The arginine deiminase pathway of Lactobacillus fermentum IMDO 130101 responds to growth under stress conditions of both temperature and salt

Microbial Dynamics and Metabolite Profiles in Different Types of Salted Seafood (Jeotgal) During Fermentation

Salted and fermented seafood (jeotgal) is known for its long shelf life and unique flavor. Despite the existence of various types of salted seafood, the factors influencing this quality have yet to be identified. These factors are essential for improving the quality of salted seafood, optimizing the fermentation process, and advancing the industrialization of fermented foods. Therefore, in this study, we explored microbial dynamics and changes in quality characteristics in three salted seafood items - salted anchovies (MJ), salted cutlass offal (GJ), and salted croakers (HJ), over a 24-month fermentation period. Distinct microbial community profiles, dominated by Tetragenococcus halophilus, Halanaerobium fermentans, and Chromohalobacter canadensis in MJ, GJ, and HJ, respectively, affect the metabolic pathways and the corresponding flavor profiles. The pH of all samples ranged from 5.7-6.0. The titratable acidity was highest in MJ at 1.4% and lowest in HJ at approximately 0.7%. Salinity was below 25% in all samples but slightly lower in MJ. Significant differences were observed in the amino acid, nucleotide, and overall metabolite profiles. MJ exhibited the highest amino acid and nitrogen-related factor levels, such as glutamic acid and hypoxanthine, enhancing flavor complexity. Correlation analysis revealed significant associations among the types, metabolites, and microbial communities. Microbial survival mechanisms in high-salt environments result in the production of unique metabolites, including umami and aroma components as well as precursors of biogenic amines, which can affect the overall quality of the final product. These differences were primarily influenced by the fish type rather than the fermentation time. Our findings provide foundational insights for enhancing fermentation strategies, improving product consistency, and advancing the industrial application of microbial management in seafood fermentation. This study not only fills a significant gap in the current understanding of fermented seafood but also outlines practical approaches for industry applications for the optimization of product quality.

Halophilic lactic acid bacteria - Play a vital role in the fermented food industry

Halophilic lactic acid bacteria have been widely found in various high-salt fermented foods. The distribution of these species in salt-fermented foods contributes significantly to the development of the product's flavor. Besides, these bacteria also have the ability to biosynthesize bioactive components which potentially apply to different areas. In this review, insights into the metabolic properties, salt stress responses, and potential applications of these bacteria have been have been elucidated. The purpose of this review highlights the important role of halophilic lactic acid bacteria in improving the quality and safety of salt-fermented products and explores the potential application of these bacteria.

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.

Key Stress Response Mechanisms of Probiotics During Their Journey Through the Digestive System: A Review

The survival of probiotic microorganisms during their exposure to harsh environments plays a critical role in the fulfillment of their functional properties. In particular, transit through the human gastrointestinal tract (GIT) is considered one of the most challenging habitats that probiotics must endure, because of the particularly stressful conditions (e.g., oxygen level, pH variations, nutrient limitations, high osmolarity, oxidation, peristalsis) prevailing in the different sections of the GIT, which in turn can affect the growth, viability, physiological status, and functionality of microbial cells. Consequently, probiotics have developed a series of strategies, called "mechanisms of stress response," to protect themselves from these adverse conditions. Such mechanisms may include but are not limited to the induction of new metabolic pathways, formation/production of particular metabolites, and changes of transcription rates. It should be highlighted that some of such mechanisms can be conserved across several different strains or can be unique for specific genera. Hence, this review attempts to review the state-of-the-art knowledge of mechanisms of stress response displayed by potential probiotic strains during their transit through the GIT. In addition, evidence whether stress responses can compromise the biosafety of such strains is also discussed.

Arginine deiminase pathway of Tetragenococcus halophilus contributes to improve the acid tolerance of lactic acid bacteria

Arginine deiminase pathway, controlled by arginine deiminase, ornithine carbamoyltransferase and carbamate kinase, could affect and modulate the intracellular pH homeostasis of lactic acid bacteria under acid stress. Herein, strategy based on exogenous addition of arginine had been proposed to improve the robustness of Tetragenococcus halophilus during acid stressed condition. Results indicated cells cultured in the presence of arginine acquired high tolerance to acid stress mainly through maintaining the homeostasis of intracellular microenvironment. Additionally, metabolomic analysis and q-PCR showed the content of intracellular metabolites and expression levels of genes involved in ADI pathway significantly increased when cells encountered acid stress with the presence of exogenous arginine. Furthermore, Lactococcus lactis NZ9000 with heterologous overexpression of arcA and arcC from T. halophilus exhibited high stress tolerance to acidic condition. This study may provide an insight into the systematical understanding about the mechanism underlying acid tolerance and improve the fermentation performance of LAB during harsh condition.

Shotgun Metagenomic Sequencing Revealed the Prebiotic Potential of a Fruit Juice Drink with Fermentable Fibres in Healthy Humans

Fibre-based dietary interventions are at the forefront of gut microbiome modulation research, with a wealth of 16S rRNA information to demonstrate the prebiotic effects of isolated fibres. However, there is a distinct lack of data relating to the effect of a combination of soluble and insoluble fibres in a convenient-to-consume fruit juice food matrix on gut microbiota structure, diversity, and function. Here, we aimed to determine the impact of the MOJU Prebiotic Shot, an apple, lemon, ginger, and raspberry fruit juice drink blend containing chicory inulin, baobab, golden kiwi, and green banana powders, on gut microbiota structure and function. Healthy adults (n = 20) were included in a randomised, double-blind, placebo-controlled, cross-over study, receiving 60 mL MOJU Prebiotic Shot or placebo (without the fibre mix) for 3 weeks with a 3-week washout period between interventions. Shotgun metagenomics revealed significant between-group differences in alpha and beta diversity. In addition, the relative abundance of the phyla Actinobacteria and Desulfobacteria was significantly increased as a result of the prebiotic intervention. Nine species were observed to be differentially abundant (uncorrected p-value of <0.05) as a result of the prebiotic treatment. Of these, Bifidobacterium adolescentis and CAG-81 sp900066785 (Lachnospiraceae) were present at increased abundance relative to baseline. Additionally, KEGG analysis showed an increased abundance in pathways associated with arginine biosynthesis and phenylacetate degradation during the prebiotic treatment. Our results show the effects of the daily consumption of 60 mL MOJU Prebiotic Shot for 3 weeks and provide insight into the functional potential of B. adolescentis.

Changes in nutrient consumption patterns of Lactobacillus fermentum mediated by sodium lactate

BACKGROUND

During high-cell-density culture of Lactobacillus fermentum, the optimal pH is often maintained by adding NaOH. During cultivation at controlled pH, L. fermentum experiences osmotic stress due to the continuous accumulation of sodium lactate as a neutralizer product, affecting its survival in subsequent processing. The purpose of this study was to evaluate the nutrient consumption patterns of L. fermentum ATCC 14931 under sodium lactate stress and to screen nutrients that help it resist osmotic stress.

RESULTS

The consumption and consumption rates of amino acids, purines, pyrimidines, vitamins, and metal ions were analyzed in chemically defined media containing 0.13, 0.31, or 0.62 mm L^-1 sodium lactate. The highest consumption rates were found for arginine, guanine, folic acid, and Mn²⁺ , and the most consumed nutrients were glutamate + glutamine, guanine, ascorbic acid, and Na⁺ . Arginine 2.58 mm L^-1 , guanine 0.23 mm L^-1 , and Mn²⁺ 0.25 mm L^-1 were added to the medium at sodium lactate concentrations of 0.13 and 0.62 mm L^-1 , and arginine 2.58 mm L^-1 , guanine 0.26 mm L^-1 , and Mn²⁺ 0.25 mm L^-1 at a sodium lactate concentration of 0.31 mm L^-1 . The viable cell counts of L. fermentum ATCC 14931 were approximately 1.02-fold (P < 0.05) of the counts observed in control medium at all three concentrations of sodium lactate.

CONCLUSION

The present results suggest that certain nutrients accelerate the growth of L. fermentum under sodium lactate stress and enhance its resistance to this adverse condition. © 2022 Society of Chemical Industry.

Functional genomics of the lactic acid bacterium Limosilactobacillus fermentum LAB-1: metabolic, probiotic and biotechnological perspectives

A genome-based systematic analysis was conducted to characterize the metabolic, probiotic, fitness, and safety properties of Limosilactobacillus fermentum LAB-1, a lactic acid bacterium demonstrating strong antimicrobial effects against clinical pathogens. Gene functional characterization revealed a large number of genes for carbohydrate metabolism and a heterofermentative system for carbon dissimilation. Genes for intact pyruvate oxidation, pentose phosphate, and PRPP biosynthetic pathways were identified. Substantial carbohydrate-active enzymes and transporters were also predicted. Metabolic reconstruction revealed complete sets of enzymes for arginine, lysine, methionine, threonine, proline, and ornithine biosynthesis. The bacterium harbors a diverse range of peptidases, and a large variety of peptide and amino acid uptake systems. It encodes restriction-modification and CRISPR-Cas systems for protection against phage infections and carries a wide spectrum of stress proteins for adaptation in the gut and industrial conditions. Genes related to the biosynthesis of B-group and K vitamins were identified allowing its application for novel bio-enriched food production. Other beneficial traits of probiotic and industrial importance such as production of flavor compounds, exopolysaccharide, acetoin, and butanediol were identified. Three antimicrobial peptides were predicted which showed >98% sequence-identity to experimentally validated bacteriocins. Negative traits such as transmissible antibiotic resistance, pathogenicity or virulence appeared to be absent suggesting the strain to be considered safe. The genome analysis will allow precisely targeted laboratory research and full exploitation of the probiotic potentials towards functional-food, biotechnology and health-related applications.

Evaluating the effect of lactic acid bacterial fermentation on salted soy whey for development of a potential novel soy sauce-like condiment

There were two main objectives of this study: (1) to understand the effect of salt concentration on the growth of four lactic acid bacteria (LAB) in soy whey and determine the non-volatile and volatile profiles generated after fermentation; (2) to evaluate the potential of using salted soy whey to develop a sauce-like condiment through LAB fermentation. The four LAB included non-halophilic Lactiplantibacillus plantarum ML Prime, Limosilactobacillus fermentum PCC, Oenococcus oeni Enoferm Beta and halophilic Tetragenococcus halophilus DSM20337. At 2% salt, all LAB grew remarkably from day 0 to day 1, except for T. halophilus, while at 6% salt, the growth of L. plantarum, L. fermentum and O. oeni was suppressed. Conversely, the higher salt concentration enhanced the growth of T. halophilus in soy whey as the cell count only increased from 6.36 to 6.60 log CFU/mL at 2% salt but it elevated from 6.61 to 7.55 log CFU/mL at 6% salt. Similarly, the higher salt content negatively affected the sugar and amino acids metabolism and organic acids production by non-halophilic LAB. L. plantarum and O. oeni generated significantly (p < 0.05) more lactic acid (3.83 g/L and 4.17 g/L, respectively) than L. fermentum and T. halophilus (2.02 g/L and 0 g/L, respectively) at 2% salt. In contrast, a higher amount of acetic acid was generated by L. fermentum (0.72 g/L at 2% salt) and T. halophilus (0.51 g/L at 6% salt). LAB could remove the green and beany off-flavours in soy whey by metabolizing C6 and C7 aldehydes. However, to develop a novel soy sauce-like condiment, yeast fermentation and Maillard reaction may be required to generate more characteristic soy sauce-associated aroma compounds.

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Soy whey with 2% and 6% NaCl supported the growth of lactic acid bacteria (LAB).

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At 6% NaCl, T. halophilus grew better while the growth of other LAB was impeded.

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T. halophilus and L. fermentum produced significant amounts of acetic acid.

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Through LAB fermentation, green and beany off-odour of soy whey could be removed.

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Yeast fermentation and heating are required to produce key aroma soy sauce compounds.

Microbiota and Mycobiota of Soy Sauce-Supplied Lactic Acid Bacteria Treated with High Pressure

Background: Ethyl carbamate (EC), a byproduct that naturally forms in fermented foods, can cause tumors and cell death and is classified as a probable human carcinogen (Group 2A). EC is naturally formed through the alcoholysis reaction between ethanol and carbamyl compounds. The major precursors and dominantly emerging stages of EC differ with disparate food types, including soy sauce. This work aimed to clarify the formation of EC and its influence factors throughout the soy sauce production process with or without high-pressure process (HPP) treatment. Methods: Tetragenococcus halophilus, Pediococcus acidilactici, Zygosaccharomyces rouxii, and Candida versatilis were added to soy sauce. The levels of citrulline and EC were measured, and a 16S and ITS assay investigated the microbiota. Results: L-citrulline production was found in each group after fermentation for one month. In addition, L-citrulline levels were generated the most in group D (500 MPa treated raw soy sauce with 12% saltwater and mixed fermentation bacteria, including T. halophilus,P. acidilactici,Z. rouxii, and C. versatilis) and group E (soy sauce fermentation with 12% saltwater without HPP treatment) compared to group F (soy sauce fermentation with 18% saltwater without HPP treatment). Conclusions: These results indicated that salt concentration and mixed fermentation bacteria (T. halophilus,P. acidilactici,Z. rouxii,C. versatilis) might not be major factors for L-citrulline production.

Comparative genomics-based probiotic relevance of Limosilactobacillus fermentum KUB-D18

Limosilactobacillus fermentum KUB-D18 is a heterofermentative lactic acid bacterium that its potential probiotic relevance originally isolated from the chicken intestine. This study sequenced a whole-genome of L. fermentum KUB-D18 and annotated its genes and functions in relation to probiotic properties. As a result, the genome sequence of L. fermentum KUB-D18 approximately contained 2.02 Mbps with GC content of51.7%. After annotating the genome by integrated protein and pathway databases, 2,158 protein-encoding genes were majorly annotated for metabolisms of amino acids, carbohydrates and cofactors as well as vitamins which showed a versatile metabolic capability to gastrointestinal microhabitats. According to the comparative genome analysis of L. fermentum KUB-D18 and the other related strains, L. fermentum KUB-D18 showed common characteristics e.g., folate biosynthesis and bile salt hydrolase enzymes-related cholesterol lowering effect as well as a unique gene cluster involved in metabolism of L-ascorbic acid of L. fermentum KUB-D18. Taken together, L. fermentum KUB-D18 genome provides the genetic basis towards cellular capability for further elucidating the functional mechanisms of its probiotic properties. This study serves for designing desirable targets for the development of probiotic foods and feeds.

The Arginine Biosynthesis Pathway of Candida albicans Regulates Its Cross-Kingdom Interaction with Actinomyces viscosus to Promote Root Caries

The cross-kingdom interactions between Candida albicans and Actinomyces viscosus play critical roles in root caries. However, the key pathway by which C. albicans regulates its interactions with A. viscosus is unclear. Here, we first employed 39 volunteers with root caries and 37 caries-free volunteers, and found that the abundances of C. albicans and A. viscosus were significantly increased in the individuals with root caries and showed a strong positive correlation. Their dual-species combination synergistically promoted biofilm formation and root caries in rats. The arginine biosynthesis pathway of C. albicans was significantly upregulated in dual-species biofilms and dental plaques from another 10 root caries volunteers compared with the 10 caries-free volunteers. The exogenous addition of arginine increased the cariogenicity of the dual-species biofilm. The C. albicansARG4, a key gene from the arginine biosynthesis pathway, null mutant failed to promote dual-species biofilm formation and root caries in rats; however, the addition of arginine restored its synergistic actions with A. viscosus. Our results identified the critical roles of the C. albicans arginine biosynthesis pathway in its cross-kingdom interactions with A. viscosus for the first time and indicated that targeting this pathway was a practical way to treat root caries caused by multiple species.

IMPORTANCE Root caries is a critical problem that threatens the oral health of the elderly population. Our results identified the essential roles of the C. albicans arginine biosynthesis pathway in its cross-kingdom interactions with A. viscosus in root caries for the first time and indicated that targeting this pathway was a practical way to treat root caries caused by multiple species.

Fermentation in Pineapple Juice Significantly Enhances Ornithine and Citrulline Production in Lactococcus lactis MSC-3G Isolated from Sugarcane

Lactic acid bacterial (LAB) fermentation of functional amino acids using fruit juices as a cultivation medium is not well-documented. In the present study, we successfully isolated a high ornithine- and citrulline-producing Lactococcus lactis strain, designated MSC-3G, from sugarcane and investigated the ornithine and citrulline production profile using various fruit juices as a cultivation medium. Among fruit juices, pineapple juice exhibited the highest potentiality to initiate ornithine production (56 mM), while the highest citrulline yield was obtained during lime juice cultivation (34.5 mM). Under the optimal cultivation condition, the highest yield of ornithine and citrulline in pineapple juice reached 98.9 ± 2.2 mM and 211.1 ± 35.7 mM, respectively, both of which were significantly higher than that in the well-known industrial strain of Corynebacterium (C.) glutamicum. Additionally, citrulline production was dependent on oxygen supplementation and increased twofold when grown aerobically. Whole genome sequencing showed that the MSC-3G genome possesses the arginine deiminase (ADI) gene cluster arcABD1C1C2TD2. The results of the ADI pathway enzyme activities of MSC-3G showed a significant increase in arginine deiminase activity, while ornithine carbamoyl transferase activity was decreased, which in turn indicates the high citrulline-accumulation ability of MSC-3G when cultivated in pineapple juice.

The arginine deaminase system plays distinct roles in Borrelia burgdorferi and Borrelia hermsii

Borrelia species are amino acid auxotrophs that utilize di- and tri- peptides obtained through their oligopeptide transport system to supply amino acids for replicative growth during their enzootic cycles. However, Borrelia species from both the Lyme disease (LD) and relapsing fever (RF) groups harbor an amino acid transport and catabolism system, the Arginine Deiminase System (ADI), that could potentially augment intracellular L-arginine required for growth. RF spirochetes contain a “complete”, four gene ADI (arcA, B, D, and C) while LD spirochetes harbor arcA, B, and sometimes D but lack arcC (encoding carbamate kinase). In this study, we evaluated the role of the ADI system in bacterial survival and virulence and discovered important differences in RF and LD ADIs. Both in vitro and in a murine model of infection, B. hermsii cells significantly reduced extracellular L-arginine levels and that reduction was dependent on arginine deiminase expression. Conversely, B. burgdorferi did not reduce the concentration of L-arginine during in vitro growth experiments nor during infection of the mammalian host, suggesting a fundamental difference in the ability to directly utilize L-arginine compared to B. hermsii. Further experiments using a panel of mutants generated in both B. burgdorferi and B. hermsii, identified important differences in growth characteristics and ADI transcription and protein expression. We also found that the ADI system plays a key role in blood and spleen colonization in RF spirochetes. In this study we have identified divergent metabolic strategies in two closely related human pathogens, that ultimately impacts the host-pathogen interface during infection.

Reports of tick-borne diseases have been steadily increasing in the US and the number of Lyme disease cases caused by B. burgdorferi have tripled since the late 1990’s. Although less common, cases of tick-borne relapsing fever, caused by B. hermsii and B. turicatae in the US, have increased as well. While transmitted by different ticks and maintained in unique enzootic cycles, the closely related spirochetes B. burgdorferi and B. hermsii share numerous genetic features including a truncated and streamlined capacity for metabolic activity. In this study we combine genetic and biochemical assays to define the role of the ADI in the infective cycles of B. burgdorferi and B. hermsii. When we compared B. burgdorferi and B. hermsii, we identified important differences in their respective ADI’s including operon arrangement, sensitivity to L-arginine and L-ornithine levels, as well as gene and protein expression. In addition, we show that arginine deiminase is required to reduce host L-arginine levels during murine infection with B. hermsii. This study provides new insights into the metabolic activities of two medically relevant spirochetes and highlights the dynamic nature of host-pathogen interactions.

In silico, in vitro and in vivo safety evaluation of Limosilactobacillus reuteri strains ATCC PTA-126787 & ATCC PTA-126788 for potential probiotic applications

The last two decades have witnessed a tremendous growth in probiotics and in the numbers of publications on their potential health benefits. Owing to their distinguishing beneficial effects and long history of safe use, species belonging to the Lactobacillus genus are among the most widely used probiotic species in human food and dietary supplements and are finding increased use in animal feed. Here, we isolated, identified, and evaluated the safety of two novel Limosilactobacillus reuteri (L. reuteri) isolates, ATCC PTA-126787 & ATCC PTA-126788. More specifically, we sequenced the genomes of these two L. reuteri strains using the PacBio sequencing platform. Using a combination of biochemical and genetic methods, we identified the two strains as belonging to L. reuteri species. Detailed in silico analyses showed that the two strains do not encode for any known genetic sequences of concern for human or animal health. In vitro assays confirmed that the strains are susceptible to clinically relevant antibiotics and do not produce potentially harmful by-products such as biogenic amines. In vitro bile and acid tolerance studies demonstrated that the two strains have similar survival profiles as the commercial L. reuteri probiotic strain DSM 17938. Most importantly, daily administration of the two probiotic strains to broiler chickens in drinking water for 26 days did not induce any adverse effect, clinical disease, or histopathological lesions, supporting the safety of the strains in an in vivo avian model. All together, these data provide in silico, in vitro and in vivo evidence of the safety of the two novel candidates for potential probiotic applications in humans as well as animals.

Citrulline Accumulation Mechanism of Pediococcus acidilactici and Weissella confusa in Soy Sauce and the Effects of Phenolic Compound on Citrulline Accumulation

Citrulline is one of the major precursors of ethyl carbamate in soy sauce, and the accumulation of citrulline is attributed to the metabolism of arginine by bacteria with the arginine deiminase (ADI) pathway. However, key strains and factors affecting citrulline accumulation are not yet clear. In this study, two key strains of Pediococcus acidilactici and Weissella confusa were isolated from soy sauce moromi, and the regularity of citrulline formation was studied. Results showed that the conversion rates from arginine to citrulline (A/C rate) and the citrulline accumulation ability of W. confusa and P. acidilactici significantly increased in the presence of different concentrations of NaCl, indicating that salt stress was the main factor for citrulline accumulation. The inconsistent expression of arc genes by salt stress was the reason for citrulline accumulation for P. acidilactici, but for W. confusa, it may be due to the influence of arginine/citrulline on the transportation system: the intracellular citrulline could neither transport to extracellular space nor convert into ornithine. Environmental factors greatly influenced citrulline accumulation of the two key bacteria; A/C rate and citrulline formation in both strains decreased at low temperature (15°C) under high salt stress, but opposite effects were observed for the two key strains under anaerobic light condition. Moreover, quercetin and gallic acid significantly decreased the A/C rate and citrulline accumulation ability of the two key strains. The optimal quercetin and gallic acid as suggested by simulation experiment were 100 and 10 mg/l, respectively, and the lowest A/C rate of 28.4% and citrulline level of 1326.7 mg/l were achieved in the simulation system. This study explored the main factors for citrulline formation by the two key strains and proposed a targeted way to control citrulline in soy sauce.

Sourdough production: fermentation strategies, microbial ecology, and use of non-flour ingredients

Sourdough production is an ancient method to ferment flour from cereals for the manufacturing of baked goods. This review deals with the state-of-the-art of current fermentation strategies for sourdough production and the microbial ecology of mature sourdoughs, with a particular focus on the use of non-flour ingredients. Flour fermentation processes for sourdough production are typically carried out by heterogeneous communities of lactic acid bacteria and yeasts. Acetic acid bacteria may also occur, although their presence and role in sourdough production can be criticized. Based on the inoculum used, sourdough productions can be distinguished in fermentation processes using backslopping procedures, originating from a spontaneously fermented flour-water mixture (Type 1), starter culture-initiated fermentation processes (Type 2), and starter culture-initiated fermentation processes that are followed by backslopping (Type 3). In traditional recipes for the initiation and/or propagation of Type 1 sourdough productions, non-flour ingredients are often added to the flour-water mixture. These ingredients may be the source of an additional microbial inoculum and/or serve as (co-)substrates for fermentation. An example of the former is the addition of yoghurt; an example of the latter is the use of fruit juices. The survival of microorganisms transferred from the ingredients to the fermenting flour-water mixture depends on the competitiveness toward particular strains of the microbial species present under the harsh conditions of the sourdough ecosystem. Their survival and growth is also determined by the presence of the appropriate substrates, whether or not carried over by the ingredients added.

Metagenome-Assembled Genomes Contribute to Unraveling of the Microbiome of Cocoa Fermentation

Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of operational taxonomic units. However, it is also important to determine metagenome-assembled genomes (MAGs), which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five data sets: one from Ghana and four from Brazil. In addition, in silico approaches were used to describe putative phenotypes and the metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) for fungi, Yamadazyma tenuis (n = 1); (ii) lactic acid bacteria, Limosilactobacillus fermentum (n = 5), Liquorilactobacillus cacaonum (n = 1), Liquorilactobacillus nagelli (n = 1), Leuconostoc pseudomesenteroides (n = 1), and Lactiplantibacillus plantarum subsp. plantarum (n = 1); (iii) acetic acid bacteria, Acetobacter senegalensis (n = 2) and Kozakia baliensis (n = 1); and (iv) Bacillus subtilis (n = 1), Brevundimonas sp. (n = 2), and Pseudomonas sp. (n = 1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some that, to our knowledge, were not previously detected in this environment (Liquorilactobacillus vini, Komagataeibacter saccharivorans, and Komagataeibacter maltaceti) and others previously described (Fructobacillus pseudoficulneus and Acetobacter pasteurianus). Taken together, the MAGs were useful for providing an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways. IMPORTANCE The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds in a microbial succession that depends on yeasts, lactic acid bacteria, and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely known, and yet it advanced from culture-based studies to the advent of next-generation DNA sequencing, with the generation of a myriad of data that need bioinformatic approaches to be properly analyzed. Although the majority of metagenomic studies have been based on short reads (operational taxonomic units), it is also important to analyze entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose; here, MAGs from cocoa fermentation microbiomes are described, and the possible implications of their phenotypic and metabolic potentials are discussed.

Diversity and dynamics of sourdough lactic acid bacteriota created by a slow food fermentation system

Sourdough is a naturally fermented dough that is used worldwide to produce a variety of baked foods. Various lactic acid bacteria (LAB), which can determine the quality of sourdough baked foods by producing metabolites, have been found in the sourdough ecosystem. However, spontaneous fermentation of sourdough leads to unpredictable growth of various micro-organisms, which result in unstable product quality. From an ecological perspective, many researchers have recently studied sourdough LAB diversity, particularly the elucidation of LAB community interactions and the dynamic mechanisms during the fermentation process, in response to requests for the control and design of a desired sourdough microbial community. This article reviews recent advances in the study of sourdough LAB diversity and its dynamics in association with unique characteristics of the fermentation system; it also discusses future perspectives for better understanding of the complex sourdough microbial ecosystem, which can be attained efficiently by both in vitro and in situ experimental approaches.

Sensory profile, functional properties and molecular weight distribution of fermented pea protein isolate

Pea protein isolate (PPI, from Pisum sativum L.) was fermented with six different lactic acid bacteria strains for 24 ​h and 48 ​h. The fermented samples were analyzed regarding their retronasal aroma and taste, their protein solubility, emulsifying and foaming capacity. Changes in the molecular weight distribution were analyzed to monitor potential effects of fermentation on the main allergenic protein fractions of PPI. After 24-h fermentation, PPI's characteristic aroma attributes and bitter taste decreased for all fermented PPI. However, after 48-h fermentation, cheesy aroma, and acid and salty tastes were increased. The PPI fermented with L. plantarum showed the most neutral taste and the panel's highest preference; instead, fermentation with L. fermentum led to a fecal aroma and was the least preferred. The protein solubility and emulsifying capacity decreased after PPI fermentation, while foaming capacity remained constant in comparison to the untreated PPI. The electrophoretic results showed a reduction in the intensity of the allergenic protein fractions; however, these changes might be attributed to the reduced protein solubility rather than to a high proteolytic effect of the strains. Fermentation of PPI for 24 ​h and 48 ​h might not be a suitable method for the production of highly functional pea proteins. Further modification methods have to be investigated in the future.

Characterization of the two nonidentical ArgR regulators of Tetragenococcus halophilus and their regulatory effects on arginine metabolism

The halophilic lactic acid bacterium Tetragenococcus halophilus has been widely used in high-salinity fermentation processes of food. Previous studies have indicated that the catabolism of arginine may contribute to the osmotic stress adaptation of T. halophilus. Unusually, in the chromosome of T. halophilus, preceding the arginine deiminase (ADI) operon, locate two co-transcribed genes, both encoding an ArgR regulator; similar structure was rarely found and the roles of the regulators have not been demonstrated. In the current study, regulatory roles of these two nonidentical ArgR regulators on the arginine metabolism of T. halophilus were investigated. The results show that these two regulators play different roles in arginine metabolism, ArgR1 acts as a negative regulator of the ADI pathway by binding to the promoter sequences and repressing the transcription of genes, and the addition of arginine or hyper-osmotic stress conditions can abolish the ArgR1 repression, whereas ArgR2 negatively regulates the genes involved in arginine biosynthesis. Our study found that despite the commonly known roles of the ArgR regulators as the activator of arginine catabolism and the repressor of arginine biosynthesis, which are found in most studied bacteria possessed one ArgR regulator, the two nonidentical ArgR regulators of T. halophilus both act as repressors, and the repression by which is regulated when sensing changes of environments. By revealing the regulation of arginine metabolism, the current study provides molecular insights and potential tools for future applications of halophiles in biotechnology. KEY POINTS: • The expression of the ADI pathway of T. halophilus is regulated by carbon sources and osmotic stress. • The arginine metabolism process of T. halophilus is fine-tuned by the two ArgR regulators. • The ADI pathway may contribute to the osmotic stress adaptation by generating more energy and accumulating citrulline which acts as compatible solute.

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.

Complete Genome Sequence of Lactobacillus plantarum Strain JDARSH, Isolated from Sheep Milk

Lactobacillus plantarum strain JDARSH, a potential probiotic with a wide range of functions, was isolated from sheep milk. Here, we report the whole-genome sequence of this bacterium. The draft genome yielded a 3.20-Mb genome and 2,980 protein-coding sequences.

Lactobacillus plantarum strain JDARSH, a potential probiotic with a wide range of functions, was isolated from sheep milk. Here, we report the whole-genome sequence of this bacterium. The draft genome yielded a 3.20-Mb genome and 2,980 protein-coding sequences.

Review: Adaptation of Beneficial Propionibacteria, Lactobacilli, and Bifidobacteria Improves Tolerance Toward Technological and Digestive Stresses

This review deals with beneficial bacteria, with a focus on lactobacilli, propionibacteria, and bifidobacteria. As being recognized as beneficial bacteria, they are consumed as probiotics in various food products. Some may also be used as starters in food fermentation. In either case, these bacteria may be exposed to various environmental stresses during industrial production steps, including drying and storage, and during the digestion process. In accordance with their adaptation to harsh environmental conditions, they possess adaptation mechanisms, which can be induced by pretreatments. Adaptive mechanisms include accumulation of compatible solutes and of energy storage compounds, which can be largely modulated by the culture conditions. They also include the regulation of energy production pathways, as well as the modulation of the cell envelop, i.e., membrane, cell wall, surface layers, and exopolysaccharides. They finally lead to the overexpression of molecular chaperones and of stress-responsive proteases. Triggering these adaptive mechanisms can improve the resistance of beneficial bacteria toward technological and digestive stresses. This opens new perspectives for the improvement of industrial processes efficiency with regard to the survival of beneficial bacteria. However, this bibliographical survey evidenced that adaptive responses are strain-dependent, so that growth and adaptation should be optimized case-by-case.

Genomic and metabolic features of Tetragenococcus halophilus as revealed by pan-genome and transcriptome analyses

The genomic and metabolic diversity and features of Tetragenococcus halophilus, a moderately halophilic lactic acid bacterium, were investigated by pan-genome, transcriptome, and metabolite analyses. Phylogenetic analyses based on the 16S rRNA gene and genome sequences of 15 T. halophilus strains revealed their phylogenetic distinctness from other Tetragenococcus species. Pan-genome analysis of the T. halophilus strains showed that their carbohydrate metabolic capabilities were diverse and strain dependent. Aside from one histidine decarboxylase gene in one strain, no decarboxylase gene associated with biogenic amine production was identified from the genomes. However, T. halophilus DSM 20339^T produced tyramine without a biogenic amine-producing decarboxylase gene, suggesting the presence of an unidentified tyramine-producing gene. Our reconstruction of the metabolic pathways of these strains showed that T. halophilus harbors a facultative lactic acid fermentation pathway to produce l-lactate, ethanol, acetate, and CO₂ from various carbohydrates. The transcriptomic analysis of strain DSM 20339^T suggested that T. halophilus may produce more acetate via the heterolactic pathway (including d-ribose metabolism) at high salt conditions. Although genes associated with the metabolism of glycine betaine, proline, glutamate, glutamine, choline, and citrulline were identified from the T. halophilus genomes, the transcriptome and metabolite analyses suggested that glycine betaine was the main compatible solute responding to high salt concentration and that citrulline may play an important role in the coping mechanism against high salinity-induced osmotic stresses. Our results will provide a better understanding of the genome and metabolic features of T. halophilus, which has implications for the food fermentation industry.

Arginine and Citrulline Catabolic Pathways Encoded by the arc Gene Cluster of Lactobacillus brevis ATCC 367

High concentrations of l-arginine or l-citrulline in the growth medium provided the wine bacterium Lactobacillus brevis with a significant growth advantage. The arginine deiminase pathway (ADI) arc gene cluster of Lactobacillus brevis contains three genes-arcD, arcE1, and arcE2-encoding putative l-arginine/l-ornithine exchangers. Uptake experiments with Lactococcus lactis cells expressing the genes showed that all three transported l-ornithine with affinities in the micromolar range. Similarly, ArcD and ArcE2 transported l-arginine, while ArcE1 transported l-citrulline, an intermediate of the ADI pathway. Chase experiments showed very efficient exchange of l-arginine and l-ornithine by ArcD and ArcE2 and of l-citrulline and l-ornithine by ArcE1. Low affinities (millimolar range) combined with low translocation rates were found for ArcD and ArcE2 with l-citrulline and for ArcE1 with l-arginine. Resting cells of Lactobacillus brevis grown in the presence of l-arginine and l-citrulline rapidly consumed l-arginine and l-citrulline, respectively, while producing ammonia and l-ornithine. About 10% of l-arginine degraded was excreted by the cells as l-citrulline. Degradation of l-arginine and l-citrulline was not subject to carbon catabolite repression by glucose in the medium. At a high medium pH, l-citrulline in the medium was required for induction of the l-citrulline degradation pathway. Pathways are proposed for the catabolic breakdown of l-arginine and l-citrulline that merge at the level of ornithine transcarbamylase in the ADI pathway. l-Arginine uptake is catalyzed by ArcD and/or ArcE2, l-citrulline by ArcE1. l-Citrulline excretion during l-arginine breakdown is proposed to be catalyzed by ArcD and/or ArcE2 through l-arginine/l-citrulline exchange.IMPORTANCELactobacillus brevis, a bacterium isolated from wine, as well as other food environments, expresses a catabolic pathway for the breakdown of l-citrulline in the medium that consists of the l-citrulline/l-ornithine exchanger ArcE1 and part of the catabolic arginine deiminase (ADI) pathway enzymes. The proposed pathways for l-arginine and l-citrulline breakdown provide a mechanism for l-citrulline accumulation in fermented food products that is the precursor of the carcinogen ethyl carbamate.

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.

Profiles of Streptococcus thermophilus MN-ZLW-002 nutrient requirements in controlled pH batch fermentations

This study aimed to evaluate the profiles of Streptococcus thermophilus nutrient requirements to guide the design of media for high cell density culturing. The growth kinetics, physiological state, and nutrient requirement profiles of S. thermophilus were analyzed in chemically defined media. The results showed that the intracellular ATP concentration, H⁺‐ATPase activity, NADH/NAD⁺, and NH₃ concentrations varied with intracellular pH. The nutrient components with the highest amounts required were Leu and Asp; ascorbic acid and p‐amino benzoic acid; K⁺ and PO₄³⁻; and guanine and uracil. The nutrient components with the largest required ratios were Arg, His, and Met; folic acid, cyanocobalamine, biotin, and nicotinic acid; Ca²⁺ and Mg²⁺; and guanine and uracil. In this study, different nutrient components were primarily used at different phase. Trp, Tyr, calcium pantothenate, thiamine, guanine, and Mg²⁺ were mainly used from late‐lag to midexponential phase. Met, Pro, Phe, Ala, Gly, nicotinic acid, and riboflavin were mainly used from midexponential to late‐exponential phase. The highest bioavailabilities of nutrient components were also found at diverse phase. Met, Leu, Ile, Asn, Glu, Lys, Pro, Gly, riboflavin, nicotinic acid, adenine, uracil, inosine, and Ca²⁺ had the highest bioavailability from late‐lag to midexponential phase. Lactose, Glu, Asp, His, Trp, Cys, Val, Arg, Phe, Ala, Ser, Thr, Tyr, folate and cobalamin, calcium pantothenate, ascorbic acid, thiamine, biotin, p‐amino benzoic acid, vitamin B₆, K⁺, Mg²⁺, guanine, xanthine, and PO₄³⁻ had the highest bioavailability from midexponential to late‐exponential phase. This study elucidated the nutrient requirement profiles with culture time and biomass at various average growth rates during the growth of S. thermophilus. The present results will help to formulate complex media for high cell density cultivation and provide the theoretical basis for S. thermophilus feeding strategies.

Accumulation of Citrulline by Microbial Arginine Metabolism during Alcoholic Fermentation of Soy Sauce

Citrulline, the major precursor of ethyl carbamate in soy sauce, is an intermediate catabolite of arginine produced by bacteria present in soy sauce moromi mash. Pediococcus acidilactici is responsible for the formation of citrulline during the lactic acid fermentation process of soy sauce. However, citrulline accumulation during the alcoholic fermentation process and the corresponding bacteria involved have not been identified. Salt-tolerant, arginine-utilizing bacteria were isolated from moromi mash during the alcoholic fermentation process. Under normal cultivation conditions, arginine utilization by these strains did not contribute to citrulline accumulation. However, the conversion of arginine to citrulline by these bacteria increased when cultivated during the alcoholic fermentation process. Additionally, the ethanol-enhanced solubility of free fatty acids in moromi mash stimulated the accumulation of citrulline. Staphylococcus exhibited the highest capability in the conversion of arginine to citrulline.

Global Analysis of Mannitol 2-Dehydrogenase in Lactobacillus reuteri CRL 1101 during Mannitol Production through Enzymatic, Genetic and Proteomic Approaches

Several plants, fungi, algae, and certain bacteria produce mannitol, a polyol derived from fructose. Mannitol has multiple industrial applications in the food, pharmaceutical, and medical industries, being mainly used as a non-metabolizable sweetener in foods. Many heterofermentative lactic acid bacteria synthesize mannitol when an alternative electron acceptor such as fructose is present in the medium. In previous work, we reported the ability of Lactobacillus reuteri CRL 1101 to efficiently produce mannitol from sugarcane molasses as carbon source at constant pH of 5.0; the activity of the enzyme mannitol 2-dehydrogenase (MDH) responsible for the fructose conversion into mannitol being highest during the log cell growth phase. Here, a detailed assessment of the MDH activity and relative expression of the mdh gene during the growth of L. reuteri CRL 1101 in the presence of fructose is presented. It was observed that MDH was markedly induced by the presence of fructose. A direct correlation between the maximum MDH enzyme activity and a high level of mdh transcript expression during the log-phase of cells grown in a fructose-containing chemically defined medium was detected. Furthermore, two proteomic approaches (2DE and shotgun proteomics) applied in this study confirmed the inducible expression of MDH in L. reuteri. A global study of the effect of fructose on activity, mdh gene, and protein expressions of MDH in L. reuteri is thus for the first time presented. This work represents a deep insight into the polyol formation by a Lactobacillus strain with biotechnological potential in the nutraceutics and pharmaceutical areas.

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.

Influence of arginine on the growth, arginine metabolism and amino acid consumption profiles of Streptococcus thermophilus T1C2 in controlled pH batch fermentations

AIMS

The aim of this study was to elucidate the effect of arginine on the growth, arginine metabolism and amino acid consumption profiles of Streptococcus thermophilus T1C2.

METHODS AND RESULTS

The growth kinetics, intracellular pH, extracellular osmotic pressure, expression of key genes in the arginine metabolism pathway and amino acid consumption profiles were analysed in chemically defined medium with different initial arginine concentrations. The results showed that arginine stimulated the growth of Strep. thermophilus T1C2 under low intracellular pH and high extracellular osmotic pressure. The expression of key genes in the arginine degradation pathway indicated that arginine relieved the drop in the intracellular pH by consuming protons and generating NH3 . Additionally, the results showed that arginine degradation did not occur via the arginine deiminase pathway but through the arginine decarboxylase-urease pathway. Furthermore, the utilization efficiency of amino acids was improved in the presence of arginine.

CONCLUSIONS

Arginine improved the growth of Strep. thermophilus due to protecting Strep. thermophilus against intracellular acid stress, which was revealed at the transcriptional level of key genes. This study showed that the acid resistance of Strep. thermophilus was achieved through the arginine decarboxylase-urease pathway.

SIGNIFICANCE AND IMPACT OF THE STUDY

The arginine-stimulated growth of Strep. thermophilus improved the utilization efficiency of amino acids and reduced nitrogen waste, which could be useful for the optimization of cultivation media.

Lysozyme affects the microbial catabolism of free arginine in raw-milk hard cheeses

Lysozyme (LZ) is used in several cheese varieties to prevent late blowing which results from fermentation of lactate by Clostridium tyrobutyricum. Side effects of LZ on lactic acid bacteria population and free amino acid pattern were studied in 16 raw-milk hard cheeses produced in eight parallel cheese makings conducted at four different dairies using the same milk with (LZ+) or without (LZ-) addition of LZ. The LZ-cheeses were characterized by higher numbers of cultivable microbial population and lower amount of DNA arising from lysed bacterial cells with respect to LZ + cheeses. At both 9 and 16 months of ripening, Lactobacillus delbrueckii and Lactobacillus fermentum proved to be the species mostly affected by LZ. The total content of free amino acids indicated the proteolysis extent to be characteristic of the dairy, regardless to the presence of LZ. In contrast, the relative patterns showed the microbial degradation of arginine to be promoted in LZ + cheeses. The data demonstrated that the arginine-deiminase pathway was only partially adopted since citrulline represented the main product and only trace levels of ornithine were found. Differences in arginine degradation were considered for starter and non-starter lactic acid bacteria, at different cheese ripening stages.

Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract

Rodent-derived strains of Lactobacillus reuteri densely colonize the forestomach of mice and possess several genes whose predicted functions constitute adaptations towards an acidic environment. The objective of this study was to systematically determine which genes of L. reuteri 100-23 contribute to tolerance towards host gastric acid secretion. Genes predicted to be involved in acid resistance were inactivated, and their contribution to survival under acidic conditions was confirmed in model gastric juice. Fitness of five mutants that showed impaired in vitro acid resistance were then compared through competition experiments in ex-germ-free mice that were either treated with omeprazole, a proton-pump inhibitor that suppresses acid secretion in the stomach, or left untreated. This analysis revealed that the urease cluster was the predominant factor in mediating resistance to gastric acid production. Population levels of the mutant, which were substantially decreased in untreated mice, were almost completely restored through omeprazole, demonstrating that urease production in L. reuteri is mainly devoted to overcome gastric acid. The findings provide novel information on the mechanisms by which L. reuteri colonizes its gastric niche and demonstrate that in silico gene predictions and in vitro tests have limitations for predicting the ecological functions of colonization factors in bacterial symbionts.

Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate

Lactococcus lactis is essential for most cheese making, and this mesophilic bacterium has its growth optimum around 30 °C. We have, through adaptive evolution, isolated a mutant TM29 that grows well up to 39 °C, and continuous growth at 40 °C is possible if pre-incubated at a slightly lower temperature. At the maximal permissive temperature for the wild-type, 38 °C, TM29 grows 33% faster and has a 12% higher specific lactate production rate than its parent MG1363, which results in fast lactate accumulation. Genome sequencing was used to reveal the mutations accumulated, most of which were shown to affect thermal tolerance. Of the mutations with more pronounced effects, two affected expression of single proteins (chaperone; riboflavin transporter), two had pleiotropic effects (RNA polymerase) which changed the gene expression profile, and one resulted in a change in the coding sequence of CDP-diglyceride synthase. A large deletion containing 10 genes was also found to affect thermal tolerance significantly. With this study we demonstrate a simple approach to obtain non-GMO derivatives of the important L. lactis that possess properties desirable by the industry, e.g. thermal robustness and increased rate of acidification. The mutations we have identified provide a genetic basis for further investigation of thermal tolerance.

The arginine deiminase pathway of koji bacteria is involved in ethyl carbamate precursor production in soy sauce

Ethyl carbamate (EC) is a group 2A carcinogen generated from a few precursors in many fermented foods and alcoholic beverages. Citrulline, urea, carbamoyl phosphate, and ethanol are common precursors detected in fermented foods. In this study, citrulline was proved to be the main EC precursor in soy sauce, which was found to be accumulated in moromi mash period and correlated with the utilization of arginine by koji bacteria. Six koji isolates belonging to three genera were identified to be able to accumulate citrulline via the arginine deiminase (ADI) pathway. Among these strains, only Pediococcus acidilactici retained high activities in synthesis and accumulation of citrulline in the presence of high concentration of sodium chloride. These results suggested that P. acidilactici is responsible for the accumulation of citrulline, one of the EC precursors, in the process of soy sauce fermentation.

Listeria monocytogenes ArcA contributes to acid tolerance

The foodborne pathogen Listeria monocytogenes is able to colonize the human and animal intestinal tracts and subsequently crosses the intestinal barrier, causing systemic infection. For successful establishment of infection, L. monocytogenes must survive and adapt to the low pH environment of the stomach. Gene sequence analysis indicates that lmo0043, an orthologue of arcA, encodes a protein containing conserved motifs and critical active amino acids characteristic of arginine deiminase that mediates an arginine deimination reaction. We attempted to characterize the role of ArcA in acid tolerance in vitro and in mice models. Transcription of arcA was significantly increased in L. monocytogenes culture subjected to acid stress at pH 4.8, as compared with that at pH 7.0. Deletion of arcA impaired growth of L. monocytogenes under mild acidic conditions at pH 5.5, and reduced its survival in synthetic human gastric fluid at pH 2.5 and in the murine stomach. Bacterial load in the spleen of mice intraperitoneally inoculated with an arcA deletion mutant was significantly lower than that of the wild-type strain. These phenotypic changes were recoverable by genetic complementation. Thus, we conclude that L. monocytogenes arcA not only mediates acid tolerance in vitro but also participates in gastric survival and virulence in mice.

Suppression subtractive hybridization reveals transcript profiling of Chlorella under heterotrophy to photoautotrophy transition

BACKGROUND

Microalgae have been extensively investigated and exploited because of their competitive nutritive bioproducts and biofuel production ability. Chlorella are green algae that can grow well heterotrophically and photoautotrophically. Previous studies proved that shifting from heterotrophy to photoautotrophy in light-induced environments causes photooxidative damage as well as distinct physiologic features that lead to dynamic changes in Chlorella intracellular components, which have great potential in algal health food and biofuel production. However, the molecular mechanisms underlying the trophic transition remain unclear.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, suppression subtractive hybridization strategy was employed to screen and characterize genes that are differentially expressed in response to the light-induced shift from heterotrophy to photoautotrophy. Expressed sequence tags (ESTs) were obtained from 770 and 803 randomly selected clones among the forward and reverse libraries, respectively. Sequence analysis identified 544 unique genes in the two libraries. The functional annotation of the assembled unigenes demonstrated that 164 (63.1%) from the forward library and 62 (21.8%) from the reverse showed significant similarities with the sequences in the NCBI non-redundant database. The time-course expression patterns of 38 selected differentially expressed genes further confirmed their responsiveness to a diverse trophic status. The majority of the genes enriched in the subtracted libraries were associated with energy metabolism, amino acid metabolism, protein synthesis, carbohydrate metabolism, and stress defense.

CONCLUSIONS/SIGNIFICANCE

The data presented here offer the first insights into the molecular foundation underlying the diverse microalgal trophic niche. In addition, the results can be used as a reference for unraveling candidate genes associated with the transition of Chlorella from heterotrophy to photoautotrophy, which holds great potential for further improving its lipid and nutrient production.