement in the fermented dairy products (FDP). A diverse range of lactic acid bacteria (LAB) is being utilized for the development of FDP with specific desirable techno-functional attributes. This review contributes to the knowledge of basic pathways and changes during fermentation process and the current research on techniques used for identification and quantification of metabolites. The focus of this article is mainly on the metabolites responsible for maintaining the desired attributes and health benefits of FDP as well as their characterization from raw milk. LAB genera including Lactobacillus, Streptococcus, Leuconostoc, Pediococcus and Lactococcus are involved in the fermentation of milk and milk products. LAB species accrue these benefits and desirable properties of FDP producing the bioactive compounds and metabolites using homo-fermentative and heterofermentative pathways. Generation of metabolites vary with incubation and other processing conditions and are analyzed and quantified using highly advanced and sophisticated instrumentation including nuclear magnetic resonance, mass-spectrometry based techniques. Health benefits of FDP are mainly possible due to the biological roles of such metabolites that also cause technological improvements desired by dairy manufacturers and consumers.

Genomic diversity of Serratia proteamaculans and Serratia liquefaciens predominant in seafood products and spoilage potential analyses

Serratia sp. cause food losses and waste due to spoilage; it is noteworthy that they represent a dominant population in seafood. The main spoilage associated species comprise S. liquefaciens, S. grimesii, S. proteamaculans and S. quinivorans, also known as S. liquefaciens-like strains. These species are difficult to discriminate since classical 16S rRNA gene-based sequences do not possess sufficient resolution. In this study, a phylogeny based on the short-length luxS gene was able to speciate 47 Serratia isolates from seafood, with S. proteamaculans being the main species from fresh salmon and tuna, cold-smoked salmon, and cooked shrimp while S. liquefaciens was only found in cold-smoked salmon. The genome of the first S. proteamaculans strain isolated from the seafood matrix (CD3406 strain) was sequenced. Pangenome analyses of S. proteamaculans and S. liquefaciens indicated high adaptation potential. Biosynthetic pathways involved in antimicrobial compounds production and in the main seafood spoilage compounds were also identified. The genetic equipment highlighted in this study contributed to gain further insights into the predominance of Serratia in seafood products and their capacity to spoil.

Probiotic potential of Enterococcus hirae in goat milk and its survival in canine gastrointestinal conditions simulated in vitro

In canine nutrition, the use of goat nutraceutical dairy products is an innovative proposal. Therefore, the objective of this study was to prepare fermented goat milk with probiotic potential in dogs in an in vitro model. A total of 40 lactic acid bacteria (LAB) species were grown, of which 30 were CAP isolates originally from goat milk and 10 were CAN isolates originally from fecal material of newborn dogs. The isolates were selected based on resistance to the simulated canine gastrointestinal condition and acidifying ability. After this preliminary screening, the analyses were performed regarding β-galactosidase and exopolysaccharide formation, diacetyl production, adhesion proteins Mub and mapa, hydrophobicity, DPPH assay, virulence and antibiotic resistance. With these evaluations, four LAB isolates were identified using sequencing of the 16S rRNA gene. These were identified as Enterococcus hirae and were used to produce fermented goat milk. For statistical analysis, the data were analyzed using the Scott-Knott test and also submitted to analysis of variance and the Tukey test (P < 0.05). In the evaluation of goat milk fermented with E. hirae and control, over the 36-day storage period there was a reduction in pH and an increase in acidity, and higher levels of LAB were observed in goat milk fermented with E. hirae. Therefore, both these E. hirae isolates and the fermented goat milk produced showed satisfactory results in vitro, demonstrating probiotic efficiency and food safety for dogs.

Unravelling the Potential of Lactococcus lactis Strains to Be Used in Cheesemaking Production as Biocontrol Agents

This research, developed within an exchange program between Italy and Canada, represents the first step of a three-year project intended to evaluate the potential of nisin-producing Lactococcus lactis strains isolated from Italian and Canadian dairy products to select a consortium of strains to be used as biocontrol agents in Crescenza and Cheddar cheese production. In this framework, the acidification and the production of nisin in milk, and the volatile molecule profiles of the fermented milk, were recorded. The strains were further tested for their anti-Listeria monocytogenes activity in milk. The data obtained highlighted good potential for some of the tested strains, which showed production of nisin beginning within 12 h after the inoculation and reaching maximum levels between 24 and 48 h. The highest inactivation levels of L. monocytogenes in milk was reached in the presence of the strains 101877/1, LBG2, 9FS16, 11FS16, 3LC39, FBG1P, UL36, UL720, UL35. The strains generated in milk-specific volatile profiles and differences in the presence of fundamental aromatic molecules of dairy products, such as 2-butanone and diacetyl. The results highlight the interesting potential of some L. lactis strains, the producer of nisin, to be further used as biocontrol agents, although the strains need to be tested for interaction with traditional thermophilic starters and tested in real cheesemaking conditions.

Determination of volatile organic compounds in Slovak bryndza cheese by the electronic nose and the headspace solid-phase microextraction gas chromatography-mass spectrometry

The aim of the present study was to describe volatile organic compounds of the traditional Slovak bryndza cheese determined by using an electronic nose (e-nose) and a gas chromatography mass spectrometry (GCMS) with head-space solid phase microextraction (HS-SPME). For the first time, e-nose based on the gas chromatography principle with a flame ionization detector was described to identify and quantify aroma active compounds of bryndza cheese from Slovakia. The e-nose detects aroma compounds of very small concentrations in real-time of a few minutes and identifies them by comparing Kovats´ retention indices with the NIST library. Bryndza cheese produced from unpasteurized ewe´s milk and from a mixture of raw ewe´s and pasteurized cow´s types of milk were collected from 2 different Slovak farms beginning in May through to September 2019. The flavour and aroma of bryndza cheese are apparently composed of compounds contained in milk and the products of fermentation of the substrate by bacteria and fungi. Regarding volatile organic compounds, 25 compounds were detected and identified by an electronic nose with a discriminant >0.900 with ethyl acetate, isopentyl acetate, 2-butanone, acetic acid, butanoic acid, and butane-2,3-dione confirmed by gas chromatography. We confirm the suitability of the electronic nose to be used for monitoring of bryndza cheese quality.

The Impact of Different Factors on the Quality and Volatile Organic Compounds Profile in "Bryndza" Cheese

The aim of this study was to evaluate the influence of different factors on the basic physicochemical and microbiological parameters, as well as volatile organic compounds of traditionally (farm) and industrially produced "bryndza" cheese. The samples were obtained from eight producers in different areas of Slovakia during the ewe's milk production season, from May to September. The physicochemical parameters set by the legislation were monitored by reference methods. The "bryndza" cheese microbiota was determined by using the plate cultivation method. There was analysis of volatile organic compounds carried out by electronic nose, as well as gas chromatography mass spectrometry. Seasonality and production technology (traditional and industrial ones) are the main factors that affect the standard quality of "bryndza" cheese. Lactic acid bacteria were dominated from bacterial microbiota, mostly presumptive lactococci, followed presumptive lactobacilli and enterococci. The numbers of coliform bacteria were higher in traditionally produced "bryndza" cheese than in industrially produced "bryndza" cheese. The presence of Dipodascus geotrichum was detected in all samples. There were key volatile organic compounds such as ethyl acetate, isoamyl acetate, 2-butanone, hexanoic acid, D-limonene, and 2,3-butanedione. The statistically significant differences were found among "bryndza" cheese samples and these differences were connected with the type of milk and dairies.

Microbial Diversity Associated with Gwell, a Traditional French Mesophilic Fermented Milk Inoculated with a Natural Starter

Gwell is a traditional mesophilic fermented milk from the Brittany region of France. The fermentation process is based on a back-slopping method. The starter is made from a portion of the previous Gwell production, so that Gwell is both the starter and final product for consumption. In a participatory research framework involving 13 producers, Gwell was characterized from both the sensory and microbial points of view and was defined by its tangy taste and smooth and dense texture. The microbial community of typical Gwell samples was studied using both culture-dependent and culture-independent approaches. Lactococcus lactis was systematically identified in Gwell, being represented by both subspecies cremoris and lactis biovar diacetylactis which were always associated. Geotrichum candidum was also found in all the samples. The microbial composition was confirmed by 16S and ITS2 metabarcoding analysis. We were able to reconstruct the history of Gwell exchanges between producers, and thus obtained the genealogy of the samples we analyzed. The samples clustered in two groups which were also differentiated by their microbial composition, and notably by the presence or absence of yeasts identified as Kazachstania servazii and Streptococcus species.

Suitability of the Nisin Z-producer Lactococcus lactis subsp. lactis CBM 21 to be Used as an Adjunct Culture for Squacquerone Cheese Production

This research investigated the technological and safety effects of the nisin Z producer Lactococcus lactis subsp. lactis CBM 21, tested as an adjunct culture for the making of Squacquerone cheese in a pilot-scale plant. The biocontrol agent remained at a high level throughout the cheese refrigerated storage, without having a negative influence on the viability of the conventional Streptococcus thermophilus starter. The inclusion of CBM 21 in Squacquerone cheesemaking proved to be more effective compared to the traditional one, to reduce total coliforms and Pseudomonas spp. Moreover, the novel/innovative adjunct culture tested did not negatively modify the proteolytic patterns of Squacquerone cheese, but it gave rise to products with specific volatile and texture profiles. The cheese produced with CBM 21 was more appreciated by the panelists with respect to the traditional one.

Lactic Fermented Fruit or Vegetable Juices: Past, Present and Future

Numerous traditional low-alcohol fermented beverages produced from fruit or vegetables are described around the world. Fruit and vegetables and lactic fermented products both present nutritional benefits, which give reasons for the recent expansion of non-dairy lactic fermented juices on the market. In addition, fruit and vegetable juices are new carriers for probiotic bacteria. Specific phenotypic traits of lactic acid bacteria (LAB) are required so that LAB can effectively grow in fruit or vegetable juices, increase their safety and improve their sensory and nutritional quality. From the diversity of microbiota of spontaneous fermentations, autochthonous starters can be selected, and their higher performance than allochthonous LAB was demonstrated. Achieving long-term storage and constant high quality of these beverages requires additional processing steps, such as heat treatment. Alternatives to conventional treatments are investigated as they can better preserve nutritional properties, extract bioactive compounds and promote the growth and metabolism of LAB. Specific processing approaches were shown to increase probiotic viability of fruit and vegetable juices. More knowledge on the metabolic activity of lactic acid bacterium consortium in fruit or vegetable juices has become a bottleneck for the understanding and the prediction of changes in bioactive compounds for functional beverages development. Hopefully, the recent developments of metabolomics and methods to describe enzymatic machinery can result in the reconstruction of fermentative pathways.

Investigation of genomic characteristics and carbohydrates' metabolic activity of Lactococcus lactis subsp. lactis during ripening of a Swiss-type cheese

Genetic diversity and metabolic properties of Lactococcus lactis subsp. lactis were explored using phylogenetic, pan-genomic and metatranscriptomic analysis. The genomes, used in the current study, were available and downloaded from the GenBank which were primarily related with microorganisms isolated from dairy products and secondarily from other foodstuffs. To study the genetic diversity of the microorganism, various bioinformatics tools were employed such as average nucleotide identity, digital DNA-DNA hybridization, phylogenetic analysis, clusters of orthologous groups analysis, KEGG orthology analysis and pan-genomic analysis. The results showed that Lc. lactis subsp. lactis strains cannot be sufficiently separated into phylogenetic lineages based on the 16S rRNA gene sequences and core genome-based phylogenetic analysis was more appropriate. Pan-genomic analysis of the strains indicated that the core, accessory and unique genome comprised of 1036, 3146 and 1296 genes, respectively. Considering the results of pan-genomic and KEGG orthology analyses, the metabolic network of Lc. lactis subsp. lactis was rebuild regarding its carbohydrates' metabolic capabilities. Based on the metatranscriptomic data during the ripening of the Swiss-type Maasdam cheese at 20 °C and 5 °C, it was shown that the microorganism performed mixed acid fermentation producing lactate, formate, acetate, ethanol and 2,3-butanediol. Mixed acid fermentation was more pronounced at higher ripening temperatures. At lower ripening temperatures, the genes involved in mixed acid fermentation were repressed while lactate production remained unaffected resembling to a homolactic fermentation. Comparative genomics and metatranscriptomic analysis are powerful tools to gain knowledge on the genomic diversity of the lactic acid bacteria used as starter cultures as well as on the metabolic activities occurring in fermented dairy products.

Technological properties of Lactococcus lactis subsp. lactis bv. diacetylactis obtained from dairy and non-dairy niches

Lactococcus lactis subsp. lactis bv. diacetylactis strains are often used as starter cultures by the dairy industry due to their production of acetoin and diacetyl, important substances that add buttery flavor notes in dairy products. Twenty-three L. lactis subsp. lactis isolates were obtained from dairy products (milk and cheese) and dairy farms (silage), identified at a biovar level, fingerprinted by rep-PCR and characterized for some technological features. Fifteen isolates presented molecular and phenotypical (diacetyl and citrate) characteristics coherent with L. lactis subsp. lactis bv. diacetylactis and rep-PCR allowed the identification of 12 distinct profiles (minimum similarity of 90%). Based on technological features, only two isolates were not able to coagulate skim milk and 10 were able to produce proteases. All isolates were able to acidify skim milk: two isolates, in special, presented high acidifying ability due to their ability in reducing more than two pH units after 24 h. All isolates were also able to grow at different NaCl concentrations (0 to 10%, w/v), and isolates obtained from peanut and grass silages presented the highest NaCl tolerance (10%, w/v). These results indicate that the L. lactis subsp. lactis bv. diacetylactis isolates presented interesting technological features for potential application in fermented foods production. Despite presenting promising technological features, the isolates must be assessed according to their safety before being considered as starter cultures.

Biopreservation as a potential hurdle for Bacillus cereus growth in fresh cheese

This study aimed to evaluate the possible inhibitory effect of natural lactic acid bacteria on the growth of 2 Bacillus cereus strains. First, we evaluated the behavior of spores of B. cereus GPe2 and D43 when inoculated before cheesemaking using pasteurized or raw milk; no statistical differences were observed between cheese produced with the 2 types of milk. Then, lactic acid bacteria (LAB) were isolated from cheese at the last sampling time, identified, and tested in vitro for their antagonistic activity and organic acid production by using an HPLC method, showing antimicrobial potential. The LAB that produced larger inhibition halos (>9 mm) against B. cereus strains (LAB 3, 6, 9, 10: Lactococcus lactis ssp. lactis; LAB 7: Lactococcus lactis ssp. cremoris) were selected to produce a LAB mixture for subsequent tests. Spores of B. cereus GPe2 and D43 were inoculated in pasteurized milk before cheesemaking with or without addition of the LAB mixture at a high dosage. Bacillus cereus grew more slowly when LAB were added to the dairy matrix (with differences from 2.36 to 2.66 log cfu/g in B. cereus GPe2 and D43 growth).

Screening of aroma-producing lactic acid bacteria and their application in improving the aromatic profile of yogurt

The development of yogurt flavor is a complicated and dynamic biochemical process. In addition to traditional starter cultures, adjunct cultures could also make significant contributions to the flavor profiles of yogurt. In the current study, two Lactobacillus plantarum strains (1-33 and 1-34) were isolated based on their abilities to produce acetaldehyde and diacetyl. In co-fermentation with traditional starters, these isolated strains were able to maintain viability without affecting the yogurt's acidification profiles. Furthermore, they positively influenced the aroma quality of the yogurt samples. They promoted the formation of volatile metabolites, especially acetaldehyde, diacetyl, and acetoin, which are recognized as characteristic compounds. The results of this work provide novel knowledge about the contributions of isolated strains on the flavor profiles of yogurt, which will help to improve the organoleptic properties of the final products. PRACTICAL APPLICATIONS: Using lactic acid bacteria (LAB) as adjunct cultures co-fermented with traditional yogurt starter cultures can increase the quantities of flavor compounds in yogurt. This study enriches our understanding of the effects of adjunct cultures on yogurt flavor. Researchers and manufacturers that specialize in yogurt making can use the results of this study to improve the aromatic profile and organoleptic quality of yogurt.

Comparative Genome Analysis of Lactococcus lactis Indicates Niche Adaptation and Resolves Genotype/Phenotype Disparity

Lactococcus lactis is one of the most important micro-organisms in the dairy industry for the fermentation of cheese and buttermilk. Besides the conversion of lactose to lactate it is responsible for product properties such as flavor and texture, which are determined by volatile metabolites, proteolytic activity and exopolysaccharide production. While the species Lactococcus lactis consists of the two subspecies lactis and cremoris their taxonomic position is confused by a group of strains that, despite of a cremoris genotype, display a lactis phenotype. Here we compared and analyzed the (draft) genomes of 43 L. lactis strains, of which 19 are of dairy and 24 are of non-dairy origin. Machine-learning algorithms facilitated the identification of orthologous groups of protein sequences (OGs) that are predictors for either the taxonomic position or the source of isolation. This allowed the unambiguous categorization of the genotype/phenotype disparity of ssp. lactis and ssp. cremoris strains. A detailed analysis of phenotypic properties including plasmid-encoded genes indicates evolutionary changes during niche adaptations. The results are consistent with the hypothesis that dairy isolates evolved from plant isolates. The analysis further suggests that genomes of cremoris phenotype strains are so eroded that they are restricted to a dairy environment. Overall the genome comparison of a diverse set of strains allowed the identification of niche and subspecies specific genes. This explains evolutionary relationships and will aid the identification and selection of industrial starter cultures.

Symposium review: Genomic investigations of flavor formation by dairy microbiota

Flavor is one of the most important attributes of any fermented dairy product. Dairy consumers are known to be willing to experiment with different flavors; thus, many companies producing fermented dairy products have looked at culture manipulation as a tool for flavor diversification. The development of flavor is a complex process, originating from a combination of microbiological, biochemical, and technological aspects. A key driver of flavor is the enzymatic activities of the deliberately inoculated starter cultures, in addition to the environmental or "nonstarter" microbiota. The contribution of microbial metabolism to flavor development in fermented dairy products has been exploited for thousands of years, but the availability of the whole genome sequences of the bacteria and yeasts involved in the fermentation process and the possibilities now offered by next-generation sequencing and downstream "omics" technologies is stimulating a more knowledge-based approach to the selection of desirable cultures for flavor development. By linking genomic traits to phenotypic outputs, it is now possible to mine the metabolic diversity of starter cultures, analyze the metabolic routes to flavor compound formation, identify those strains with flavor-forming potential, and select them for possible commercial application. This approach also allows for the identification of species and strains not previously considered as potential flavor-formers, the blending of strains with complementary metabolic pathways, and the potential improvement of key technological characteristics in existing strains, strains that are at the core of the dairy industry. An in-depth knowledge of the metabolic pathways of individual strains and their interactions in mixed culture fermentations can allow starter blends to be custom-made to suit industry needs. Applying this knowledge to starter culture research programs is enabling research and development scientists to develop superior starters, expand flavor profiles, and potentially develop new products for future market expansion.

Genomic and metabolic features of the Bacillus amyloliquefaciens group- B. amyloliquefaciens, B. velezensis, and B. siamensis- revealed by pan-genome analysis

The genomic and metabolic features of the Bacillus amyloliquefaciens group comprising B. amyloliquefaciens, B. velezensis, and B. siamensis were investigated through a pan-genome analysis combined with an experimental verification of some of the functions identified. All B. amyloliquefaciens group genomes were retrieved from GenBank and their phylogenetic relatedness was subsequently investigated. Genome comparisons of B. amyloliquefaciens, B. siamensis, and B. velezensis showed that their genomic and metabolic features were similar; however species-specific features were also identified. Energy metabolism-related genes are more enriched in B. amyloliquefaciens, whereas secondary metabolite biosynthesis-related genes are enriched in B. velezensis. Compared to B. amyloliquefaciens and B. siamensis, B. velezensis harbors more genes in its core-genome which are involved in the biosynthesis of antimicrobial compounds, as well as genes involved in d-galacturonate and d-fructuronate metabolism. B. amyloliquefaciens, B. siamensis, and B. velezensis all harbor a xanthine oxidase gene cluster (xoABCDE) in their core-genomes that is involved in metabolizing xanthine and uric acid to glycine and oxalureate. A reconstruction of B. amyloliquefaciens group metabolic pathways using their individual pan-genomes revealed that the B. amyloliquefaciens group strains have the ability to metabolize diverse carbon sources aerobically, or anaerobically, and can produce various metabolites such as lactate, ethanol, acetate, CO₂, xylitol, diacetyl, acetoin, and 2,3-butanediol. This study therefore provides insights into the genomic and metabolic features of the B. amyloliquefaciens group.

Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation

The genomic and metabolic features of Leuconostoc (Leu) mesenteroides were investigated through pan-genomic and transcriptomic analyses. Relatedness analysis of 17 Leu. mesenteroides strains available in GenBank based on 16S rRNA gene sequence, average nucleotide identity, in silico DNA-DNA hybridization, molecular phenotype, and core-genome indicated that Leu. mesenteroides has been separated into different phylogenetic lineages. Pan-genome of Leu. mesenteroides strains, consisting of 999 genes in core-genome, 1,432 genes in accessory-genome, and 754 genes in unique genome, and their COG and KEGG analyses showed that Leu. mesenteroides harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The reconstruction of fermentative metabolic pathways for Leu. mesenteroides strains showed that Leu. mesenteroides produces various metabolites such as lactate, ethanol, acetate, CO₂, mannitol, diacetyl, acetoin, and 2,3-butanediol through an obligate heterolactic fermentation from various carbohydrates. Fermentative metabolic features of Leu. mesenteroides during kimchi fermentation were investigated through transcriptional analyses for the KEGG pathways and reconstructed metabolic pathways of Leu. mesenteroides using kimchi metatranscriptomic data. This was the first study to investigate the genomic and metabolic features of Leu. mesenteroides through pan-genomic and metatranscriptomic analyses, and may provide insights into its genomic and metabolic features and a better understanding of kimchi fermentations by Leu. mesenteroides.

From Genome to Phenotype: An Integrative Approach to Evaluate the Biodiversity of Lactococcus lactis

Lactococcus lactis is one of the most extensively used lactic acid bacteria for the manufacture of dairy products. Exploring the biodiversity of L. lactis is extremely promising both to acquire new knowledge and for food and health-driven applications. L. lactis is divided into four subspecies: lactis, cremoris, hordniae and tructae, but only subsp. lactis and subsp. cremoris are of industrial interest. Due to its various biotopes, Lactococcus subsp. lactis is considered the most diverse. The diversity of L. lactis subsp. lactis has been assessed at genetic, genomic and phenotypic levels. Multi-Locus Sequence Type (MLST) analysis of strains from different origins revealed that the subsp. lactis can be classified in two groups: “domesticated” strains with low genetic diversity, and “environmental” strains that are the main contributors of the genetic diversity of the subsp. lactis. As expected, the phenotype investigation of L. lactis strains reported here revealed highly diverse carbohydrate metabolism, especially in plant- and gut-derived carbohydrates, diacetyl production and stress survival. The integration of genotypic and phenotypic studies could improve the relevance of screening culture collections for the selection of strains dedicated to specific functions and applications.

Production of Acetoin through Simultaneous Utilization of Glucose, Xylose, and Arabinose by Engineered Bacillus subtilis

Glucose, xylose and arabinose are the three most abundant monosaccharide found in lignocellulosic biomass. Effectively and simultaneously utilization of these sugars by microorganisms for production of the biofuels and bio-chemicals is essential toward directly fermentation of the lignocellulosic biomass. In our previous study, the recombinant Bacillus subtilis 168ARSRCPΔacoAΔbdhA strain was already shown to efficiently utilize xylose for production of acetoin, with a yield of 0.36 g/g xylose. In the current study, the Bacillus subtilis168ARSRCPΔacoAΔbdhA strain was further engineered to produce acetoin from a glucose, xylose, and arabinose mixtures. To accomplish this, the endogenous xylose transport protein AraE, the exogenous xylose isomerase gene xylA and the xylulokinase gene xylB from E. coli were co-overexpressed in the Bacillus subtilis 168ARSRCPΔacoAΔbdhA strain, which enabled the resulting strain, denoted ZB02, to simultaneously utilize glucose and xylose. Unexpectedly, the ZB02 strain could simultaneously utilize glucose and arabinose also. Further results indicated that the transcriptional inhibition of the arabinose transport protein gene araE was the main limiting factor for arabinose utilization in the presence of glucose. Additionally, the arabinose operon in B. subtilis could be activated by the addition of arabinose, even in the presence of glucose. Through fed-batch fermentation, strain ZB02 could simultaneously utilize glucose, xylose, and arabinose, with an average sugar consumption rate of 3.00 g/l/h and an average production of 62.2 g/l acetoin at a rate of 0.864 g/l/h. Finally, the strain produced 11.2 g/l acetoin from lignocellulosic hydrolysate (containing 20.6g/l glucose, 12.1 g/l xylose and 0.45 g/l arabinose) in flask cultivation, with an acetoin yield of 0.34 g/g total sugar. The result demonstrates that this strain has good potential for the utilization of lignocellulosic hydrolysate for production of acetoin.

Lactococcus lactis V7 inhibits the cell invasion of bovine mammary epithelial cells by Escherichia coli and Staphylococcus aureus

Bovine mastitis, an inflammatory disease of the mammary gland often associated to bacterial infection, is the first cause of antibiotic use in dairy cattle. Because of the risk of antibioresistance emergence, alternative non-antibiotic strategies are needed to prevent or to cure bovine mastitis and reduce the antibiotic use in veterinary medicine. In this work, we investigated Lactococcus lactis V7, a strain isolated from the mammary gland, as a probiotic option against bovine mastitis. Using bovine mammary epithelial cell (bMEC) culture, and two representative strains for Escherichia coli and for Staphylococcus aureus, two major mastitis pathogens, we investigated L. lactis V7 ability to inhibit cell invasion (i.e. adhesion and internalization) of these pathogens into bMEC. L. lactis V7 ability to modulate the production of CXCL8, a key chemokine IL-8 responsible for neutrophil influx, in bMEC upon challenge with E. coli was investigated by an ELISA dosage of CXCL8 in bMEC culture supernatants. We showed that L. lactis V7 inhibited the internalisation of both E. coli and S. aureus strains into bMEC, whereas it inhibited the adhesion of only one out of the two S. aureus strains and of none of the E. coli strains tested. Investigation of the bMEC immune response showed that L. lactis V7 alone induced a slight increase in CXCL8 production in bMEC and that it increased the inflammatory response in bMEC challenged with the E. coli strains. Altogether these features of L. lactis V7 make it a potential promising candidate for a probiotic prevention strategy against bovine mastitis.

From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment

Lactococcus lactis is an organism of substantial economic importance, used extensively in the production of fermented foods and widely held to have evolved from plant strains. The domestication of this organism to the milk environment is associated with genome reduction and gene decay, and the acquisition of specific genes involved in protein and lactose utilisation by horizontal gene transfer. In recent years, numerous studies have focused on uncovering the physiology and molecular biology of lactococcal strains from the wider environment for exploitation in the dairy industry. This in turn has facilitated comparative genome analysis of lactococci from different environments and provided insight into the natural phenotypic and genetic diversity of L. lactis. This diversity may be exploited in dairy fermentations to develop products with improved quality and sensory attributes. In this review, we discuss the classification of L. lactis and the problems that arise with phenotype/genotype designation. We also discuss the adaptation of non-dairy lactococci to milk, the traits associated with this adaptation and the potential application of non-dairy lactococci to dairy fermentations.

Two-stage pH control strategy based on the pH preference of acetoin reductase regulates acetoin and 2,3-butanediol distribution in Bacillus subtilis

Acetoin reductase/2,3-butanediol dehydrogenase (AR/BDH), which catalyzes the interconversion between acetoin and 2,3-butanediol, plays an important role in distribution of the products pools. This work characterized the Bacillus subtilis AR/BDH for the first time. The enzyme showed very different pH preferences of pH 6.5 for reduction and pH 8.5 for oxidation. Based on these above results, a two-stage pH control strategy was optimized for acetoin production, in which the pH was controlled at 6.5 for quickly converting glucose to acetoin and 2,3-butanediol, and then 8.0 for reversely transforming 2,3-butanediol to acetoin. By over-expression of AR/BDH in the wild-type B. subtilis JNA 3-10 and applying fed-batch fermentation based on the two-stage pH control strategy, acetoin yield of B. subtilis was improved to a new record of 73.6 g/l, with the productivity of 0.77 g/(l·h). The molar yield of acetoin was improved from 57.5% to 83.5% and the ratio of acetoin/2,3-butanediol was switched from 2.7∶1 to 18.0∶1.

The rebalanced pathway significantly enhances acetoin production by disruption of acetoin reductase gene and moderate-expression of a new water-forming NADH oxidase in Bacillus subtilis

Bacillus subtilis produces acetoin as a major extracellular product. However, the by-products of 2,3-butanediol, lactic acid and ethanol were accompanied in the NADH-dependent pathways. In this work, metabolic engineering strategies were proposed to redistribute the carbon flux to acetoin by manipulation the NADH levels. We first knocked out the acetoin reductase gene bdhA to block the main flux from acetoin to 2,3-butanediol. Then, among four putative candidates, we successfully screened an active water-forming NADH oxidase, YODC. Moderate-expression of YODC in the bdhA disrupted B. subtilis weakened the NADH-linked pathways to by-product pools of acetoin. Through these strategies, acetoin production was improved to 56.7g/l with an increase of 35.3%, while the production of 2,3-butanediol, lactic acid and ethanol were decreased by 92.3%, 70.1% and 75.0%, respectively, simultaneously the fermentation duration was decreased 1.7-fold. Acetoin productivity by B. subtilis was improved to 0.639g/(lh).

Technological properties of bacteriocin-producing lactic acid bacteria isolated from Pico cheese an artisanal cow's milk cheese

AIM

Evaluate technologically relevant properties from bacteriocin-producing strains to use as starter/adjunct cultures in cheese making.

METHODS AND RESULTS

Eight isolates obtained from Pico cheese produced in Azores (Portugal) were found to produce bacteriocins against Listeria monocytogenes and three isolates against Clostridium perfringens. They were identified as Lactococcus lactis and Enterococcus faecalis and submitted to technological tests: growth at different conditions of temperature and salt, acid production, proteolysis, lipolysis, coexistence, enzymatic profile and autolytic capacity. Safety evaluation was performed by evaluating haemolytic, gelatinase and DNase activity, resistance to antibiotics and the presence of virulence genes. Some isolates presented good technological features such as high autolytic activity, acid and diacetyl production. Lactococcus lactis was negative for all virulence genes tested and inhibit the growth of all Lactic acid bacteria (LAB) isolates. Enterococci were positive for the presence of some virulence genes, but none of the isolates were classified as resistant to important antibiotics.

CONCLUSIONS

The bacteriocin-producing Lc. lactis present good potential for application in food as adjunct culture in cheese production. The study also reveals good technological features for some Enterococcus isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacteriocin-producing strains presented important technological properties to be exploited as new adjunct culture for the dairy industry, influencing flavour development and improve safety.

The carbohydrate metabolism signature of lactococcus lactis strain A12 reveals its sourdough ecosystem origin

Lactococcus lactis subsp. lactis strain A12 was isolated from sourdough. Combined genomic, transcriptomic, and phenotypic analyses were performed to understand its survival capacity in the complex sourdough ecosystem and its role in the microbial community. The genome sequence comparison of strain A12 with strain IL1403 (a derivative of an industrial dairy strain) revealed 78 strain-specific regions representing 23% of the total genome size. Most of the strain-specific genes were involved in carbohydrate metabolism and are potentially required for its persistence in sourdough. Phenotype microarray, growth tests, and analysis of glycoside hydrolase content showed that strain A12 fermented plant-derived carbohydrates, such as arabinose and α-galactosides. Strain A12 exhibited specific growth rates on raffinose that were as high as they were on glucose and was able to release sucrose and galactose outside the cell, providing soluble carbohydrates for sourdough microflora. Transcriptomic analysis identified genes specifically induced during growth on raffinose and arabinose and reveals an alternative pathway for raffinose assimilation to that used by other lactococci.

Genotypic and phenotypic analysis of dairy Lactococcus lactis biodiversity in milk: volatile organic compounds as discriminating markers

The diversity of nine dairy strains of Lactococcus lactis subsp. lactis in fermented milk was investigated by both genotypic and phenotypic analyses. Pulsed-field gel electrophoresis and multilocus sequence typing were used to establish an integrated genotypic classification. This classification was coherent with discrimination of the L. lactis subsp. lactis bv. diacetylactis lineage and reflected clonal complex phylogeny and the uniqueness of the genomes of these strains. To assess phenotypic diversity, 82 variables were selected as important dairy features; they included physiological descriptors and the production of metabolites and volatile organic compounds (VOCs). Principal-component analysis (PCA) demonstrated the phenotypic uniqueness of each of these genetically closely related strains, allowing strain discrimination. A method of variable selection was developed to reduce the time-consuming experimentation. We therefore identified 20 variables, all associated with VOCs, as phenotypic markers allowing discrimination between strain groups. These markers are representative of the three metabolic pathways involved in flavor: lipolysis, proteolysis, and glycolysis. Despite great phenotypic diversity, the strains could be divided into four robust phenotypic clusters based on their metabolic orientations. Inclusion of genotypic diversity in addition to phenotypic characters in the classification led to five clusters rather than four being defined. However, genotypic characters make a smaller contribution than phenotypic variables (no genetic distances selected among the most contributory variables). This work proposes an original method for the phenotypic differentiation of closely related strains in milk and may be the first step toward a predictive classification for the manufacture of starters.