Thiamine-Starved Lactococcus lactis for Producing Food-Grade Pyruvate

Lactococcus lactis is a safe lactic acid bacterium widely used in dairy fermentations. Normally, its main fermentation product is lactic acid; however, L. lactis can be persuaded into producing other compounds, e.g., through genetic engineering. Here, we have explored the possibility of rewiring the metabolism of L. lactis into producing pyruvate without using genetic tools. Depriving the thiamine-auxotrophic and lactate dehydrogenase-deficient L. lactis strain RD1M5 of thiamine efficiently shut down two enzymes at the pyruvate branch, the thiamine pyrophosphate (TPP) dependent pyruvate dehydrogenase (PDHc) and α-acetolactate synthase (ALS). After eliminating the remaining enzyme acting on pyruvate, the highly oxygen-sensitive pyruvate formate lyase (PFL), by simple aeration, the outcome was pyruvate production. Pyruvate could be generated by nongrowing cells and cells growing in a substrate low in thiamine, e.g., Florisil-treated milk. Pyruvate is a precursor for the butter aroma compound diacetyl. Using an α-acetolactate decarboxylase deficient L. lactis strain, pyruvate could be converted to α-acetolactate and diacetyl. Summing up, by starving L. lactis for thiamine, secretion of pyruvate could be attained. The food-grade pyruvate produced has many applications, e.g., as an antioxidant or be used to make butter aroma.

Citrate metabolism in lactic acid bacteria: is there a beneficial effect for Oenococcus oeni in wine?

Lactic acid bacteria (LAB) are Gram positive bacteria frequently used in the food industry for fermentation, mainly transformation of carbohydrates into lactic acid. In addition, these bacteria also have the capacity to metabolize citrate, an organic acid commonly found in food products. Its fermentation leads to the production of 4-carbon compounds such as diacetyl, resulting in a buttery flavor desired in dairy products. Citrate metabolism is known to have several beneficial effects on LAB physiology. Nevertheless, a controversial effect of citrate has been described on the acid tolerance of the wine bacterium Oenococcus oeni. This observation raises questions about the effect of citrate on the capacity of O. oeni to conduct malolactic fermentation in highly acidic wines. This review aims to summarize the current understanding of citrate metabolism in LAB, with a focus on the wine bacterium O. oeni. Metabolism with the related enzymes is detailed, as are the involved genes organized in cit loci. The known systems of cit locus expression regulation are also described. Finally, the beneficial effects of citrate catabolism on LAB physiology are reported and the negative impact observed in O. oeni is discussed.

Lebanese fermented goat milk products: From tradition to meta-omics

Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.

Co-fermentation of non-Saccharomyces yeasts with Lactiplantibacillus plantarum FST 1.7 for the production of non-alcoholic beer

The non-alcoholic beer (NAB) sector has experienced steady growth in recent years, with breweries continuously seeking new ways to fulfil consumer demands. NAB can be produced by limited fermentation of non-Saccharomyces yeasts; however, beer produced in this manner is often critiqued for its sweet taste and wort-like off-flavours due to high levels of residual sugars and lack of flavour metabolites. The use of Lactobacillus in limited co-fermentation with non-Saccharomyces yeasts is a novel approach to produce NABs with varying flavour and aroma characteristics. In this study, lab-scale fermentations of Lachancea fermentati KBI 12.1 and Cyberlindnera subsufficiens C6.1 with Lactiplantibacillus plantarum FST 1.7 were performed and compared to a brewer's yeast, Saccharomyces cerevisiae WLP001. Fermentations were monitored for pH, TTA, extract reduction, alcohol production, and microbial cell count. The final beers were analysed for sugar and organic acid concentration, free amino nitrogen content (FAN), glycerol, and levels of volatile metabolites. The inability of the non-Saccharomyces yeasts to utilise maltotriose as an energy source resulted in extended fermentation times compared to S. cerevisiae WLP001. Co-fermentation of yeasts with lactic acid bacteria (LAB) resulted in a decreased pH, higher TTA and increased levels of lactic acid in the final beers. The overall acceptability of the NABs produced by co-fermentation was higher than or similar to that of the beers fermented with the yeasts alone, indicating that LAB fermentation did not negatively impact the sensory attributes of the beer. C. subsufficiens C6.1 and L. plantarum FST 1.7 NAB was characterised as fruity tasting with the significantly higher ester concentrations masking the wort-like flavours resulting from limited fermentation. NAB produced with L. fermentati KBI12.1 and L. plantarum FST1.7 had decreased levels of the undesirable volatile compound diacetyl and was described as 'fruity' and 'acidic', with the increased sourness masking the sweet, wort-like characteristics of the NAB. Moreover, this NAB was ranked as the most highly acceptable in the sensory evaluation. In conclusion, the limited co-fermentation of non-Saccharomyces yeasts with LAB is a promising strategy for the production of NAB.

Fermentation of cv. Kalamata Natural Black Olives with Potential Multifunctional Yeast Starters

The purpose of this study was to explore the inoculated fermentation of cv. Kalamata natural black olives using selected strains of yeast cultures with multifunctional potential. For this purpose, five yeast starters belonging to Candida boidinii (four starters) and Saccharomyces cerevisiae (one starter), previously isolated from table olive fermentation of the same variety and screened for their technological characteristics and probiotic potential, were inoculated in brines at the beginning of fermentation. Microbial populations (lactic acid bacteria, yeasts, and Enterobacteriaceae), pH, titratable acidity, organic acids, and ethanol were monitored during fermentation for a period of 5 months. At the same time, the survival of each starter was assessed by culture-dependent molecular identification at the beginning (0 days), middle (75 days), and final stages (150 days) of fermentation in the brines and olives (at the end of the process only). The results revealed the coexistence of yeasts and lactic acid bacteria (LAB) throughout fermentation in most processes and also the absence of Enterobacteriaceae after the first 20 days of brining. The population of yeasts remained 2 log cycles below LAB counts, except for in the inoculated treatment with C. boidinii Y28, where the yeast starter prevailed from day 60 until the end of the fermentation, as well as in the inoculated treatment with C. boidinii Y30, where no LAB could be detected in the brines after 38 days. At the end of the process, LAB ranged between 4.6 and 6.8 log₁₀ CFU/mL, while yeasts were close to 5.0 log₁₀ CFU/mL, except for the inoculated fermentation with C. boidinii Y27 and spontaneous fermentation (control), in which the yeast counts were close to 3.5 log₁₀ CFU/mL. At the end of fermentation, the recovery percentage of C. boidinii Y27 was 50% in the brines and 45% in the olives. C. boidinii Y28 and S. cerevisiae Y34 could be recovered at 25% and 5% in the brine, respectively, whereas neither starter could be detected in the olives. For C. boidinii Y30, the recovery percentage was 25% in the brine and 10% in the olives. Finally, C. boidinii Y31 could not be detected in the brines and survived at a low percentage (10%) in the olives.

Lentil-Based Yogurt Alternatives Fermented with Multifunctional Strains of Lactic Acid Bacteria—Techno-Functional, Microbiological, and Sensory Characteristics

A milk-alternative produced from lentil protein isolate was fermented with three multifunctional strains of lactic acid bacteria, Leuconostoc citreum TR116, Leuconostoc pseudomesenteroides MP070, and Lacticaseibacillus paracasei FST 6.1. As a control, a commercial starter culture containing Streptococcus thermophilus was used. The metabolic performance of these strains and the techno-functional properties of the resulting yogurt alternatives (YA) were studied. Microbial growth was evaluated by cell counts, acidification, and carbohydrate metabolization. The structure of the YA was investigated by textural and rheological analyses and confocal laser scanning microscopy (CLSM). Production of antifungal compounds, the influence of fermentation on the content of FODMAPs, and typical metabolites were analyzed, and a sensory analysis was performed. The results revealed an exponential microbial growth in the lentil base substrate supported by typical acidification, which indicates a suitable environment for the selected strains. The resulting YA showed a gel-like texture typical for non-stirred yogurts, and high water holding capacity. The tested strains produced much higher levels of antifungal phenolic compounds than the commercial control and are therefore promising candidates as adjunct cultures for shelf-life extension. The Leuconostoc strains produced mannitol from fructose and could thus be applied in sugar-reduced YA. Preliminary sensory analysis showed high acceptance for YA produced with Lacticaseibacillus paracasei FST 6.1, and a yogurt-like flavor not statistically different to that produced by the control. Overall, each tested strain possessed promising functionalities with great potential for application in fermented plant-based dairy-alternatives.

Fermented Foods, Health and the Gut Microbiome

Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.

Niche partitioning facilitates coexistence of closely related honey bee gut bacteria

Ecological processes underlying bacterial coexistence in the gut are not well understood. Here, we disentangled the effect of the host and the diet on the coexistence of four closely related Lactobacillus species colonizing the honey bee gut. We serially passaged the four species through gnotobiotic bees and in liquid cultures in the presence of either pollen (bee diet) or simple sugars. Although the four species engaged in negative interactions, they were able to stably coexist, both in vivo and in vitro. However, coexistence was only possible in the presence of pollen, and not in simple sugars, independent of the environment. Using metatranscriptomics and metabolomics, we found that the four species utilize different pollen-derived carbohydrate substrates indicating resource partitioning as the basis of coexistence. Our results show that despite longstanding host association, gut bacterial interactions can be recapitulated in vitro providing insights about bacterial coexistence when combined with in vivo experiments.

Global cocoa fermentation microbiome: revealing new taxa and microbial functions by next generation sequencing technologies

This review provides an overview of the application of next-generation sequencing (NGS) technologies for microbiome analysis of cocoa beans fermentation. The cocoa-producing regions where NGS has been applied include Brazil, Ghana, Ivory Coast, Cameroon, Nicaragua, and Colombia. The data collected were processed by principal component analysis (PCA) and Venn diagrams to perform a multivariate association between microbial diversity and cocoa-producing regions. NGS studies have confirmed the dominance of three major microbial groups revealed by culture-dependent approaches, i.e., lactic acid bacteria, acetic acid bacteria, and yeasts. However, a more complex microbial diversity has been revealed, comprising sub-dominant populations, late-growing species, and uncultivable microorganisms. A total of 99 microbial genera and species were for the first time reported in cocoa beans fermentation, such as Brevibacillus sp., Halomonas meridiana, Methylobacterium sp., Novosphingobium sp., and Paenibacillus pabuli. PCA and Venn diagrams showed that species composition is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies between different cocoa-producing regions. Understanding these differences will provide further directions for exploring the functional and metabolic activity of rare and abundant taxa, as well as their use as starter cultures to obtain high-quality cocoa beans.

Development of Lactococcus lactis Biosensors for Detection of Diacetyl

Some secondary metabolites of fermentative bacteria are desired compounds for the food industry. Examples of these compounds are diacetyl and acetaldehyde, which are produced by species of the lactic acid bacteria (LAB) family. Diacetyl is an aromatic compound, giving the buttery flavor associated with dairy products, and acetaldehyde is the compound responsible for the yogurt flavor and aroma. The quantification of these compounds in food matrices is a laborious task that involves sample preparation and specific analytical methods. The ability of bacteria to naturally sense metabolites has successfully been exploited to develop biosensors that facilitate the identification and quantification of certain metabolites (Mahr and Frunzke, 2016). The presence of a specific metabolite is sensed by the biosensors, and it is subsequently translated into the expression of one or more reporter genes. In this study we aimed to develop fluorescence-based biosensors to detect diacetyl and acetaldehyde. Since the metabolic pathways for production and degradation of these compounds are present in Lactococcus lactis, the sensing mechanisms in this bacterium are expected. Thus, we identified diacetyl and acetaldehyde responsive promoters by performing transcriptome analyses in L. lactis. The characterization of the biosensors showed their response to the presence of these compounds, and a further analysis of the diacetyl-biosensors (its dynamics and orthogonality) was performed. Moreover, we attempted to produce natural diacetyl from producer strains, namely L. lactis subsp. lactis biovar diacetylactis, to benchmark the performance of our biosensors. The diacetyl-biosensors responded linearly to the amounts of diacetyl obtained in the bacterial supernatants, i.e., the increases in GFP expression were proportional to the amounts of diacetyl present in the supernatants of L. lactis subsp. lactis biovar diacetylactis MR3-T7 strain. The biosensors developed in this study may eventually be used to engineer strains or pathways for increased diacetyl and acetaldehyde production, and may facilitate the detection of these metabolites in complex food matrices.

Evolution of Bacterial Communities, Physicochemical Changes and Sensorial Attributes of Natural Whole and Cracked Picual Table Olives During Spontaneous and Inoculated Fermentation

Table olives are one of the most well-known traditionally fermented products, and their global consumption is exponentially increasing. In direct brining, table olives are produced spontaneously, without any debittering pre-treatment. Up to date, fermentation process remains empirical and inconstant, as it is affected by the physicochemical attributes of the fruit, tree and fruit management of pro and post-harvest. In the present study, whole and cracked Picual table olives were fermented at industrial scale for 120 days, using three distinct methods (natural fermentation, inoculation with lactic acid bacteria (LAB) at a 7 or a 10% NaCl concentration). Microbial, physicochemical and sensorial alterations monitored during the whole process, and several differences were observed between treatments. Results indicated that in all treatments, the dominant microflora were LAB. Yeasts also detected in noteworthy populations, especially in non-inoculated samples. However, LAB population was significantly higher in inoculated compared to non-inoculated samples. Microbial profiles identified by metagenomic approach showed meaningful differences between spontaneous and inoculated treatments. As a result, the profound dominance of starter culture had a severe effect on olives fermentation, resulting in lower pH and higher acidification, which was mainly caused by the higher levels of lactic acid produced. Furthermore, the elimination of Enterobacteriaceae was shortened, even at lower salt concentration. Although no effect observed concerning the quantitated organoleptic parameters such as color and texture, significantly higher levels in terms of antioxidant capacity were recorded in inoculated samples. At the same time, the degradation time of oleuropein was shortened, leading to the production of higher levels of hydroxytyrosol. Based on this evidence, the establishment of starter culture driven Picual olives fermentation is strongly recommended. It is crucial to mention that the inoculated treatment with reducing sodium content was highly appreciated by the sensory panel, enhancing the hypothesis that the production of Picual table olives at reduced NaCl levels is achievable.

Efficient production of α-acetolactate by whole cell catalytic transformation of fermentation-derived pyruvate

Background

Diacetyl provides the buttery aroma in products such as butter and margarine. It can be made via a harsh set of chemical reactions from sugarcane bagasse, however, in dairy products it is normally formed spontaneously from α-acetolactate, a compound generated by selected lactic acid bacteria in the starter culture used. Due to its bacteriostatic properties, it is difficult to achieve high levels of diacetyl by fermentation. Here we present a novel strategy for producing diacetyl based on whole-cell catalysis, which bypasses the toxic effects of diacetyl.

Results

By expressing a robust α-acetolactate synthase (ALS) in a metabolically optimized Lactococcus lactis strain we obtained a whole-cell biocatalyst that efficiently converted pyruvate into α-acetolactate. After process optimization, we achieved a titer for α-acetolactate of 172 ± 2 mM. Subsequently we used a two-stage production setup, where pyruvate was produced by an engineered L. lactis strain and subsequently used as the substrate for the biocatalyst. Using this approach, 122 ± 5 mM and 113 ± 3 mM α-acetolactate could be made from glucose or lactose in dairy waste, respectively. The whole-cell biocatalyst was robust and fully active in crude fermentation broth containing pyruvate.

Conclusions

An efficient approach for converting sugar into α-acetolactate, via pyruvate, was developed and tested successfully. Due to the anaerobic conditions used for the biotransformation, little diacetyl was generated, and this allowed for efficient biotransformation of pyruvate into α-acetolactate, with the highest titers reported to date. The use of a two-step procedure for producing α-acetolactate, where non-toxic pyruvate first is formed, and subsequently converted into α-acetolactate, also simplified the process optimization. We conclude that whole cell catalysis is suitable for converting lactose in dairy waste into α-acetolactate, which favors resource utilization.

Benefits of the Use of Lactic Acid Bacteria Starter in Green Cracked Cypriot Table Olives Fermentation

Table olives are one of the most established Mediterranean vegetables, having an exponential increase consumption year by year. In the natural-style processing, olives are produced by spontaneous fermentation, without any chemical debittering. This natural fermentation process remains empirical and variable since it is strongly influenced by physicochemical parameters and microorganism presence in olive drupes. In the present work, Cypriot green cracked table olives were processed directly in brine (natural olives), using three distinct methods: spontaneous fermentation, inoculation with lactic acid bacteria at a 7% or a 10% NaCl concentration. Sensory, physicochemical, and microbiological alterations were monitored at intervals, and major differences were detected across treatments. Results indicated that the predominant microorganisms in the inoculated treatments were lactic acid bacteria, while yeasts predominated in control. As a consequence, starter culture contributed to a crucial effect on olives fermentation, leading to faster acidification and lower pH. This was attributed to a successful lactic acid fermentation, contrasting the acetic and alcoholic fermentation observed in control. Furthermore, it was established that inhibition of enterobacteria growth was achieved in a shorter period and at a significantly lower salt concentration, compared to the spontaneous fermentation. Even though no significant variances were detected in terms of the total phenolic content and antioxidant capacity, the degradation of oleuropein was achieved faster in inoculated treatments, thus, producing higher levels of hydroxytyrosol. Notably, the reduction of salt concentration, in combination with the use of starter, accented novel organoleptic characteristics in the final product, as confirmed from a sensory panel; hence, it becomes obvious that the production of Cypriot table olives at reduced NaCl levels is feasible.

Comparison of Volatile and Nonvolatile Compounds in Rice Fermented by Different Lactic Acid Bacteria

The production of rice-based beverages fermented by lactic acid bacteria (LAB) can increase the consumption of rice in the form of a dairy replacement. This study investigated volatile and nonvolatile components in rice fermented by 12 different LABs. Volatile compounds of fermented rice samples were analyzed using gas chromatography-mass spectrometry (GC-MS) combined with solid-phase microextraction (SPME), while nonvolatile compounds were determined using gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) after derivatization. The 47 identified volatile compounds included acids, aldehydes, esters, furan derivatives, ketones, alcohols, benzene and benzene derivatives, hydrocarbons, and terpenes, while the 37 identified nonvolatile components included amino acids, organic acids, and carbohydrates. The profiles of volatile and nonvolatile components generally differed significantly between obligatorily homofermentative/facultatively heterofermentative LAB and obligatorily heterofermentative LAB. The rice sample fermented by Lactobacillus sakei (RTCL16) was clearly differentiated from the other samples on principal component analysis (PCA) plots. The results of PCA revealed that the rice samples fermented by LABs could be distinguished according to microbial strains.

Implications of the expression of Enterococcus faecalis citrate fermentation genes during infection

Citrate is an ubiquitous compound in nature. However, citrate fermentation is present only in a few pathogenic or nonpathogenic microorganisms. The citrate fermentation pathway includes a citrate transporter, a citrate lyase complex, an oxaloacetate decarboxylase and a regulatory system. Enterococcus faecalis is commonly present in the gastro-intestinal microbiota of warm-blooded animals and insect guts. These bacteria can also cause infection and disease in immunocompromised individuals. In the present study, we performed whole genome analysis in Enterococcus strains finding that the complete citrate pathway is present in all of the E. faecalis strains isolated from such diverse habitats as animals, hospitals, water, milk, plants, insects, cheese, etc. These results indicate the importance of this metabolic preservation for persistence and growth of E. faecalis in different niches. We also analyzed the role of citrate metabolism in the E. faecalis pathogenicity. We found that an E. faecalis citrate fermentation-deficient strain was less pathogenic for Galleria mellonella larvae than the wild type. Furthermore, strains with deletions in the oxaloacetate decarboxylase subunits or in the α-acetolactate synthase resulted also less virulent than the wild type strain. We also observed that citrate promoters are induced in blood, urine and also in the hemolymph of G. mellonella. In addition, we showed that citrate fermentation allows E. faecalis to grow better in blood, urine and G. mellonella. The results presented here clearly indicate that citrate fermentation plays an important role in E. faecalis opportunistic pathogenic behavior.

Evolution of Yeast Consortia during the Fermentation of Kalamata Natural Black Olives upon Two Initial Acidification Treatments

The objective of this study was to elucidate the yeast consortia structure and dynamics during Greek-style processing of Kalamata natural black olives in different brine solutions. Olives were subjected to spontaneous fermentation in 7% (w/v) NaCl brine solution (control treatment) or brine acidified with (a) 0.5% (v/v) vinegar, and (b) 0.1% (v/v) lactic acid at the onset of fermentation. Changes in microbial counts, pH, acidity, organic acids, sugars, and alcohols were analyzed for a period of 187 days. Yeast consortia diversity was evaluated at days 4, 34, 90, 140, and 187 of fermentation. A total of 260 isolates were characterized at sub-species level by rep-PCR genomic fingerprinting with the oligo-nucleotide primer (GTG)5. The characterization of yeast isolates at species level was performed by sequencing of the D1/D2 domain of 26S rRNA gene. Results showed that yeasts dominated the process presenting a relatively broad range of biodiversity composed of 11 genera and 21 species. No lactic acid bacteria (LAB) or Enterobacteriaceae could be enumerated after 20 and 10 days of fermentation, respectively. The dominant yeast species at the beginning were Aureobasidium pullulans for control and vinegar acidification treatments, and Candida naeodendra for lactic acid treatment. Between 34 and 140 days the dominant species were Candida boidinii, Candida molendinolei and Saccharomyces cerevisiae. In the end of fermentation the dominant species in all processes were C. boidinii and C. molendinolei, followed by Pichia manshurica and S. cerevisiae in lactic acid acidification treatment, P. manshurica in vinegar acidification treatment, and Pichia membranifaciens in control fermentation.