The Metabolism of Leuconostoc Genus Decoded by Comparative Genomics

Leuconostoc encompasses a number of species that frequently appear in foods where they play different roles, ranging from ripening to spoiling. The number of available Leuconostoc genomes has recently increased and enabled the precise taxonomic and phylogenetic delineation of species. Nonetheless, a thorough investigation of the functions and the metabolic potential of Leuconostoc species has never been accomplished. In this study, all the currently available 553 Leuconostoc genomes were downloaded from NCBI GenBank and annotated utilizing specific tools in order to reconstruct the metabolic potential of the genus in terms of carbohydrate hydrolysis and fermentative pathways, transporters, and anabolic potential. The analysis revealed that species cluster based on their metabolic potential, showing unique adaptation and ecological roles. Pentose phosphate and phosphoketolase pathways were highlighted as the main ones of central metabolism. The various identified PTS and ABC transporters showed adaptability to different sugars. The metabolic diversity described in this study not only supports the role of Leuconostoc spp. in natural ecosystems but also highlights their potential in industrial applications, particularly in the fermentation industry where their ability to metabolize a wide range of substrates can be harnessed for the production of various fermented foods and bioproducts.

Leuconostoc citreum: A Promising Sourdough Fermenting Starter for Low-Sugar-Content Baked Goods

This review highlights Leuconostoc citreum's promising possibilities as a proficient mannitol producer and its potential implications for sugar reduction, with a focus on its use in sourdough-based baked good products. Mannitol, a naturally occurring sugar alcohol, has gained popularity in food items due to its low calorie content and unique beneficial qualities. This study summarizes recent research findings and investigates the metabolic pathways and culture conditions that favor increased mannitol production by Leuconostoc citreum. Furthermore, it investigates the several applications of mannitol in baked goods, such as its function in increasing texture, flavor and shelf life while lowering the sugar content. Sourdough-based products provide an attractive niche for mannitol integration, as customer demand for healthier and reduced-sugar options increases.

Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios

Background

The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.

Methods

Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers.

Results

Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism.

Conclusion

We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.

A comparative study of the effect of bacteria and yeasts communities on inoculated and spontaneously fermented apple cider

Understanding bacteria and yeasts communities can reduce unpredictable changes of apple cider. In this study, apple juice inoculated with Saccharomyces cerevisiae WET 136 and fermented spontaneously were compared, the relationships of bacteria, yeasts, organic acids, and volatiles were analyzed. Results showed that microbial diversity affected the fermentation, organic acids and volatiles in apple ciders. In the first four spontaneous fermentation days, LAB (lactic acid bacteria) multiplied and reached 7.89 lg CFU/mL, and then triggered malolactic fermentation (MLF), leading to malic acid decreased by 3880.52 mg/L and lactic acid increased by 4787.55 mg/L. The citric, succinic and fumaric acids content was 2171.14, 701.51 and 8.06 mg/L lower than that in inoculated cider, respectively. Although the yeasts multiplied during spontaneous fermentation, it did not reach 7.50 lg CFU/mL until the 5th day, which led to a long lag period, as well as later and lower production of acetaldehyde and higher alcohols. The inoculated yeast inhibited LAB, acetic acid bacteria, Rahnella, and non-Saccharomyces. Yeasts were the key to produce citric acid, acetaldehyde and 3-methyl-1-butanol in apple cider; while bacteria were closely related to the formation of lactic acid, acetic acid and ethyl acetate. It suggested that low higher alcohols and acetaldehyde can be realized by selecting yeasts, and Leuconostoc pseudomesenteroides can work as candidate to reduce L-malic and citric acids in apple cider.

Unsalable Vegetables Ensiled With Sorghum Promote Heterofermentative Lactic Acid Bacteria and Improve in vitro Rumen Fermentation

This study characterized the nutritive and microbial profiles and the fermentation characteristics of silage with the following compositions on a dry matter (DM) basis: (1) 100% sorghum, (2) 70% sorghum + 30% carrot or pumpkin, and (3) 40% sorghum + 60% carrot or pumpkin. The treatments were further divided based on the addition or no addition of a probiotic inoculant. After 70 days of ensiling, the silage was incubated for 48 h using the in vitro batch culture technique. Crude protein and non-fiber carbohydrates in the silage increased (P ≤ 0.01) by 5.7 percent point (pp) and 9.6 pp, respectively, with pumpkin at 60% DM. The V4 region of the 16S rRNA gene was sequenced to profile pre-ensiled and ensiled archeal and bacterial communities. Silages containing carrot or pumpkin strongly influenced the microbial structure (PERMANOVA: R² = 0.75; P < 0.001), despite the ensiled treatments being dominated by Lactobacillus spp., except for the control, which was dominated by Weissella and Pediococcus spp. (P < 0.01). Linear discriminant analysis indicated that carrot and pumpkin silages were responsible for the increased relative abundance of Lactobacillus and Acinetobacter spp. (log LDA score ≥ 2), respectively. After 48 h of incubation, carrot and pumpkin inclusion increased (P < 0.01) the in vitro DM digestibility by 22.5 and 31.3%, increased the total volatile fatty acids (VFAs) by 16 and 20.6% (P < 0.01), respectively, and showed a tendency (P = 0.07) to increase the gas production. Therefore, this study supports the use of carrot or pumpkin in sorghum silages to maximize feed digestibility and total VFA concentrations.

Immobilization of microorganisms in activated zeolite beads and alkaline pretreated straws for ammonium-nitrogen removal from urban river water

The non-treated wastewater from residential areas contains high concentrations of ammonium-nitrogen (NH₄⁺-N). When discharged into the drainage water system, it deteriorates the water quality in urban rivers. This study used two types of materials to form eco-bags, using activated zeolite bead (AZB) and alkaline pretreated straw (APS), in geotextile bags for easy recovery and reuse. The AZB and APS provided the breeding habitat for the microorganisms that promoted biofilm formation on their surface. The immobilization of engineered denitrification microorganisms facilitated the removal of NH₄⁺-N from the urban river water. The NH₄⁺-N removal in the AZB and APS bags were in the range of 64-73%, and 56-61%, respectively, while the chemical oxygen demand (COD) removal in the AZB and APS bags ranged from 33-36%, and 30-31%, respectively. In addition, as evident from DNA and microbial community analysis, the microorganisms demonstrated a greater proclivity to grow and proliferate on the surface of AZB and APS and improved the water quality of urban rivers.

Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

Development of a yoghurt alternative, based on plant-adapted lactic acid bacteria, soy drink and the liquid fraction of brewers' spent grain

With consumers becoming more aware of sustainability, healthier lifestyles and animal welfare, plant-based food products as alternatives to dairy products have become a fast-growing industry in the last decade, and an increasing number of plant-based products are showing up on the markets. With over 88 million tons of food wasted in Europe annually, a sustainable alternative to dairy could be to use side streams for new products. Here, we tried to develop a plant-based yogurt alternative based on three ingredients: commercial soy drink and a liquid fraction of brewers' spent grain fermented with plant-adapted lactic acid bacteria. Analysis of the content and properties of the fermented product were compared to a commercial plant-based yoghurt-like product and a commercial dairy yoghurt. Results from the project show that fermentation of a commercial soy drink containing 20% of the liquid fraction of brewers' spent grain results in a product with texture and sensory characteristics that mimics a dairy yogurt.

Genomic analysis of Leuconostoc citreum TR116 with metabolic reconstruction and the effects of fructose on gene expression for mannitol production

The species Leuconostoc citreum is often isolated from grain and vegetable fermentations such as sourdough, sauerkraut and kimchi. Lc. citreum has seen an increase in its use as a starter culture for various fermentations and food applications. The strain Lc. citreum TR116 has been applied previously in this laboratory aimed at sugar depletion through metabolism resulting in the reduction of fructose to mannitol, a polyol considered as a sweet carbohydrate. Besides reducing sugar, TR116 showed flavour modulating characteristics and contributes to the extension of microbial shelf life. In order to obtain a better understanding of this strain and to fully use its set of abilities, the genome of Lc. citreum TR116 was sequenced using the Illumina MiSeq, assembly with SPAdes and annotated by the Prokaryotic Genome Annotation Pipeline. Metabolic reconstruction was employed to elucidate carbohydrate, organic acid and amino acid metabolism in the strain. Of particular interest was the gene expression analysis ascertained the influence of fructose on the genes mdh and manX involved in the uptake of fructose and its conversion to mannitol. This investigation, the first in Lc. citreum, illustrates the metabolic processes involved in fermentation used by this strain and demonstrates that in the presence of fructose, expression of the genes mdh and manX is increased. The resulting transparency of the skill set of TR116 contributes highly to future functionalisation of food systems and food ingredients.

Screening of endogenous strong promoters of Leuconostoc citreum EFEL2700 based on transcriptome analysis and its application for food-grade production of β-galactosidase

Leuconostoc citreum is a heterofermentative lactic acid bacterium frequently found in the various fermented foods. L. citreum EFEL2700 isolated from Korean kimchi has been used as a host strain for biotechnological applications. For the use as a food-grade host to over-produce food ingredients or enzymes, strong endogenous promoters guarantying high expression levels of target genes are necessary. In this study, transcriptomic analysis of L. citreum EFEL2700 was performed using RNA-Seq and three promoters of the most highly expressed genes were selected: glyceraldehyde 3-phosphate dehydrogenase (G3PD), 6-phosphogluconate dehydrogenase (6PGD), and phosphoketolase (PPK). Thereafter, they were used as promoters to express β-galactosidase gene from Lactobacillus plantarum WCFS1 in L. citreum EFEL2700 and the levels were compared with the control promoter P710 from L. mesenteroides ATCC 8293. As results, the β-galactosidase activities of the transformants were 2.73, 0.27, 37.43, and 9.25 units/mg under the P710, G3PD, 6PGD, and PPK promoters, respectively. The expression level of endogenous promoter 6PGD was superior to the heterologous P710 promoter previously used in a Leuconostoc-Escherichia coli shuttle vector. The 6PGD developed in this study can be used as the most suitable promoter for β-galactosidase expression in L. citreum EFEL2700.

Leuconostoc citreum TR116 as a Microbial Cell Factory to Functionalise High-Protein Faba Bean Ingredients for Bakery Applications

Grain legumes, such as faba beans, have been investigated as promising ingredients to enhance the nutritional value of wheat bread. However, a detrimental effect on technological bread quality was often reported. Furthermore, considerable amounts of antinutritional compounds present in faba beans are a subject of concern. Sourdough-like fermentation can positively affect baking performance and nutritional attributes of faba bean flours. The multifunctional lactic acid bacteria strain Leuconostoc citreum TR116 was employed to ferment two faba bean flours with different protein contents (dehulled flour (DF); high-protein flour (PR)). The strain’s fermentation profile (growth, acidification, carbohydrate metabolism and antifungal phenolic acids) was monitored in both substrates. The fermentates were applied in regular wheat bread by replacing 15% of wheat flour. Water absorption, gluten aggregation behaviour, bread quality characteristics and in vitro starch digestibility were compared to formulations containing unfermented DF and PR and to a control wheat bread. Similar microbial growth, carbohydrate consumption as well as production of lactic and acetic acid were observed in both faba bean ingredients. A less pronounced pH drop as well as a slightly higher amount of antifungal phenolic acids were measured in the PR fermentate. Fermentation caused a striking improvement of the ingredients’ baking performance. GlutoPeak measurements allowed for an association of this observation with an improved gluten aggregation. Given its higher potential to improve protein quality in cereal products, the PR fermentate seemed generally more promising as functional ingredient due to its positive impact on bread quality and only moderately increased starch digestibility in bread.

Effects of imidacloprid on the oxidative stress, detoxification and gut microbiota of Chinese mitten crab, Eriocheir sinensis

Imidacloprid (IMI) is used in integrated aquaculture systems for pest control and the toxicity of IMI to non-target aquatic animals such as fish and microcrustaceans has been recognised. However, knowledge about the toxic effect of IMI on commercial crabs is still scarce. In the present study, effects of IMI on the acute toxicity, antioxidative status, detoxification systems and gut microbiota in Chinese mitten crab, Erocheir sinensis were investigated. In the present study, the 96-h LC₅₀ of IMI for E. sinensis was 24.97 mg/L. Under sublethal exposure, superoxide dismutase (SOD) activities increased under low concentration (LC, 5 μg/L) and median concentration (MC, 50 μg/L) exposure, but decreased in high concentration group (HC, 500 μg/L). Activities of catalyse (CAT) decreased in a dose-dependent manner. Detoxification-related enzymes aminopyrine N-demethylase (APND) and erythromycin N-demethylase (ERND) increased in all treatments whereas glutathione-S-transferase (GST) decreased dose-dependently. The relative mRNA expression of the cytochrome P4502 (cyp2) gene was induced significantly in LC and HC groups while no significant change was observed in cytochrome P4503 (cyp3) gene. The expression of gst was also significantly decreased in HC group. Up-regulation of heat shock protein hsp70 and 90 was observed in MC and HC groups whereas hsp60 up-regulated only in LC group. In addition, significant changes of composition of microbial communities at both phylum and genus levels were found in this test. In particular, beneficial bacteria were found to decrease and pathogens increased after exposure to IMI. These results indicate that high concentration of IMI could induce oxidative stress and suppress the detoxification system mainly by down-regulation of gst mRNA expression, inhibition of enzyme activities and dysbiosis of gut microbiota.

Large microbiota survey reveals how the microbial ecology of cooked ham is shaped by different processing steps

Cooked ham production involves numerous steps shaping the microbial communities of the final product, with consequences on spoilage metabolites production. To identify the main factors driving the ecology of ham and its spoilage, we designed a study encompassing five variables related to ham production: type of storage during meat transportation, churning speed, drain-off time, slicing line and O₂ packaging permeability. About 200 samples from the same facility were obtained and characterized with respect to i) their microbiota based on gyrB amplicon sequencing ii) their production of spoilage-related metabolites based on E-Nose analysis and enzymatic assays. The slicing was the most critical step, shaping two general types of microbiota according to the slicing line: one dominated by Carnobacterium divergens and another one dominated by Leuconostoc carnosum and Serratia proteamaculans. Regarding metabolites production, L. carnosum was associated to d-lactic acid, ethanol and acetic acid production, whereas Serratia proteamaculans was associated to acetic acid production. This last species prevailed with highly O₂-permeable packaging. Within a given slicing line, campaign-based variations were observed, with Lactobacillus sakei, Leuconostoc mesenteroides and Carnobacterium maltaromaticum prevalent in summer. L. sakei was associated with l-lactic acid production and C. maltaromaticum with formic and acetic acid productions.

Salmon Gravlax Biopreservation With Lactic Acid Bacteria: A Polyphasic Approach to Assessing the Impact on Organoleptic Properties, Microbial Ecosystem and Volatilome Composition

Seafood and fishery products are very perishable commodities with short shelf-lives owing to rapid deterioration of their organoleptic and microbiological quality. Microbial growth and activity are responsible for up to 25% of food losses in the fishery industry. In this context and to meet consumer demand for minimally processed food, developing mild preservation technologies such as biopreservation represents a major challenge. In this work, we studied the use of six lactic acid bacteria (LAB), previously selected for their properties as bioprotective agents, for salmon dill gravlax biopreservation. Naturally contaminated salmon dill gravlax slices, with a commercial shelf-life of 21 days, were purchased from a French industrial company and inoculated by spraying with the protective cultures (PCs) to reach an initial concentration of 106 log CFU/g. PC impact on gravlax microbial ecosystem (cultural and acultural methods), sensory properties (sensory profiling test), biochemical parameters (pH, TMA, TVBN, biogenic amines) and volatilome was followed for 25 days of storage at 8°C in vacuum packaging. PC antimicrobial activity was also assessed in situ against Listeria monocytogenes. This polyphasic approach underlined two scenarios depending on the protective strain. Carnobacterium maltaromaticum SF1944, Lactococcus piscium EU2229 and Leuconostoc gelidum EU2249, were very competitive in the product, dominated the microbial ecosystem, and displayed antimicrobial activity against the spoilage microbiota and L. monocytogenes. The strains also expressed their own sensory and volatilome signatures. However, of these three strains, C. maltaromaticum SF1944 did not induce strong spoilage and was the most efficient for L. monocytogenes growth control. By contrast, Vagococcus fluvialis CD264, Carnobacterium inhibens MIP2551 and Aerococcus viridans SF1044 were not competitive, did not express strong antimicrobial activity and produced only few organic volatile compounds (VOCs). However, V. fluvialis CD264 was the only strain to extend the sensory quality, even beyond 25 days. This study shows that C. maltaromaticum SF1944 and V. fluvialis CD264 both have a promising potential as bioprotective cultures to ensure salmon gravlax microbial safety and sensorial quality, respectively.

Metagenomic analysis and characterization of acidogenic microbiome and effect of pH on organic acid production

Organic acid production including lactate and acetate is an economically attractive technology that has gained momentum worldwide over the past years. These series of action need to be performed by an esoteric and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. In this study, we analyzed the bioma from bioreactors with various pH conditions of 4.0, 5.0 and 6.0 (R₁, R₂ and R₃), respectively, involved in acidogenic digestion for stable production of various organic acids by means of high-throughput Illumina sequencing, disclosing thousands of genes and extracting more than 53 microbial genomes. At pH 5.0, the hydrolysis reaction was enhanced and thus the lactic acid fermentation was stably improved to 45.96 mm/L and acetic acid to 73.77 mm/L. R₂ was found with the most suitable pH condition for stable organic acids production as Lactobacilli and Bifidobacteria were the major members. Both the members have the key roles in heterofermentation and produce higher transcripts of key encoding enzymes involved in the dominant heterofermentation pathways.

Aroma formation in retentostat co-cultures of Lactococcus lactis and Leuconostoc mesenteroides

Lactococcus lactis subsp. lactis biovar diacetylactis and Leuconostoc mesenteroides are considered to be the main aroma producers in Dutch-type cheeses. Both species of lactic acid bacteria were grown in retentostat mono- and co-cultures to investigate their interaction at near-zero growth rates and to determine if co-cultivation enhances the aroma complexity compared to single species performance. During retentostat mono-cultures, the growth rates of both species decreased to less than 0.001 h^-1 and a large fraction of the cells became viable but not culturable. Compared to Lc. mesenteroides, L. lactis reached a 3.4-fold higher biomass concentration caused by i) a higher ATP yield on substrate, ii) a higher biomass yield on ATP and iii) a lower maintenance requirement (m_ATP). Dynamic models estimated that the m_ATP of both species decreased approximately 7-fold at near-zero growth rates compared to high growth rates. Extension of these models by assuming equal substrate distribution resulted in excellent prediction of the biomass accumulation in retentostat co-cultures with L. lactis dominating (100:1) as observed in ripened cheese. Despite its low abundance (∼1%), Lc. mesenteroides contributed to aroma production in co-cultures as indicated by the presence of all 5 specific Lc. mesenteroides compounds. This study provides insights in the production of cheese aroma compounds outside the cheese matrix by co-cultures of L. lactis and Lc. mesenteroides, which could be used as food supplements in dairy or non-dairy products.

High Levels of CO2 Induce Spoilage by Leuconostoc mesenteroides by Upregulating Dextran Synthesis Genes

During nonventilated storage of carrots, CO2 gradually accumulates to high levels and causes modifications in the carrot's microbiome toward dominance of Lactobacillales and Enterobacteriales The lactic acid bacterium Leuconostoc mesenteroides secretes a slimy exudate over the surface of the carrots. The objective of this study was to characterize the slime components and the potential cause for its secretion under high CO2 levels. A proteomic analysis of the exudate revealed bacterial glucosyltransferases as the main proteins, specifically, dextransucrase. A chemical analysis of the exudate revealed high levels of dextran and several simple sugars. The exudate volume and dextran amount were significantly higher when L. mesenteroides was incubated under high CO2 levels than when incubated in an aerated environment. The treatment of carrot medium plates with commercial dextransucrase or exudate protein extract resulted in similar sugar profiles and dextran production. Transcriptome analysis demonstrated that dextran production is related to the upregulation of the L. mesenteroides dextransucrase-encoding genes dsrD and dsrT during the first 4 to 8 h of exposure to high CO2 levels compared to aerated conditions. A phylogenetic analysis of L. mesenteroides YL48 dsrD revealed a high similarity to other dsr genes harbored by different Leuconostoc species. The ecological benefit of dextran production under elevated CO2 requires further investigation. However, this study implies an overlooked role of CO2 in the physiology and fitness of L. mesenteroides in stored carrots, and perhaps in other food items, during storage under nonventilated conditions.IMPORTANCE The bacterium Leuconostoc mesenteroides is known to cause spoilage of different types of foods by secreting a slimy fluid that damages the quality and appearance of the produce. Here, we identified a potential mechanism by which high levels of CO2 affect the spoilage caused by this bacterium by upregulating dextran synthesis genes. These results have broader implications for the study of the physiology, degradation ability, and potential biotechnological applications of Leuconostoc.

Extrusion of Dissolved Oxygen by Exopolysaccharide From Leuconostoc mesenteroides and Its Implications in Relief of the Oxygen Stress

Strains of Leuconostoc are generally facultatively anaerobic and exposure to oxygen might be detrimental; therefore, strategies to combat the oxygen stress are essential for these bacteria to survive and flourish in the oxygenic atmosphere. Despite the extensive applications in industry, the fundamental issues concerning the aerobic life of Leuconostocs remain to be addressed. In this study, we have demonstrated that Leuconostoc mesenteroides CGMCC10064 cultivated in sucrose medium would acquire a growth advantage over that in glucose medium under oxygenic conditions, as reflected by more viable cells and less accumulation of reactive oxygen species. Further analysis showed that the growth advantage was dependent on exopolysaccharide (EPS) synthesized by a secreted glucansucrase. Determination of the dissolved oxygen in the culture suggested that the growth improvement was mediated by extrusion of dissolved oxygen from the aqueous circumstances. Growth experiments performed with the purified EPS showed that supplementation of 5 g/L EPS in the medium could improve the aerobic growth of L. mesenteroides by ∼10-fold. Moreover, the purified EPS was also effective in promoting the aerobic growth of oxygen-sensitive Lactobacillus and Bifidobacterium. These results demonstrate that EPS of L. mesenteroides plays a critical role in relief of the oxygen stress, and suggest the potential of the EPS in manufacture as well as preservation of oxygen-sensitive probiotics.

A high-throughput qPCR system for simultaneous quantitative detection of dairy Lactococcus lactis and Leuconostoc bacteriophages

Simultaneous quantitative detection of Lactococcus (Lc.) lactis and Leuconostoc species bacteriophages (phages) has not been reported in dairies using undefined mixed-strain DL-starters, probably due to the lack of applicable methods. We optimized a high-throughput qPCR system that allows simultaneous quantitative detection of Lc. lactis 936 (now SK1virus), P335, c2 (now C2virus) and Leuconostoc phage groups. Component assays are designed to have high efficiencies and nearly the same dynamic detection ranges, i.e., from ~1.1 x 10⁵ to ~1.1 x 10¹ phage genomes per reaction, which corresponds to ~9 x 10⁷ to ~9 x 10³ phage particles mL^-1 without any additional up-concentrating steps. The amplification efficiencies of the corresponding assays were 100.1±2.6, 98.7±2.3, 101.0±2.3 and 96.2±6.2. The qPCR system was tested on samples obtained from a dairy plant that employed traditional mother-bulk-cheese vat system. High levels of 936 and P335 phages were detected in the mother culture and the bulk starter, but also in the whey samples. Low levels of phages were detected in the cheese milk samples.

Genomic Characterization of Dairy Associated Leuconostoc Species and Diversity of Leuconostocs in Undefined Mixed Mesophilic Starter Cultures

Undefined mesophilic mixed (DL-type) starter cultures are composed of predominantly Lactococcus lactis subspecies and 1-10% Leuconostoc spp. The composition of the Leuconostoc population in the starter culture ultimately affects the characteristics and the quality of the final product. The scientific basis for the taxonomy of dairy relevant leuconostocs can be traced back 50 years, and no documentation on the genomic diversity of leuconostocs in starter cultures exists. We present data on the Leuconostoc population in five DL-type starter cultures commonly used by the dairy industry. The analyses were performed using traditional cultivation methods, and further augmented by next-generation DNA sequencing methods. Bacterial counts for starter cultures cultivated on two different media, MRS and MPCA, revealed large differences in the relative abundance of leuconostocs. Most of the leuconostocs in two of the starter cultures were unable to grow on MRS, emphasizing the limitations of culture-based methods and the importance of careful media selection or use of culture independent methods. Pan-genomic analysis of 59 Leuconostoc genomes enabled differentiation into twelve robust lineages. The genomic analyses show that the dairy-associated leuconostocs are highly adapted to their environment, characterized by the acquisition of genotype traits, such as the ability to metabolize citrate. In particular, Leuconostoc mesenteroides subsp. cremoris display telltale signs of a degenerative evolution, likely resulting from a long period of growth in milk in association with lactococci. Great differences in the metabolic potential between Leuconostoc species and subspecies were revealed. Using targeted amplicon sequencing, the composition of the Leuconostoc population in the five commercial starter cultures was shown to be significantly different. Three of the cultures were dominated by Ln. mesenteroides subspecies cremoris. Leuconostoc pseudomesenteroides dominated in two of the cultures while Leuconostoc lactis, reported to be a major constituent in fermented dairy products, was only present in low amounts in one of the cultures. This is the first in-depth study of Leuconostoc genomics and diversity in dairy starter cultures. The results and the techniques presented may be of great value for the dairy industry.

Gsy, a novel glucansucrase from Leuconostoc mesenteroides, mediates the formation of cell aggregates in response to oxidative stress

Leuconostoc mesenteroides is a member of lactic acid bacteria (LAB) with wide applications in the food and medical industries. Species in the genus Leuconostoc are catalase-negative and generally regarded as facultative anaerobic or aerotolerant organisms. Despite their extensive use in industry, certain issues concerning the aerobic life of L. mesenteroides, e.g., the mechanism involved in the tolerance to oxygen, remain to be addressed. In this manuscript, a survival strategy employed by L. mesenteroides BD3749 in response to oxidative stress was elucidated. BD3749 cells cultivated in medium with sucrose available synthesized large amounts of exopolysaccharides, mostly consisting of insoluble EPS. When BD3749 cells were challenged with oxidative stress, the amount of insoluble EPS was greatly enhanced. The synthesized EPSs reduced the accumulation of reactive oxygen species (ROS) in bacterial cells and improved their survival during chronic oxidative stress. Another study showed that Gsy, a novel glucansucrase in the GH70 family that is induced by sucrose and up-regulated following exposure to oxygen, was responsible for the synthesis of insoluble EPS. Gsy was subsequently demonstrated to play pivotal roles in the formation of aggregates to alleviate the detrimental effects on BD3749 cells exerted by oxygen.

Whey powders are a rich source and excellent storage matrix for dairy bacteriophages

Thirteen whey powders and 5 whey powder formulations were screened for the presence of dairy bacteriophages using a representative set of 8 acid-producing Lactococcus lactis and 5 Streptococcus thermophilus, and 8 flavour-producing Leuconostoc pseudomesenteroides and Leuconostoc mesenteroides strains. Lytic L. lactis phages were detected in all samples, while S. thermophilus and Leuconostoc phages were present in 50% or 40% of the samples, respectively. Maximal phage titers were 6×10⁷ plaque-forming units (pfu)/g of whey powder for L. lactis phages, 1×10⁷pfu/g for Leuconostoc phages and 1×10⁵pfu/g for S. thermophilus phages. In total, 55 phages were isolated and characterized. Thirty one of the 33 lactococcal phages tested belonged to the wide-spread 936 phage group. In the course of this study, a PCR detection method for Leuconostoc phages (Ali et al., 2013) was adapted to new phage isolates. Furthermore, a remarkably high stability of phages in whey powder samples was documented during a long-term storage period of 4 years.

Leuconostoc spp. Associated with Root Rot in Sugar Beet and Their Interaction with Rhizoctonia solani

Rhizoctonia root and crown rot is an important disease problem in sugar beet caused by Rhizoctonia solani and also shown to be associated with Leuconostoc spp. Initial Leuconostoc studies were conducted with only a few isolates and the relationship of Leuconostoc with R. solani is poorly understood; therefore, a more thorough investigation was conducted. In total, 203 Leuconostoc isolates were collected from recently harvested sugar beet roots in southern Idaho and southeastern Oregon during 2010 and 2012: 88 and 85% Leuconostoc mesenteroides, 6 and 15% L. pseudomesenteroides, 2 and 0% L. kimchi, and 4 and 0% unrecognized Leuconostoc spp., respectively. Based on 16S ribosomal RNA sequencing, haplotype 11 (L. mesenteroides isolates) comprised 68 to 70% of the isolates in both years. In pathogenicity field studies with commercial sugar beet 'B-7', all Leuconostoc isolates caused more rot (P < 0.0001; α = 0.05) when combined with R. solani than when inoculated alone in both years. Also, 46 of the 52 combination treatments over the 2 years had significantly more rot (P < 0.0001; α = 0.05) than the fungal check. The data support the conclusion that a synergistic interaction leads to more rot when both Leuconostoc spp. and R. solani are present in sugar beet roots.

Avoiding Buffer Interference in ITC Experiments: A Case Study from the Analysis of Entropy-Driven Reactions of Glucose-6-Phosphate Dehydrogenase

Isothermal titration calorimetry (ITC) is a label-free technique that allows the direct determination of the heat absorbed or released in a reaction. Frequently used to determining binding parameters in biomolecular interactions, it is very useful to address enzyme-catalyzed reactions as both kinetic and thermodynamic parameters can be obtained. Since calorimetry measures the total heat effects of a reaction, it is important to consider the contribution of the heat of protonation/deprotonation that is possibly taking place. Here, we show a case study of the reaction catalyzed by the glucose-6-phosphate dehydrogenase (G6PD) from Leuconostoc mesenteroides. This enzyme is able to use either NAD(+) or NADP(+) as a cofactor. The reactions were done in five buffers of different enthalpy of protonation. Depending on the buffer used, the observed calorimetric enthalpy (ΔH(cal)) of the reaction varied from -22.93 kJ/mol (Tris) to 19.37 kJ/mol (phosphate) for the NADP(+)-linked reaction, and -11.67 kJ/mol (Tris) to 7.32 kcal/mol or 30.63 kJ/mol (phosphate) for the NAD(+) reaction. We will use this system as an example of how to extract proton-independent reaction enthalpies from kinetic data to ensure that the reported accurately represent the intrinsic heat of reaction.

Functional implications of the microbial community structure of undefined mesophilic starter cultures

This review describes the recent advances made in the studies of the microbial community of complex and undefined cheese starter cultures. We report on work related to the composition of the cultures at the level of genetic lineages, on the presence and activity of bacteriophages and on the population dynamics during cheese making and during starter culture propagation. Furthermore, the link between starter composition and starter functionality will be discussed. Finally, recent advances in predictive metabolic modelling of the multi-strain cultures will be discussed in the context of microbe-microbe interactions.

Technological characterisation, antibiotic susceptibility and antimicrobial activity of wild-type Leuconostoc strains isolated from North Italian traditional cheeses

Genotypic and technological properties, antibiotic susceptibility and antimicrobial activity of 35 Leuconostoc strains, isolated from different Italian raw milk cheeses, were investigated. RAPD-PCR was used to study genetic variability and to distinguish closely related strains. The results showed a high degree of heterogeneity among isolates. All the strains had weak acidifying activity and showed low proteolytic and lipolytic activities. Reduction activity, was generally low. All the Leuconostoc were susceptible to ampicillin, mupirocin, erythromycin, quinupristin/dalfopristin and tetracycline. Many strains were classified as resistant to oxacillin, ciprofloxacin and nitrofurantonin, while all isolates were found resistant to vancomycin. PCR-based detection did not identify any of the common genetic determinants for vancomycin (vanA, vanB, vanC1, vanC2, vanC3, vanD, vanE, vanG) or erythromycin (ermB and ermC). Tetracycline resistance genes were detected in 25 tetracycline susceptible strains, the most frequent one being tetM. One strain, belonging to Ln. pseudomesenteroides species, was positive for the presence of the int gene of the Tn916/Tn1545 trasposon family. This is the first time the conjugative transposon Tn916 has been detected inside the Leuconostoc species. All strains showed antimicrobial activity against Enterococcus faecalis and Ent. faecium. The presence of genes encoding amino-acid decarboxylases (hdc and tdc) was not detected. Some strains are interesting in view of their use in cheese production as starter and non starter cultures.

Classification of lytic bacteriophages attacking dairy Leuconostoc starter strains

A set of 83 lytic dairy bacteriophages (phages) infecting flavor-producing mesophilic starter strains of the Leuconostoc genus was characterized, and the first in-depth taxonomic scheme was established for this phage group. Phages were obtained from different sources, i.e., from dairy samples originating from 11 German dairies (50 Leuconostoc pseudomesenteroides [Ln. pseudomesenteroides] phages, 4 Ln. mesenteroides phages) and from 3 external phage collections (17 Ln. pseudomesenteroides phages, 12 Ln. mesenteroides phages). All phages belonged to the Siphoviridae family of phages with isometric heads (diameter, 55 nm) and noncontractile tails (length, 140 nm). With the exception of one phage (i.e., phage ΦLN25), all Ln. mesenteroides phages lysed the same host strains and revealed characteristic globular baseplate appendages. Phage ΦLN25, with different Y-shaped appendages, had a unique host range. Apart from two phages (i.e., phages P792 and P793), all Ln. pseudomesenteroides phages shared the same host range and had plain baseplates without distinguishable appendages. They were further characterized by the presence or absence of a collar below the phage head or by unique tails with straight striations. Phages P792 and P793 with characteristic fluffy baseplate appendages could propagate only on other specific hosts. All Ln. mesenteroides and all Ln. pseudomesenteroides phages were members of two (host species-specific) distinct genotypes but shared a limited conserved DNA region specifying their structural genes. A PCR detection system was established and was shown to be reliable for the detection of all Leuconostoc phage types.

Selection for Resistance to the Rhizoctonia-Bacterial Root Rot Complex in Sugar Beet

The Rhizoctonia-bacterial root rot complex continues to be a concerning problem in sugar beet production areas. To investigate resistance to this complex in 26 commercial sugar beet cultivars, field studies and greenhouse studies with mature roots from the field were conducted with Rhizoctonia solani anastomosis group 2-2 IIIB strains and Leuconostoc mesenteroides. Based on means for the 26 cultivars in the 2010 and 2011 field studies, fungal rot ranged from 0 to 8%, bacterial rot ranged from 0 to 37%, total internal rot ranged from 0 to 44%, and surface rot ranged from 0 to 52%. All four rot variables resulted in significant (P < 0.0001) cultivar differences. Based on regression analysis, strong positive relationships (r² from 0.6628 to 0.9320; P < 0.0001) were present among the rot variables. When ranking cultivars, the most consistent rot variable was surface rot, because 12 of 13 variable-year combinations had significant (P ≤ 0.05) correlations. When cultivar ranking in greenhouse assays was compared, there was frequently a positive correlation with storage data but no relationship with field results. Thus, the greenhouse assays will identify storage rot resistance but field screening will be required to find resistance to this rot complex in the field.

Characterization of a Leuconostoc bacteriophage infecting flavor producers of cheese starter cultures

Dairy siphovirus φLmd1, which infects starter culture isolate Leuconostoc mesenteroides subsp. dextranicum A1, showed resistance to pasteurization and was able to grow on 3 of the 4 commercial starter cultures tested. Its 26,201-bp genome was similar to that of Leuconostoc phage of vegetable origin but not to those of dairy phages infecting Lactococcus.

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Background

The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in the gastrointestinal microbiome during IBD remain unclear. We analyzed the microbiota of intestinal biopsies and stool samples from 231 IBD and healthy subjects by 16S gene pyrosequencing and followed up a subset using shotgun metagenomics. Gene and pathway composition were assessed, based on 16S data from phylogenetically-related reference genomes, and associated using sparse multivariate linear modeling with medications, environmental factors, and IBD status.

Results

Firmicutes and Enterobacteriaceae abundances were associated with disease status as expected, but also with treatment and subject characteristics. Microbial function, though, was more consistently perturbed than composition, with 12% of analyzed pathways changed compared with 2% of genera. We identified major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways.

Conclusions

This inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis.

A potent probiotic strain from cheddar cheese

A lactic acid bacteria Leuconostoc paramesenteroides was isolated and characterized from cheddar cheese and was adapted to grow at low pH (2.0) and high bile salt concentration (2%) by sequential sub-culturing so that it can survive the extreme environmental condition of gut. Cell hydrophobicity assay shows the maximum adherence of the culture to toluene (46.11%). Adhesion ability was confirmed by in vitro assay using rat intestinal epithelial layer. The culture has an antimicrobial activity against food borne pathogens and is vancomycin sensitive. The culture shows a β-galactosidase activity of 3.42 μM/mg protein, which indicates the ability of the culture to hydrolyze lactose for easy absorption. All these properties determine the ability of the culture to be used as a probiotic.

Artificial intelligence based optimization of exocellular glucansucrase production from Leuconostoc dextranicum NRRL B-1146

Two different artificial intelligence techniques namely artificial neural network (ANN) and genetic algorithm (GA) were integrated for optimizing fermentation medium for the production of glucansucrase. The experimental data reported in a previous study were used to build the neural network. The ANN was trained using the back propagation algorithm. The ANN predicted values showed good agreement with the experimentally reported ones from a response surface based experiment. The concentrations of three medium components: viz Tween 80, sucrose and K2HPO4 served as inputs to the neural network model and the enzyme activity as the output of the model. A model was generated with a coefficient of correlation (R2) of 1.0 for the training set and 0.90 for the test data. A genetic algorithm was used to optimize the input space of the neural network model to find the optimum settings for maximum enzyme activity. This artificial neural network supported genetic algorithm predicted a maximum glucansucrase activity of 6.92U/ml at medium composition of 0.54% (v/v) Tween 80, 5.98% (w/v) sucrose and 1.01% (w/v) K2HPO4. ANN-GA predicted model gave a 6.0% increase of enzyme activity over the regression based prediction for optimized enzyme activity. The maximum enzyme activity experimentally obtained using the ANN-GA designed medium was 6.75+/-0.09U/ml which was in good agreement with the predicted value.