Kinetic analysis of growth and sugar consumption by Lactobacillus fermentum IMDO 130101 reveals adaptation to the acidic sourdough ecosystem

Various cold storage-backslopping cycles show the robustness of Limosilactobacillus fermentum IMDO 130101 as starter culture for Type 3 sourdough production

Type 3 sourdoughs, which are starter culture-initiated and subsequently backslopped, are less studied than other sourdough types. Yet, they can serve as a model to assess how competitive starter culture strains for sourdough production are and how the microbial composition of such sourdoughs may evolve over time. In the present study, Limosilactobacillus fermentum IMDO 130101 was used to produce Type 3 sourdoughs, prepared from wheat and wholemeal wheat flours. Therefore, an initial fermentation of the flour-water mixture was performed at 30 °C for 48 h. This was followed by cold storage-backslopping cycles, consisting of refreshments (50 %, v/v), fermentation steps of 16 h, and storage at 4 °C each week, every three weeks, and every six weeks. The microbial dynamics (culture-dependent and -independent approaches) and metabolite dynamics were measured. In all sourdoughs produced, starter culture strain monitoring, following an amplicon sequence variant approach, showed that Liml. fermentum IMDO 130101 prevailed during one month when the sourdoughs were refreshed each week, during 24 weeks when the sourdoughs were refreshed every three weeks, and during 12 weeks when the sourdoughs were refreshed every six weeks. This suggested the competitiveness and robustness of Liml. fermentum IMDO 130101 for a considerable duration but also showed that the strain is prone to microbial interference. For instance, Levilactobacillus brevis and Pediococcus spp. prevailed upon further cold storage and backslopping. Also, although no yeasts were inoculated into the flour-water mixtures, Kazachstania unispora, Torulaspora delbrueckii, and Wickerhamomyces anomalus were the main yeast species found. They appeared after several weeks of storage and backslopping, which however indicated the importance of an interplay between LAB and yeast species in sourdoughs. The main differences among the mature sourdoughs obtained could be explained by the different flours used, the refreshment conditions applied, and the sampling time (before and after backslopping). Finally, the metabolite quantifications revealed continued metabolite production during the cold storage periods, which may impact the sourdough properties and those of the breads made thereof.

Cyclic pairwise interaction representing a rock-paper-scissors game maintains the population of the vulnerable yeast Saccharomyces cerevisiae within a multispecies sourdough microbiome

IMPORTANCE

Traditionally, multispecies consisting of lactic acid bacteria and yeasts collaboratively engage sourdough fermentation, which determines the quality of the resulting baked goods. Nonetheless, the successive transfer of these microbial communities can result in undesirable community dynamics that prevent the formation of high-quality sourdough bread. Thus, a mechanistic understanding of the community dynamics is fundamental to engineer sourdough complex fermentation. This study describes the population dynamics of five species of lactic acid bacteria-yeast communities in vitro using a generalized Lotka-Volterra model that examines interspecies interactions. A vulnerable yeast species was maintained within up to five species community dynamics by obtaining support with a cyclic interspecies interaction. Metaphorically, it involves a rock-paper-scissors game between two lactic acid bacteria species. Application of the generalized Lotka-Volterra model to real food microbiomes including sourdoughs will increase the reliability of the model prediction and help identify key microbial interactions that drive microbiome dynamics.

Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions

Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.

Inactivation of Foodborne Pathogens by Lactiplantibacillus Strains during Meat Fermentation: Kinetics and Mathematical Modelling

This study examined the effect of beef fermentation with Lactiplantibacillus paraplantarum (L) PTCC 1965, Lactiplantibacillus (L) plantarum subsp. plantarum PTCC 1745, and Lactiplantibacillus (L) pentosus PTCC 1872 bacteria on the growth of pathogenic bacteria, including Salmonella (S) Typhi PTCC 1609 and Staphylococcus (S) aureus PTCC 1826. The growth of lactic acid bacteria (LAB) and the effect of fermentation on pathogenic bacteria were studied using Weibull: biphasic linear and competitive models. The results showed that the rate of pH reduction was lower in the early stages and increased as the microbial population grew. The α parameter was lower for L. plantarum subsp. plantarum compared to L. paraplantarum and L. pentosus. The comparison of the α parameter for bacterial growth and pH data showed that the time interval required to initiate the rapid growth phase of the bacteria was much shorter than that for the rapid pH reduction phase. The pH value had a 50% greater effect on the inactivation of S. Typhi when compared to the samples containing L. plantarum subsp. plantarum and L. pentosus. The same parameter was reported to be 72% for the inactivation of St. aureus. In general, during the fermentation process, LAB strains caused a decrease in pH, and as a result, reduced the growth of pathogens, which improves consumer health and increases the food safety of fermented meat.

Characterization of autochthonous lactobacilli from goat dairy products with probiotic potential for metabolic diseases

The present study aimed to design functional fermented goat milk with probiotic potential for metabolic diseases. Thereby, autochthonous lactobacilli from goat dairy products that target improving the inflammatory, lipid, and glycemic profile were characterized. We designed fermented goat milk using Lactobacillus delbrueckii subsp. indicus CRL1447 as starter strain, supplemented with different probiotic consortia formed by Limosilactobacillus fermentum CRL1446, Lactiplantibacillus paraplantarum CRL1449, and CRL1472 strains. These lactobacilli were selected for their positive effects on inhibition of α-glucosidase, bile salts hydrolase activity, cholesterol assimilation, and decreased triglyceride percentage in Caenorhabditis elegans. Furthermore, the lactobacilli oral administration to obese mice caused a significant decrease in body weight gain and ameliorated hyperglycemia and hyperlipemia. These results reveal the potential of this goat dairy product as a functional food to prevent obesity and related pathologies. Goat milk-derived products stand out for their marketing potential. Hence, fermented goat milk incorporating novel probiotics represents a group of food products with broad prospects by their promising nutritive and therapeutic properties for metabolic diseases. The goat dairy product designed in this study could be used in the prevention of dyslipidemia and hyperglycemia in obese people.

•

New probiotic consortium (CRL1449, CRL1472, and ​CRL1446) was selected.

•

The probiotic consortium showed in vitro immuno and adipomodulatory properties.

•

Lactobacillus delbrueckii subsp. indicus CRL1447 was selected as a starter culture for fermented milk elaboration.

•

Manufacturing of a functional fermented goat milk with a new probiotic consortium.

Mechanistic Insight into Yeast Bloom in a Lactic Acid Bacteria Relaying-Community in the Start of Sourdough Microbiota Evolution

The spontaneous microbiota of wheat sourdough, often comprising one yeast species and several lactic acid bacteria (LAB) species, evolves over repeated fermentation cycles, which bakers call backslopping. The final product quality largely depends on the microbiota functions, but these fluctuate sometimes during the initial months of fermentation cycles due to microbiota evolution in which three phases of LAB relay occur. In this study, the understanding of yeast-LAB interactions in the start of the evolution of the microbiota was deepened by exploring the timing and trigger interactions when sourdough yeast entered a preestablished LAB-relaying community. Monitoring of 32 cycles of evolution of 6 batches of spontaneous microbiota in wheat sourdoughs revealed that sourdough yeasts affected the LAB community when the 2nd- or 3rd-relaying types of LAB genera emerged. In in vitro pairwise cocultures, all 12 LAB strains containing the 3 LAB-relaying types arrested the growth of a Saccharomyces cerevisiae strain, a frequently found species in sourdoughs, to various extents by sugar-related interactions. These findings suggest competition due to different affinities of each LAB and a S. cerevisiae strain for each sugar. In particular, maltose was the driver of S. cerevisiae growth in all pairwise cocultures. The functional prediction of sugar metabolism in sourdough LAB communities showed a positive correlation between maltose degradation and the yeast population. Our results suggest that maltose-related interactions are key factors that enable yeasts to enter and then settle in the LAB-relaying community during the initial part of evolution of spontaneous sourdough microbiota.

IMPORTANCE Unpredictable evolution of spontaneous sourdough microbiota sometimes prevents bakers from making special-quality products because the unstable microbiota causes the product quality to fluctuate. Elucidation of the evolutionary mechanisms of the sourdough community, comprising yeast and lactic acid bacteria (LAB), is fundamental to control fermentation performance. This study investigated the mechanisms by which sourdough yeasts entered and settled in a bacterial community in which a three-phase relay of LAB occurred. Our results showed that all three layers of LAB restricted the cohabiting yeast population by competing for the sugar sources, particularly maltose. During the initial evolution of spontaneous sourdough microbiota, yeasts tended to grow synchronously with the progression of the lactic acid bacterial relay, which was predictably associated with changes in the maltose degradation functions in the bacterial community. Further study of ≥3 species’ interactions while considering yeast diversity can uncover additional interaction mechanisms driving the initial evolution of sourdough microbiota.

Sourdough yeast-bacteria interactions can change ferulic acid metabolism during fermentation

The metabolism of ferulic acid (FA) was studied during fermentation with different species and strains of lactic acid bacteria (LAB) and yeasts, in synthetic sourdough medium. Yeast strains of Kazachstania humilis, Kazachstania bulderi, and Saccharomyces cerevisiae, as well as lactic acid bacteria strains of Fructilactobacillus sanfranciscensis, Lactiplantibacillus plantarum, Lactiplantibacillus xiangfangensis, Levilactobacillus hammesii, Latilactobacillus curvatus and Latilactobacillus sakei were selected from French natural sourdoughs. Fermentation in presence or absence of FA was carried out in LAB and yeasts monocultures, as well as in LAB/yeast co-cultures. Our results indicated that FA was mainly metabolized into 4-vinylguaiacol (4-VG) by S. cerevisiae strains, and into dihydroferulic acid (DHFA) and 4-VG in the case of LAB. Interactions of LAB and yeasts led to the modification of FA metabolism, with a major formation of DHFA, even by the strains that do not produce it in monoculture. Interestingly, FA was almost completely consumed by the F. sanfranciscensis bFs17 and K. humilis yKh17 pair and converted into DHFA in 89.5 ± 19.6% yield, while neither bFs17, nor yKh17 strains assimilated FA in monoculture.

Sourdough Fermentation of Carob Flour and Its Application in Wheat Bread

Research background

Carob is widely cultivated Mediterranean plant, but its flour is scarcely used in bread making. Previous studies investigated the quality of wheat bread with added carob flour showing discrepant results. This study aims to investigate the fermentation performance, antioxidant activity, rheological behaviour and baking application of carob sourdough.

Experimental approach

Carob sourdough was fermented with Lactobacillus brevis or Lactobacillus fermentum combined with Saccharomyces cerevisiae for 24 h at 30 °C. At the end of sourdough fermentation, number of viable lactic acid bacteria and yeast cells, total titratable acidity, pH value, antioxidant activity, phenolics and sugar content were determined. Carob flour (12% flour mass fraction) or sourdough equivalent (22.5% dough mass fraction) was applied in making composite partially baked frozen bread. Dough rheology was monitored using a farinograph. Nutritive value, physical properties and sensory attributes of the rebaked bread samples were evaluated using a hedonic test.

Results and conclusions

By the end of fermentation, carob sourdough reached pH=4.2-4.5 and total acidity 9.9-12.3 mL of 0.1 M NaOH, sugar content on dry mass basis was reduced by 8 g/100 g, while total phenolics and antioxidant activity were increased up to 21%, depending on the starter culture. Addition of carob flour or sourdough to wheat dough resulted in firmer consistency, longer development time, and lower quality number. Regardless, bread with carob flour had significantly improved specific volume. Compared with common wheat bread, carob bread had increased dietary fibre content (46%), total phenolics (140-200%) and antioxidant activity (240-300%), higher shape, larger volume, reduced crumbliness, unchanged firmness and darker crumb colour. Consumer preference and overall acceptability scores of carob sour bread were comparable to those of wheat bread, falling into the category of ’liking very much’.

Novelty and scientific contribution

To our knowledge, this is the first study that proved the feasibility of carob sourdough fermentation using mixed starter cultures, where L. brevis together with S. cerevisiae was better adapted to the substrate than L. fermentum. The carob sourdough could be used as a natural ingredient for improvement of nutritive value and reduction of crumbliness of partially baked frozen bread.

Potential of Bacteria from Alternative Fermented Foods as Starter Cultures for the Production of Wheat Sourdoughs

Microbial strains for starter culture-initiated sourdough productions are commonly isolated from a fermenting flour-water mixture. Yet, starter culture strains isolated from matrices other than sourdoughs could provide the dough with interesting metabolic properties and hence change the organoleptic properties of the concomitant breads. Furthermore, the selection of sourdough starter cultures does not need to be limited to lactic acid bacteria (LAB), as other food-grade microorganisms are sometimes found in sourdoughs. Therefore, different strains belonging to LAB, acetic acid bacteria (AAB), and coagulase-negative staphylococci (CNS) that originated from different fermented food matrices (fermenting cocoa pulp-bean mass, fermented sausage, and water kefir), were examined as to their prevalence in a wheat sourdough ecosystem during 72-h fermentations. Limosilactobacillus fermentum IMDO 222 (fermented cocoa pulp-bean mass isolate) and Latilactobacillus sakei CTC 494 (fermented sausage isolate) seemed to be promising candidates as sourdough starter culture strains, as were the AAB strains Acetobacter pasteurianus IMDO 386B and Gluconobacter oxydans IMDO A845 (both isolated from fermented cocoa pulp-bean mass), due to their competitiveness in the wheat flour-water mixtures. Wheat breads made with G. oxydans IMDO A845 sourdoughs were significantly darker than reference wheat breads.

Impact of pH on succession of sourdough lactic acid bacteria communities and their fermentation properties

Sourdough, a traditional fermented dough, is made via natural fermentation by lactic acid bacteria (LAB). Its pH changes from near neutral to acid during the subculture process. However, the product quality of subcultured sourdough depends on the unpredictable succession of LAB communities, the influential factors of which are still unclear. To elucidate one end of the LAB community succession mechanism, we evaluated the effect of pH by designing four subculture experiments using a model medium adjusted to pH 6.7, 5.5, and 4.5, as well as a natural sourdough subculture. All experiments began by inoculating a sourdough LAB mixture, and both bacterial successions and fermentative properties were monitored until ten subculture steps. In media subcultures, lactic acid production was higher in higher pH media. Three LAB genera, Weissella, Pediococcus, and Lactobacillus, each represented by one operational taxonomic unit (OTU), were successively detected in all subcultures. In later steps with lower pH media, an OTU closely related to Lactobacillus brevis dominated, replacing an OTU closely related to the Weissella cibaria-confusa group that was more dominant than the L. brevis OTU in the near-neutral pH medium. In the sourdough subculture, the three genera were also detected, while Lactobacillus was dominant in earlier steps due to the emergence of an OTU closely related to Lactobacillus sanfranciscensis. These results suggest that a lower pH is favorable for the sequence of sourdough bacterial community evolution finalizing with Lactobacillus domination. Further research is needed to elucidate additional factors other than pH that influence the pattern of LAB community shift.

Comparative genomics of Lactobacillus fermentum suggests a free-living lifestyle of this lactic acid bacterial species

Lactobacillus fermentum is a lactic acid bacterium frequently isolated from mammal tissues, milk, and plant material fermentations, such as sourdough. A comparative genomics analysis of 28 L. fermentum strains enabled the investigation of the core and accessory genes of this species. The core protein phylogenomic tree of the strains examined, consisting of five clades, did not exhibit clear clustering of strains based on isolation source, suggesting a free-living lifestyle. Based on the presence/absence of orthogroups, the largest clade, containing most of the human-related strains, was separated from the rest. The extended core genome included genes necessary for the heterolactic fermentation. Many traits were found to be strain-dependent, for instance utilisation of xylose and arabinose. Compared to other strains, the genome of L. fermentum IMDO 130101, a candidate starter culture strain capable of dominating sourdough fermentations, contained unique genes related to the metabolism of starch degradation products, which could be advantageous for growth in sourdough matrices. This study explained the traits that were previously demonstrated for L. fermentum IMDO 130101 at the genetic level and provided future avenues of research regarding L. fermentum strains isolated from sourdough.

The addition of citrate stimulates the production of acetoin and diacetyl by a citrate-positive Lactobacillus crustorum strain during wheat sourdough fermentation

In traditional sourdough fermentation recipes of artisan bakeries, often extra ingredients are added to the flour-water mixture. This may accentuate the aroma and taste of the baked products produced from such sourdoughs. This is made possible, for instance, by stimulating certain microbial activities during fermentation. This study examined the effects of the addition of citrate (a food-grade organic acid present in milk and lemons) on wheat sourdough fermentation in the presence of a citrate-positive, homofermentative, lactic acid bacterial starter culture strain, namely Lactobacillus crustorum LMG 23699. Both liquid and firm wheat sourdoughs were produced. The starter culture strain was able to steer all wheat sourdough fermentations performed, as it always prevailed due to its competitiveness, as shown through culture-dependent microbiological plating and culture-independent bacterial community profiling. Moreover, it possessed all enzyme-encoding genes (as unraveled through genome mining) necessary to convert citrate into desirable compounds such as lactic acid, acetic acid, succinate, acetoin, diacetyl, and 2,3-butanediol. Indeed, citrate addition to the wheat flour-water mixture had an impact on the sourdough fermentation dynamics and thus on the aroma profile of the liquid and firm sourdoughs produced and breads made thereof. A higher final pH, higher total titratable acidity values, and low yeast counts were found in wheat sourdoughs produced with citrate. In particular, the starter culture strain added converted the supplemented citrate into more l-lactic acid as well as acetoin and diacetyl (buttery aroma compounds), which was independent of the dough yield. The buttery aroma compounds were also accentuated in the concomitant breads produced. Further, organic acid production was stimulated in the sourdoughs, whereas increased pyrazine concentrations occurred in the breads. Consequently, citrate supplementation to wheat sourdoughs could be of interest to produce baked goods with enhanced buttery aroma compounds and notes.

Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria

Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, their microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice fermentations were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that Enterobacteriaceae were outcompeted by lactic acid bacteria (LAB) between 3 and 13 days of fermentation. Metabolite-target analysis showed that lactic acid and mannitol were highly produced, as well as the biogenic amine cadaverine. High-throughput 16S rRNA gene sequencing revealed that mainly species of Leuconostoc and Lactobacillus (as identified by 8 and 20 amplicon sequence variants [ASVs], respectively) mediated the fermentations in subsequent order. The analyses at the DNA level still detected a high number of Enterobacteriaceae, but their relative abundance was low when RNA-based sequencing was performed to detect presumptive metabolically active bacterial cells. In addition, this method greatly reduced host read contamination. Phylogenetic placement indicated a high LAB diversity, with ASVs from nine different phylogenetic groups of the Lactobacillus genus complex. However, fermentation experiments with isolates showed that only strains belonging to the most prevalent phylogenetic groups preserved the fermentation dynamics. The carrot juice fermentation thus forms a robust man-made microbial ecosystem suitable for studies on LAB diversity and niche specificity.

IMPORTANCE The usage of fermented food products by professional chefs is steadily growing worldwide. Meanwhile, this interest has also increased at the household level. However, many of these artisanal food products remain understudied. Here, an extensive microbial analysis was performed of spontaneous fermented carrot juices which are used as nonalcoholic alternatives for wine in a Belgian Michelin star restaurant. Samples were collected through an active citizen science approach with 38 participants, in addition to three laboratory fermentations. Identification of the main microbial players revealed that mainly species of Leuconostoc and Lactobacillus mediated the fermentations in subsequent order. In addition, a high diversity of lactic acid bacteria was found; however, fermentation experiments with isolates showed that only strains belonging to the most prevalent lactic acid bacteria preserved the fermentation dynamics. Finally, this study showed that the usage of RNA-based 16S rRNA amplicon sequencing greatly reduces host read contamination.

Complete and Annotated Genome Sequence of the Sourdough Lactic Acid Bacterium Lactobacillus fermentum IMDO 130101

Lactobacillus fermentum is a species of lactic acid bacteria that is frequently found in sourdough, a fermented flour-water mixture used in the production of bread and other baked goods. Here, we present the complete genome sequence of L. fermentum IMDO 130101, a candidate sourdough starter culture strain isolated from a backslopped rye sourdough.

Microbial Ecology and Process Technology of Sourdough Fermentation

From a microbiological perspective, sourdough is to be considered as a specific and stressful ecosystem, harboring yeasts and lactic acid bacteria (LAB), that is used for the production of baked goods. With respect to the metabolic impact of the sourdough microbiota, acidification (LAB), flavor formation (LAB and yeasts), and leavening (yeasts and heterofermentative LAB species) are most noticeable. Three distinct types of sourdough fermentation processes can be discerned based on the inocula applied, namely backslopped ones (type 1), those initiated with starter cultures (type 2), and those initiated with a starter culture followed by backslopping (type 3). A sourdough-characteristic LAB species is Lactobacillus sanfranciscensis. A sourdough-characteristic yeast species is Candida humilis. Although it has been suggested that the microbiota of a specific sourdough may be influenced by its geographical origin, region specificity often seems to be an artefact resulting from interpretation of the research data, as those are dependent on sampling, isolation, and identification procedures. It is however clear that sourdough-adapted microorganisms are able to withstand stress conditions encountered during their growth. Based on the technological setup, type 0 (predoughs), type I (artisan bakery firm sourdoughs), type II (industrial liquid sourdoughs), and type III sourdoughs (industrial dried sourdoughs) can be distinguished. The production of all sourdoughs, independent of their classification, depends on several intrinsic and extrinsic factors. Both the flour (type, quality status, etc.) and the process parameters (fermentation temperature, pH and pH evolution, dough yield, water activity, oxygen tension, backslopping procedure and fermentation duration, etc.) determine the dynamics and outcome of (backslopped) sourdough fermentation processes.

Amino acid conversions by coagulase-negative staphylococci in a rich medium: Assessment of inter- and intraspecies heterogeneity

The ability of coagulase-negative staphylococci (CNS) to convert amino acids into volatile compounds and biogenic amines was investigated after 24h and 48 h of incubation in a rich medium (brain heart infusion). Volatile compounds were measured with static-headspace gas chromatography and mass spectrometry (SH-GC-MS); biogenic amine measurements were carried out with a newly developed method based on ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS). In total, 56 CNS strains from five different species were used, namely Staphylococcus carnosus, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus. With respect to the production of volatile compounds, the leucine-derived 3-methyl butanol was produced over time by most CNS strains, up to 52 μM for S. xylosus W1-1 after 48 h of incubation. The average production by strains of S. xylosus was significantly higher than for strains of S. carnosus, whereas strains of S. epidermidis turned out to be poor producers. Yet, differences between species were blurred to a large degree because of the high strain variability. A few strains also produced 3-methyl butanal on top of the amount that was already present in the medium background, although most CNS led to a decrease of this compound. Concerning biogenic amines, the average total concentrations per species remained below 100 μM after 48 h of incubation. The most abundant variant was 2-phenylethylamine (PEA), especially within S. carnosus (average of 65 μM after 48 h of incubation). Yet, some individual strains were able to produce higher concentrations, as found for the PEA production of 295 μM by S. epidermidis ATCC 12228 after 48 h of incubation. The insights obtained during this study indicate heterogeneity and are of importance in view of both starter culture development and the evaluation of a spontaneously established CNS microbiota in artisan-type meat fermentations.

Selected ion flow tube-mass spectrometry for online monitoring of submerged fermentations: a case study of sourdough fermentation

Selected ion flow tube-mass spectrometry (SIFT-MS) has recently gained interest as an alternative method to traditional GC-MS for the detection of targeted volatile sample compounds, due to its ease of use, its speed and sensitivity, and its potential for real-time quantification. The feasibility of this technique was demonstrated using the case of the production of ethanol during sourdough fermentation. The potential of SIFT-MS as an online monitoring device for food fermentations was further demonstrated by the detection of acetoin in certain sourdough fermentations. This allowed discrimination between sourdough fermentation processes and illustrated the importance of real-time monitoring of food fermentations.

Coagulase-negative Staphylococci favor conversion of arginine into ornithine despite a widespread genetic potential for nitric oxide synthase activity

Within ecosystems that are poor in carbohydrates, alternative substrates such as arginine may be of importance to coagulase-negative staphylococci (CNS). However, the versatility of arginine conversion in CNS remains largely uncharted. Therefore, a set of 86 strains belonging to 17 CNS species was screened for arginine deiminase (ADI), arginase, and nitric oxide synthase (NOS) activities, in view of their ecological relevance. In fermented meats, for instance, ADI could improve bacterial competitiveness, whereas NOS may serve as an alternative nitrosomyoglobin generator to nitrate and nitrite curing. About 80% of the strains were able to convert arginine, but considerable inter- and intraspecies heterogeneity regarding the extent and mechanism of conversion was found. Overall, ADI was the most commonly employed pathway, resulting in mixtures of ornithine and small amounts of citrulline. Under aerobic conditions, which are more relevant for skin-associated CNS communities, several strains shifted toward arginase activity, leading to the production of ornithine and urea. The obtained data indeed suggest that arginase occurs relatively more in CNS isolates from a dairy environment, whereas ADI seems to be more abundant in strains from a fermented meat background. With some exceptions, a reasonable match between phenotypic ADI and arginase activity and the presence of the encoding genes (arcA and arg) was found. With respect to the NOS pathway, however, only one strain (Staphylococcus haemolyticus G110) displayed phenotypic NOS-like activity under aerobic conditions, despite a wide prevalence of the NOS-encoding gene (nos) among CNS. Hence, the group of CNS displays a strain- and condition-dependent toolbox of arginine-converting mechanisms with potential implications for competitiveness and functionality.

Determination of expression and activity of genes involved in starch metabolism in Lactobacillus plantarum A6 during fermentation of a cereal-based gruel

Traditional fermented gruels prepared from cereals are widely used for complementary feeding of young children in Africa and usually have a low energy density. The amylase activity of some lactic acid bacteria (LAB) helps increase the energy content of gruels through partial hydrolysis of starch, thus enabling the incorporation of more starchy material while conserving the desired semi-liquid consistency for young children. Even if this ability is mainly related to the production of alpha-amylase (E.C. 3.2.1.1), in a recent molecular screening, genes coding for enzymes involved in starch metabolism were detected in the efficient amylolytic LAB Lactobacillus plantarum A6: alpha-glucosidase (E.C. 3.2.1.20), neopullulanase (E.C. 3.2.1.135), amylopectin phosphorylase (E.C. 2.4.1.1) and maltose phosphorylase (E.C. 2.4.1.8). The objective of this study was to investigate the expression of these genes in a model of starchy fermented food made from pearl millet (Pennisetum glaucum). Transcriptional and enzymatic analyses were performed during the 18-h fermentation period. Liquefaction was mainly caused by an extracellular alpha amylase encoded by the amyA gene specific to the A6 strain among L. plantarum species and found in both Lactobacillus amylovorus and Lactobacillus manihotivorans. The second most active enzyme was neopullulanase. Other starch metabolizing enzymes were less often detected. The dynamic detection of transcripts of gene during starch fermentation in pearl millet porridge suggests that the set of genes we investigated was not expressed continuously but transiently.

Oxidation of metabolites highlights the microbial interactions and role of Acetobacter pasteurianus during cocoa bean fermentation

Four cocoa-specific acetic acid bacterium (AAB) strains, namely, Acetobacter pasteurianus 386B, Acetobacter ghanensis LMG 23848(T), Acetobacter fabarum LMG 24244(T), and Acetobacter senegalensis 108B, were analyzed kinetically and metabolically during monoculture laboratory fermentations. A cocoa pulp simulation medium (CPSM) for AAB, containing ethanol, lactic acid, and mannitol, was used. All AAB strains differed in their ethanol and lactic acid oxidation kinetics, whereby only A. pasteurianus 386B performed a fast oxidation of ethanol and lactic acid into acetic acid and acetoin, respectively. Only A. pasteurianus 386B and A. ghanensis LMG 23848(T) oxidized mannitol into fructose. Coculture fermentations with A. pasteurianus 386B or A. ghanensis LMG 23848(T) and Lactobacillus fermentum 222 in CPSM for lactic acid bacteria (LAB) containing glucose, fructose, and citric acid revealed oxidation of lactic acid produced by the LAB strain into acetic acid and acetoin that was faster in the case of A. pasteurianus 386B. A triculture fermentation with Saccharomyces cerevisiae H5S5K23, L. fermentum 222, and A. pasteurianus 386B, using CPSM for LAB, showed oxidation of ethanol and lactic acid produced by the yeast and LAB strain, respectively, into acetic acid and acetoin. Hence, acetic acid and acetoin are the major end metabolites of cocoa bean fermentation. All data highlight that A. pasteurianus 386B displayed beneficial functional roles to be used as a starter culture, namely, a fast oxidation of ethanol and lactic acid, and that these metabolites play a key role as substrates for A. pasteurianus in its indispensable cross-feeding interactions with yeast and LAB during cocoa bean fermentation.

The use of nucleosides and arginine as alternative energy sources by coagulase-negative staphylococci in view of meat fermentation

The ability of coagulase-negative staphylococci (CNS) to use alternative energy sources in meat may partially explain their occurrence in fermented meats. Of 61 CNS strains tested, all metabolized adenosine and inosine in a meat simulation medium (MSM). The ability to catabolize arginine via the arginine deiminase (ADI) pathway varied between strains. All tested strains of Staphylococcus carnosus and Staphylococcus epidermidis possessed an arcA gene and showed ADI activity, whereas other species, such as Staphylococcus equorum and Staphylococcus succinus, did not. Arginine catabolic mobile elements (ACME), as in the positive control S. epidermidis ATCC 12228, were uncommon and only found in Staphylococcus xylosus 3PA6 (sausage isolate) and Staphylococcus chromogenes G222 (teat apex isolate). Monoculture experiments were performed in MSM with S. carnosus 833 and SS3-4, S. xylosus G211, and S. epidermidis ATCC 12228 and 2S7-4. At all pH values tested (5.3, 5.8, and 6.5), the strains of S. carnosus catabolized arginine faster than the strains of S. xylosus and S. epidermidis. Only at pH 6.5 could a low ADI activity be found for S. xylosus G211. Increased ADI activity occurred in the case of the ACME-positive S. epidermidis ATCC 12228, when compared to the ACME-negative S. epidermidis 2S7-4.

Streptococcus pyogenes arginine and citrulline catabolism promotes infection and modulates innate immunity

A bacterium's ability to acquire nutrients from its host during infection is an essential component of pathogenesis. For the Gram-positive pathogen Streptococcus pyogenes, catabolism of the amino acid arginine via the arginine deiminase (ADI) pathway supplements energy production and provides protection against acid stress in vitro. Its expression is enhanced in murine models of infection, suggesting an important role in vivo. To gain insight into the function of the ADI pathway in pathogenesis, the virulence of mutants defective in each of its enzymes was examined. Mutants unable to use arginine (ΔArcA) or citrulline (ΔArcB) were attenuated for carriage in a murine model of asymptomatic mucosal colonization. However, in a murine model of inflammatory infection of cutaneous tissue, the ΔArcA mutant was attenuated but the ΔArcB mutant was hyperattenuated, revealing an unexpected tissue-specific role for citrulline metabolism in pathogenesis. When mice defective for the arginine-dependent production of nitric oxide (iNOS(-/-)) were infected with the ΔArcA mutant, cutaneous virulence was rescued, demonstrating that the ability of S. pyogenes to utilize arginine was dispensable in the absence of nitric oxide-mediated innate immunity. This work demonstrates the importance of arginine and citrulline catabolism and suggests a novel mechanism of virulence by which S. pyogenes uses its metabolism to modulate innate immunity through depletion of an essential host nutrient.

The ability of bifidobacteria to degrade arabinoxylan oligosaccharide constituents and derived oligosaccharides is strain dependent

Arabinoxylan oligosaccharides (AXOS) are prebiotic carbohydrates with promising health-promoting properties that stimulate the activity of specific colon bacteria, in particular bifidobacteria. However, the mechanisms by which bifidobacterial strains break down these compounds in the colon is still unknown. This study investigates AXOS consumption of a large number of bifidobacterial strains (36), belonging to 11 different species, systematically. To determine their degradation mechanisms, all strains were grown on a mixture of arabinose and xylose, xylo-oligosaccharides, and complex AXOS molecules as the sole added energy sources. Based on principal component and cluster analyses of their different arabinose substituent and/or xylose backbone consumption patterns, five clusters that were species independent could be distinguished among the bifidobacterial strains tested. In parallel, the strains were screened for the presence of genes encoding several putative AXOS-degrading enzymes, but no clear-cut correlation could be made with the different degradation mechanisms. The intra- and interspecies differences in the consumption patterns of AXOS indicate that bifidobacterial strains could avoid competition among each other or even could cooperate jointly to degrade these complex prebiotics. The knowledge gained on the AXOS degradation mechanisms in bifidobacteria can be of importance in the rational design of prebiotics with tailor-made composition and thus increased specificity in the colon.

Applicability of Lactobacillus plantarum IMDO 788 as a starter culture to control vegetable fermentations

BACKGROUND

Fermentation of vegetables and fruits is a traditional preservation technique, e.g. in Eastern Europe. Although usually spontaneous fermentation processes are applied, the addition of lactic acid bacteria (LAB) starter cultures could accelerate processing and improve the consistency and quality of the end-products.

RESULTS

The application of Lactobacillus plantarum IMDO 788 as a starter culture strain for cauliflower and mixed vegetable fermentations resulted in accelerated acidification as compared with the spontaneous fermentations. The strain dominated the background microbiota throughout the process, whereas the spontaneous fermentations were characterised by widely variable species diversity. During the spontaneous fermentations, almost all carbohydrates were converted into lactic acid, ethanol, mannitol and acetic acid, indicating the participation of both heterofermentative and homofermentative LAB species. During the starter culture-added fermentations, residual carbohydrates were found and lactic acid and ethanol were the main end-metabolites. Vegetable-associated aromas, ethyl acetate and isoamyl acetate were produced during all fermentations. The high concentration of ethanol and the production of ethyl acetate and isoamyl acetate suggested the involvement of yeasts during all fermentations.

CONCLUSION

Lactobacillus plantarum IMDO 788 was an adequate starter culture strain for vegetable fermentations, prevailing over endogenous LAB communities. Further optimisation of the starter culture formulation is necessary to avoid yeast growth.

Microbial ecology of sourdough fermentations: diverse or uniform?

Sourdough is a specific and stressful ecosystem inhabited by yeasts and lactic acid bacteria (LAB), mainly heterofermentative lactobacilli. On the basis of their inocula, three types of sourdough fermentation processes can be distinguished, namely backslopped ones, those initiated with starter cultures, and those initiated with a starter culture followed by backslopping. Typical sourdough LAB species are Lactobacillus fermentum, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus sanfranciscensis. Typical sourdough yeast species are Candida humilis, Kazachstania exigua, and Saccharomyces cerevisiae. Whereas region specificity is claimed in the case of artisan backslopped sourdoughs, no clear-cut relationship between a typical sourdough and its associated microbiota can be found, as this is dependent on the sampling, isolation, and identification procedures. Both simple and very complex consortia may occur. Moreover, a series of intrinsic and extrinsic factors may influence the composition of the sourdough microbiota. For instance, an influence of the flour (type, quality status, etc.) and the process parameters (temperature, pH, dough yield, backslopping practices, etc.) occurs. In this way, the presence of Lb. sanfranciscensis during sourdough fermentation depends on specific environmental and technological factors. Also, Triticum durum seems to select for obligately heterofermentative LAB species. Finally, there are indications that the sourdough LAB are of intestinal origin.

Bacterial community dynamics, lactic acid bacteria species diversity and metabolite kinetics of traditional Romanian vegetable fermentations

BACKGROUND

Artisanal vegetable fermentations are very popular in Eastern European countries. Fresh vegetables undergo a spontaneous fermentation in the presence of salt, which is mainly carried out by lactic acid bacteria (LAB).

RESULTS

Culture-dependent and culture-independent analyses of end-samples of various spontaneous vegetable fermentations carried out in houses of the Chiodju region (central Romania) revealed Lactobacillus plantarum and Lactobacillus brevis as the most frequently isolated LAB species. Leuconostoc mesenteroides and Leuconostoc citreum were also found. Furthermore, the community dynamics of spontaneous cauliflower and mixed-vegetable (green tomatoes, carrots and cauliflower) fermentations revealed three steps: an initial phase characterised by the presence of Enterobacteriaceae and a wide LAB species diversity, encompassing Weissella species; a second phase from day 3 onwards wherein L. citreum and Lb. brevis occurred; and a final phase characterised by the prevalence of Lb. brevis and Lb. plantarum. Metabolite target analysis revealed that glucose and fructose were mostly depleted at the end of fermentation. The main products of carbohydrate metabolism were lactic acid, acetic acid, ethanol and small amounts of mannitol, indicating heterolactate fermentation.

CONCLUSION

Given their prevalence at the end of vegetable fermentations, Lb. brevis and Lb. plantarum appear to be good candidate starter cultures for controlled vegetable fermentation processes.

Kefir immobilized on corn grains as biocatalyst for lactic acid fermentation and sourdough bread making

The natural mixed culture kefir was immobilized on boiled corn grains to produce an efficient biocatalyst for lactic acid fermentation with direct applications in food production, such as sourdough bread making. The immobilized biocatalyst was initially evaluated for its efficiency for lactic acid production by fermentation of cheese whey at various temperatures. The immobilized cells increased the fermentation rate and enhanced lactic acid production compared to free kefir cells. Maximum lactic acid yield (68.8 g/100 g) and lactic acid productivity (12.6 g/L per day) were obtained during fermentation by immobilized cells at 37 °C. The immobilized biocatalyst was then assessed as culture for sourdough bread making. The produced sourdough breads had satisfactory specific loaf volumes and good sensory characteristics. Specifically, bread made by addition of 60% w/w sourdough containing kefir immobilized on corn was more resistant regarding mould spoilage (appearance during the 11(th) day), probably due to higher lactic acid produced (2.86 g/Kg of bread) compared to the control samples. The sourdough breads made with the immobilized biocatalyst had aroma profiles similar to that of the control samples as shown by headspace SPME GC-MS analysis.

Expression of the arginine deiminase pathway genes in Lactobacillus sakei is strain dependent and is affected by the environmental pH

The adaptation of Lactobacillus sakei to a meat environment is reflected in its metabolic potential. For instance, the ability to utilize arginine through the arginine deiminase (ADI) pathway, resulting in additional ATP, represents a competitive benefit. In L. sakei CTC 494, the arc operon (arcABCTDR) shows the same gene order and organization as that in L. sakei 23K, the genome sequence of which is known. However, differences in relative gene expression were found, and these seemed to be optimal in different growth phases, namely, the highest relative gene expression level was in the end exponential growth phase in the case of L. sakei CTC 494 and in the mid-exponential growth phase of L. sakei 23K. Also, the environmental pH influenced the relative expression level of the arc operon, as shown for L. sakei CTC 494, with the highest relative expression level occurring at the optimal pH for growth (pH 6.0). Deviations from this optimal pH (pH 5.0 and pH 7.0) resulted in an overall decline of the relative expression level of all genes of the arc operon. Furthermore, a differential relative expression of the individual genes of the arc operon was found, with the highest relative gene expression occurring for the first two genes of the arc operon (arcA and arcB). Finally, it was shown that some L. sakei strains were able to convert agmatine into putrescine, suggesting an operational agmatine deiminase pathway in these strains, a metabolic trait that is undesirable in meat fermentations. This study shows that this metabolic trait is most probably encoded by a previously erroneously annotated second putative arc operon.

Interesting starter culture strains for controlled cocoa bean fermentation revealed by simulated cocoa pulp fermentations of cocoa-specific lactic acid bacteria

Among various lactic acid bacterial strains tested, cocoa-specific strains of Lactobacillus fermentum were best adapted to the cocoa pulp ecosystem. They fermented glucose to lactic acid and acetic acid, reduced fructose to mannitol, and converted citric acid into lactic acid and 2,3-butanediol.

The pentose moiety of adenosine and inosine is an important energy source for the fermented-meat starter culture Lactobacillus sakei CTC 494

The genome sequence of Lactobacillus sakei 23K has revealed that the species L. sakei harbors several genes involved in the catabolism of energy sources other than glucose in meat, such as glycerol, arginine, and nucleosides. In this study, a screening of 15 L. sakei strains revealed that arginine, inosine, and adenosine could be used as energy sources by all strains. However, no glycerol catabolism occurred in any of the L. sakei strains tested. A detailed kinetic analysis of inosine and adenosine catabolism in the presence of arginine by L. sakei CTC 494, a fermented-meat starter culture, was performed. It showed that nucleoside catabolism occurred as a mixed-acid fermentation in a pH range (pH 5.0 to 6.5) relevant for sausage fermentation. This resulted in the production of a mixture of acetic acid, formic acid, and ethanol from ribose, while the nucleobase (hypoxanthine and adenine in the case of fermentations with inosine and adenosine, respectively) was excreted into the medium stoichiometrically. This indicates that adenosine deaminase activity did not take place. The ratios of the different fermentation end products did not vary with environmental pH, except for the fermentation with inosine at pH 5.0, where lactic acid was produced too. In all cases, no other carbon-containing metabolites were found; carbon dioxide was derived only from arginine catabolism. Arginine was cometabolized in all cases and resulted in the production of both citrulline and ornithine. Based on these results, a pathway for inosine and adenosine catabolism in L. sakei CTC 494 was presented, whereby both nucleosides are directly converted into their nucleobase and ribose, the latter entering the heterolactate pathway. The present study revealed that the pentose moiety (ribose) of the nucleosides inosine and adenosine is an effective fermentable substrate for L. sakei. Thus, the ability to use these energy sources offers a competitive advantage for this species in a meat environment.