Long-term adaptive evolution of Leuconostoc mesenteroides for enhancement of lactic acid tolerance and production

Unraveling the Genetic Adaptations in Cell Surface Composition and Transporters of Lactiplantibacillus plantarum for Enhanced Acid Tolerance

This study employed adaptive laboratory evolution to improve the acid tolerance of Lactiplantibacillus plantarum, a vital strain in food fermentation and a potential probiotic. Phenotype and genomic analyses identified the overexpression of stress response proteins, ATP synthases, and transporters as pivotal in conferring acid tolerance to the evolved strains. These adaptations led to a shorter lag phase, improved survival rates, and higher intracellular pH values compared to the wild-type strain under acid stress conditions. Additionally, the evolved strains showed an increased expression of genes in the fatty acid synthesis pathway, resulting in a higher production of unsaturated fatty acids. The changes in cell membrane composition possibly prevented H+ influx, while mutant genes related to cell surface structure contributed to observed elongated cells and thicker cell surface. These alterations in cell wall and membrane composition, along with improved transporter efficiency, were key factors contributing to the enhanced acid tolerance in the evolved strains.

Heterotypic stress-induced adaptive evolution enhances freeze-drying tolerance and storage stability of Leuconostoc mesenteroides WiKim33

Lactic acid bacteria (LAB) are currently being investigated for their potential use as probiotics and starter cultures. Researchers have developed powdering processes for the commercialization of LAB. Previous studies have focused on identifying innovative cryoprotective agents and freeze-drying (FD) techniques to enhance the stability of LAB. In this study, adaptive laboratory evolution (ALE) was employed to develop a strain with high FD tolerance and enhanced storage stability. Leuconostoc mesenteroids WiKim33 was subjected to heterotypic shock (heat and osmosis shock) to induce the desired phenotype and genotype. An FD-tolerant enhanced Leu. mesenteroides WiKim33 strain (ALE50) was obtained, which harbored a modified fatty acid composition and cell envelope characteristics. Specifically, ALE50 showed a lower unsaturated fatty acid (UFA)/saturated fatty acid (SFA) ratio and a higher cyclic fatty acid (CFA) composition. Moreover, the exopolysaccharide (EPS) thickness increased significantly by 331% compared to that of the wild type (WT). FD tolerance, which was evaluated using viability testing after FD, was enhanced by 33.4%. Overall, we demonstrated the feasibility of ALE to achieve desirable characteristics and provided insights into the mechanisms underlying increased FD tolerance.

Phenotype and metabolism alterations in PCB-degrading Rhodococcus biphenylivorans TG9T under acid stress

Environmental acidification impairs microorganism diversity and their functions on substance transformation. Rhodococcus is a ubiquitously distributed genus for contaminant detoxification in the environment, and it can also adapt a certain range of pH. This work interpreted the acid responses from both phenotype and metabolism in strain Rhodococcus biphenylivorans TG9^T (TG9) induced at pH 3. The phenotype alterations were described with the number of culturable and viable cells, intracellular ATP concentrations, cell shape and entocyte, degradation efficiency of polychlorinated biphenyl (PCB) 31 and biphenyl. The number of culturable cells maintained rather stable within the first 10 days, even though the other phenotypes had noticeable alterations, indicating that TG9 possesses certain capacities to survive under acid stress. The metabolism responses were interpreted based on transcription analyses with four treatments including log phase (LP), acid-induced (PER), early recovery after removing acid (RE) and later recovery (REL). With the overview on the expression regulations among the 4 treatments, the RE sample presented more upregulated and less downregulated genes, suggesting that its metabolism was somehow more active after recovering from acid stress. In addition, the response mechanism was interpreted on 10 individual metabolism pathways mainly covering protein modification, antioxidation, antipermeability, H⁺ consumption, neutralization and extrusion. Furthermore, the transcription variations were verified with RT-qPCR on 8 genes with 24-hr, 48-hr and 72-hr acid treatment. Taken together, TG9 possesses comprehensive metabolism strategies defending against acid stress. Consequently, a model was built to provide an integrate insight to understand the acid resistance/tolerance metabolisms in microorganisms.

Metabolic changes of the acetogen Clostridium sp. AWRP through adaptation to acetate challenge

In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution (ALE) under the acetate challenge. Acetate-adapted strain 46 T-a displayed acetate tolerance to acetate up to 10 g L^-1 and increased ethanol production in small-scale cultures. The adapted strain showed a higher cell density than AWRP even without exogenous acetate supplementation. 46 T-a was shown to have reduced gas consumption rate and metabolite production. It was intriguing to note that 46 T-a, unlike AWRP, continued to consume H₂ at low CO₂ levels. Genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase (Hyt) crucial for autotrophic growth in CO₂ + H₂, in addition to one in the dnaK gene. Transcriptome analysis revealed that most genes involved in the CO₂-fixation Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated in 46 T-a. Several metabolic pathways involved in dissimilation of nucleosides and carbohydrates were significantly up-regulated in 46 T-a, indicating that 46 T-a evolved to utilize organic substrates rather than CO₂ + H₂. Further investigation into degeneration in carbon fixation of the acetate-adapted strain will provide practical implications for CO₂ + H₂ fermentation using acetogenic bacteria for long-term continuous fermentation.

Redefining methods for augmenting lactic acid bacteria robustness and phenyllactic acid biocatalysis: Integration valorizes simplicity

The production of phenyllactic acid (PLA) has been reported by several researchers, but so far, no mention has been made of augmented PLA production using an orchestrated assembly of simple techniques integrated to improve lactic acid bacteria (LAB) metabolism for the same. This review summarizes sequentially tailoring LAB growth and metabolism for augmented PLA catalysis through several strategies like monitoring LAB sustenance by choosing appropriate starter PLA-producing LAB strains isolated from natural environments, with desirably fastidious growth rates, properties like acidification, proteolysis, bacteriophage-resistance, aromatic/texturing-features, etc.; entrapping chosen LAB strains in novel cryogels and/or co-cultivating two/more LAB strains to improve their biotransformation potential and promote growth dependency/sustainability; adopting adaptive evolution methods designed to improve LAB strains under selection pressure inducing desired phenotypes tolerant to stress factors like heat, salt, acid, and solvent; monitoring physico-chemical LAB fermentation factors like temperature, pH, dissolved oxygen content, enzymes, and cofactors for PLA biosynthesis; and modulating purification/downstream processes to extract substantial PLA yields. This review paper serves as a comprehensive preliminary guide that can evoke a strategic experimental plan to produce industrial-scale PLA yields using simple techniques orchestrated together in the pursuit of conserving time, effort, and resources.

Direct conversion of cellulose to L-lactic acid by a novel thermophilic Caldicellulosiruptor strain

Background

Consolidated bioprocessing (CBP) of lignocellulosic biomass to l-lactic acid using thermophilic cellulolytic/hemicellulolytic bacteria provides a promising solution for efficient lignocellulose conversion without the need for additional cellulolytic/hemicellulolytic enzymes. Most studies on the mesophilic and thermophilic CBP of lignocellulose to lactic acid concentrate on cultivation of non-cellulolytic mesophilic and thermophilic bacteria at temperatures of 30–55 °C with external addition of cellulases/hemicellulases for saccharification of substrates.

Results

l-Lactic acid was generated by fermenting microcrystalline cellulose or lignocellulosic substrates with a novel thermophilic anaerobic bacterium Caldicellulosiruptor sp. DIB 104C without adding externally produced cellulolytic/hemicellulolytic enzymes. Selection of this novel bacterium strain for lactic acid production is described as well as the adaptive evolution towards increasing the l-lactic acid concentration from 6 to 70 g/l on microcrystalline cellulose. The evolved strains grown on microcrystalline cellulose show a maximum lactic acid production rate of 1.0 g/l*h and a lactic acid ratio in the total organic fermentation products of 96 wt%. The enantiomeric purity of the l-lactic acid generated is 99.4%. In addition, the lactic acid production by these strains on several other types of cellulose and lignocellulosic feedstocks is also reported.

Conclusions

The evolved strains originating from Caldicellulosiruptor sp. DIB 104C were capable of producing unexpectedly large amounts of l-lactic acid from microcrystalline cellulose in fermenters. These strains produce l-lactic acid also from lignocellulosic feedstocks and thus represent an ideal starting point for development of a highly integrated commercial l-lactic acid production process from such feedstocks.

Microbial cell factories for the production of three-carbon backbone organic acids from agro-industrial wastes

At present, mass production of basic and valuable commodities is dependent on linear petroleum-based industries, which ultimately makes the depletion of finite natural reserves and accumulation of non-biodegradable and hazardous wastes. Therefore, an ecofriendly and sustainable solution should be established for a circular economy where infinite resources, such as agro-industrial wastes, are fully utilized as substrates in the production of target value-added chemicals. Hereby, recent advances in metabolic engineering strategies and techniques used in the development of microbial cell factories for enhanced production of three-carbon platform chemicals such as lactic acid, propionic acid, and 3-hydroxypropionic acid are discussed. Further developments and future perspectives in the production of these organic acids from agro-industrial wastes from the dairy, sugar, and biodiesel industries are also highlighted to demonstrate the importance of waste-based biorefineries for organic acid production.

A comprehensive review on current status and future perspectives of microbial volatile fatty acids production as platform chemicals

Volatile fatty acids (VFA), the secondary metabolite of microbial fermentation, are used in a wide range of industries for production of commercially valuable chemicals. In this review, the fermentative production of VFAs by both pure as well mixed microbial cultures is highlighted along with the strategies for enhancing the VFA production through innovations in existing approaches. Role of conventionally applied tools for the optimization of operational parameters such as pH, temperature, retention time, organic loading rate, and headspace pressure has been discussed. Furthermore, a comparative assessment of above strategies on VFA production has been done with alternate developments such as co-fermentation, substrate pre-treatment, and in situ removal from fermented broth. The review also highlights the applications of different bioreactor geometries in the optimum production of VFAs and how metagenomic tools could provide a detailed insight into the microbial communities and their functional attributes that could be subjected to metabolic engineering for the efficient production of VFAs.

Acid stress responses of Lactobacillus amylovorus and Candida kefyr isolated from fermented sorghum gruel and their application in food fermentation

Exposure of Lactic Acid Bacteria (LAB) and yeasts to adverse fluctuations during fermentation causes stress, consequently, microbes develop adaptive responses. In this study, the physiological and proteomic responses of LAB and yeast to acid stress, and their application in food fermentation was investigated. The physiological and proteomic responses of Lactobacillus amylovorus LS07 and Candida kefyr YS12 to acid stress were measured using turbidimetry method, SDS-PAGE and LC-MS/MS respectively. The technique previously reported by Association of Official Analytical Chemists (AOAC) were employed for evaluation of the physiocochemical and organoleptic properties of the sorghum gruel fermented using the LAB and yeast in singly and combination as starter cultures and spontaneous fermentation as control. Growth of L. amylovorus LS07 was optimal at pH 1.0 and C. kefyr YSI2 at pH 4. An increased intensity of 30S ribosomal protein S2 (L. amylovorus LS07) and 6-phosphogluconate dehydrogenase (C. kefyr YS12) was noted at pH 1 and 4 respectively suggesting increased microbial metabolism thereby reducing stress encountered. Sorghum gruel produced with combined starters had the highest crude protein (10.94 %), Iron content (0.0085 %), organoleptic acceptability (7.29) significantly different from products produced with the single starters and control. The combined starter's (L. amylovorus LS07 and C. kefyr YSI2 as starter) adapted stress yielded foods with improved sensory properties, mineral and reduced anti-nutrient contents.

In vivo evolution of lactic acid hyper-tolerant Clostridium thermocellum

Lactic acid (LA) has several applications in the food, cosmetics and pharmaceutical industries, as well as in the production of biodegradable plastic polymers, namely polylactides. Industrial production of LA is essentially based on microbial fermentation. Recent reports have shown the potential of the cellulolytic bacterium Clostridium thermocellum for direct LA production from inexpensive lignocellulosic biomass. However, C. thermocellum is highly sensitive to acids and does not grow at pH < 6.0. Improvement of LA tolerance of this microorganism is pivotal for its application in cost-efficient production of LA. In the present study, the LA tolerance of C. thermocellum strains LL345 (wild-type fermentation profile) and LL1111 (high LA yield) was increased by adaptive laboratory evolution. At large inoculum size (10 %), the maximum tolerated LA concentration of strain LL1111 was more than doubled, from 15 g/L to 35 g/L, while subcultures evolved from LL345 showed 50-85 % faster growth in medium containing 45 g/L LA. Gene mutations (pyruvate phosphate dikinase, histidine protein kinase/phosphorylase) possibly affecting carbohydrate and/or phosphate metabolism have been detected in most LA-adapted populations. Although improvement of LA tolerance may sometimes also enable higher LA production in microorganisms, C. thermocellum LA-adapted cultures showed a yield of LA, and generally of other organic acids, similar to or lower than parental strains. Based on its improved LA tolerance and LA titer similar to its parent strain (LL1111), mixed adapted culture LL1630 showed the highest performing phenotype and could serve as a framework for improving LA production by further metabolic engineering.

Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose

Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.

Rapid Enabling of Gluconobacter oxydans Resistance to High D-Sorbitol Concentration and High Temperature by Microdroplet-Aided Adaptive Evolution

Gluconobacter oxydans is important in the conversion of D-sorbitol into l-sorbose, which is an essential intermediate for industrial-scale production of vitamin C. In a previous study, the strain G. oxydans WSH-004 could directly produce 2-keto-l-gulonic acid (2-KLG). However, its D-sorbitol tolerance was poor compared with that of other common industrial G. oxydans strains, which grew well in the presence of more than 200 g/L of D-sorbitol. This study aimed to use the microbial microdroplet culture (MMC) system for the adaptive evolution of G. oxydans WSH-004 so as to improve its tolerance to high substrate concentration and high temperature. A series of adaptively evolved strains, G. oxydans MMC1-MMC10, were obtained within 90 days. The results showed that the best strain MMC10 grew in a 300 g/L of D-sorbitol medium at 40°C. The comparative genomic analysis revealed that genetic changes related to increased tolerance were mainly in protein translation genes. Compared with the traditional adaptive evolution method, the application of microdroplet-aided adaptive evolution could improve the efficiency in terms of reducing time and simplifying the procedure for strain evolution. This research indicated that the microdroplet-aided adaptive evolution was an effective tool for improving the phenotypes with undemonstrated genotypes in a short time.

Clostridium cellulovorans Proteomic Responses to Butanol Stress

Combination of butanol-hyperproducing and hypertolerant phenotypes is essential for developing microbial strains suitable for industrial production of bio-butanol, one of the most promising liquid biofuels. Clostridium cellulovorans is among the microbial strains with the highest potential for direct production of n-butanol from lignocellulosic wastes, a process that would significantly reduce the cost of bio-butanol. However, butanol exhibits higher toxicity compared to ethanol and C. cellulovorans tolerance to this solvent is low. In the present investigation, comparative gel-free proteomics was used to study the response of C. cellulovorans to butanol challenge and understand the tolerance mechanisms activated in this condition. Sequential Window Acquisition of all Theoretical fragment ion spectra Mass Spectrometry (SWATH-MS) analysis allowed identification and quantification of differentially expressed soluble proteins. The study data are available via ProteomeXchange with the identifier PXD024183. The most important response concerned modulation of protein biosynthesis, folding and degradation. Coherent with previous studies on other bacteria, several heat shock proteins (HSPs), involved in protein quality control, were up-regulated such as the chaperones GroES (Cpn10), Hsp90, and DnaJ. Globally, our data indicate that protein biosynthesis is reduced, likely not to overload HSPs. Several additional metabolic adaptations were triggered by butanol exposure such as the up-regulation of V- and F-type ATPases (involved in ATP synthesis/generation of proton motive force), enzymes involved in amino acid (e.g., arginine, lysine, methionine, and branched chain amino acids) biosynthesis and proteins involved in cell envelope re-arrangement (e.g., the products of Clocel_4136, Clocel_4137, Clocel_4144, Clocel_4162 and Clocel_4352, involved in the biosynthesis of saturated fatty acids) and a redistribution of carbon flux through fermentative pathways (acetate and formate yields were increased and decreased, respectively). Based on these experimental findings, several potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in C. cellulovorans are suggested. This includes overexpression of HSPs (e.g., GroES, Hsp90, DnaJ, ClpC), RNA chaperone Hfq, V- and F-type ATPases and a number of genes whose function in C. cellulovorans is currently unknown.

New Insight into Bacterial Interaction with the Matrix of Plant-Based Fermented Foods

Microorganisms have been harnessed to process raw plants into fermented foods. The adaptation to a variety of plant environments has resulted in a nearly inseparable association between the bacterial species and the plant with a characteristic chemical profile. Lactic acid bacteria, which are known for their ability to adapt to nutrient-rich niches, have altered their genomes to dominate specific habitats through gene loss or gain. Molecular biology approaches provide a deep insight into the evolutionary process in many bacteria and their adaptation to colonize the plant matrix. Knowledge of the adaptive characteristics of microorganisms facilitates an efficient use thereof in fermentation to achieve desired final product properties. With their ability to acidify the environment and degrade plant compounds enzymatically, bacteria can modify the textural and organoleptic properties of the product and increase the bioavailability of plant matrix components. This article describes selected microorganisms and their competitive survival and adaptation in fermented fruit and vegetable environments. Beneficial changes in the plant matrix caused by microbial activity and their beneficial potential for human health are discussed as well.

Adaptive laboratory evolution principles and applications in industrial biotechnology

Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.

High-throughput amplicon sequencing to assess the impact of processing factors on the development of microbial communities during spontaneous meat fermentation

During spontaneous meat fermentation, diverse microbial communities develop over time. These communities consist mainly of lactic acid bacteria (LAB) and coagulase-negative staphylococci (CNS), of which the species composition is influenced by the fermentation temperature and the level of acidification. Recent development and application of amplicon-based high-throughput sequencing (HTS) methods have allowed to gain deeper insights into the microbial communities of fermented meats. The aim of the present study was to investigate the effect of different fermentation temperatures and acidification profiles on the CNS communities during spontaneous fermentation, using a previously developed amplicon-based HTS method targeting both the 16S rRNA and tuf genes. Spontaneous fermentations were performed with five different lots of meat to assess inter-lot variability. The process influence was investigated by fermenting the meat batters for seven days at different fermentation temperatures (23 °C, 30 °C, and 37 °C) and in the absence or presence of added glucose to simulate different acidification levels. Additionally, the results were compared with a starter culture-initiated fermentation process. The data revealed that the fermentation temperature was the most influential processing condition in shaping the microbial communities during spontaneous meat fermentation processes, whereas differences in pH were only responsible for minor shifts in the microbial profiles. Furthermore, the CNS communities showed a great level of variability, which depended on the initial microbial communities present and their competitiveness.

Lactic acid bacteria: little helpers for many human tasks

Lactic acid bacteria (LAB) are a group of highly specialised bacteria specifically adapted to a diverse range of habitats. They are found in the gut of humans and other animals, in many food fermentations, and on plants. Their natural specialisation in close relation to human activities make them particularly interesting from an industrial point of view. They are relevant not only for traditional food fermentations, but also as probiotics, potential therapeutics and cell factories for the production of many different products. Many new tools and methods are being developed to analyse and modify these microorganisms. This review shall give an overview highlighting some of the most striking characteristics of lactic acid bacteria and our approaches to harness their potential in many respects - from home made food to industrial chemical production, from probiotic activities to the most modern cancer treatments and vaccines.

Lactic Acid Bacteria in Wine: Technological Advances and Evaluation of Their Functional Role

Currently, the main role of Lactic Acid Bacteria (LAB) in wine is to conduct the malolactic fermentation (MLF). This process can increase wine aroma and mouthfeel, improve microbial stability and reduce the acidity of wine. A growing number of studies support the appreciation that LAB can also significantly, positively and negatively, contribute to the sensorial profile of wine through many different enzymatic pathways. This is achieved either through the synthesis of compounds such as diacetyl and esters or by liberating bound aroma compounds such as glycoside-bound primary aromas and volatile thiols which are odorless in their bound form. LAB can also liberate hydroxycinnamic acids from their tartaric esters and have the potential to break down anthocyanin glucosides, thus impacting wine color. LAB can also produce enzymes with the potential to help in the winemaking process and contribute to stabilizing the final product. For example, LAB exhibit peptidolytic and proteolytic activity that could break down the proteins causing wine haze, potentially reducing the need for bentonite addition. Other potential contributions include pectinolytic activity, which could aid juice clarification and the ability to break down acetaldehyde, even when bound to SO2, reducing the need for SO2 additions during winemaking. Considering all these findings, this review summarizes the novel enzymatic activities of LAB that positively or negatively affect the quality of wine. Inoculation strategies, LAB improvement strategies, their potential to be used as targeted additions, and technological advances involving their use in wine are highlighted along with suggestions for future research.

Improvement of lactic acid tolerance by cocktail δ-integration strategy and identification of the transcription factor PDR3 responsible for lactic acid tolerance in yeast Saccharomyces cerevisiae

Although, yeast Saccharomyces cerevisiae is expected to be used as a host for lactic acid production, improvement of yeast lactic acid tolerance is required for efficient non-neutralizing fermentation. In this study, we optimized the expression levels of various transcription factors to improve the lactic acid tolerance of yeast by a previously developed cocktail δ-integration strategy. By optimizing the expression levels of various transcription factors, the maximum D-lactic acid production and yield under non-neutralizing conditions were improved by 1.2. and 1.6 times, respectively. Furthermore, overexpression of PDR3, which is known as a transcription factor involved in multi-drug resistance, effectively improved lactic acid tolerance in yeast. In addition, we clarified for the first time that high expression of PDR3 contributes to the improvement of lactic acid tolerance. PDR3 is considered to be an excellent target gene for studies on yeast stress tolerance and further researches are desired in the future.

Stimulation of Bovicin HC5 Production and Selection of Improved Bacteriocin-Producing Streptococcus equinus HC5 Variants

Bovicin HC5 is a peptide that has inhibitory activity against various pathogenic microorganisms and food spoilage bacteria. Aiming to improve the productivity of this bacteriocin, we evaluated several potential factors that could stimulate the synthesis of bovicin HC5 and selected variants of Streptococcus equinus (Streptococcus bovis) HC5 with enhanced bacteriocin production by adaptive laboratory evolution (ALE). The highest production of the bacteriocin (1.5-fold) was observed when Strep. equinus HC5 was cultivated with lactic acid (100 mmol/L). For the ALE experiment, Strep. equinus HC5 cells were subjected to acid-shock (pH 3.0 for 2 h) and maintained in continuous culture for approximately 140 generations (40 days) in media with lactic acid (100 mmol/L) and pH-controlled at 5.5 ± 0.2. An adapted variant was selected showing a distinct phenotype (sedimentation, pigmentation) compared with the parental strain. Bacteriocin production increased 2-fold in this adapted Strep. equinus HC5 variant, which appears to be associated with changes in the cell envelope of the adapted variant and enhanced bacteriocin release into the culture media. In addition, the adapted variant showed higher levels of expression of all bovicin HC5 biosynthetic genes compared with the parental strain during the early and late stages of growth. Results presented here indicate that ALE is a promising strategy for selecting strains of lactic acid bacteria with increased production of bacteriocins.

El-Seedi H. The Many Faces of Kefir Fermented Dairy Products: Quality Characteristics, Flavour Chemistry, Nutritional Value, Health Benefits, and Safety

Kefir is a dairy product that can be prepared from different milk types, such as goat, buffalo, sheep, camel, or cow via microbial fermentation (inoculating milk with kefir grains). As such, kefir contains various bacteria and yeasts which influence its chemical and sensory characteristics. A mixture of two kinds of milk promotes kefir sensory and rheological properties aside from improving its nutritional value. Additives such as inulin can also enrich kefir's health qualities and organoleptic characters. Several metabolic products are generated during kefir production and account for its distinct flavour and aroma: Lactic acid, ethanol, carbon dioxide, and aroma compounds such as acetoin and acetaldehyde. During the storage process, microbiological, physicochemical, and sensory characteristics of kefir can further undergo changes, some of which improve its shelf life. Kefir exhibits many health benefits owing to its antimicrobial, anticancer, gastrointestinal tract effects, gut microbiota modulation and anti-diabetic effects. The current review presents the state of the art relating to the role of probiotics, prebiotics, additives, and different manufacturing practices in the context of kefir's physicochemical, sensory, and chemical properties. A review of kefir's many nutritional and health benefits, underlying chemistry and limitations for usage is presented.

Development and characterization of acidic-pH-tolerant mutants of Zymomonas mobilis through adaptation and next-generation sequencing-based genome resequencing and RNA-Seq

BACKGROUND

Acid pretreatment is a common strategy used to break down the hemicellulose component of the lignocellulosic biomass to release pentoses, and a subsequent enzymatic hydrolysis step is usually applied to release hexoses from the cellulose. The hydrolysate after pretreatment and enzymatic hydrolysis containing both hexoses and pentoses can then be used as substrates for biochemical production. However, the acid-pretreated liquor can also be directly used as the substrate for microbial fermentation, which has an acidic pH and contains inhibitory compounds generated during pretreatment. Although the natural ethanologenic bacterium Zymomonas mobilis can grow in a broad range of pH 3.5 ~ 7.5, cell growth and ethanol fermentation are still affected under acidic-pH conditions below pH 4.0.

RESULTS

In this study, adaptive laboratory evolution (ALE) strategy was applied to adapt Z. mobilis under acidic-pH conditions. Two mutant strains named 3.6M and 3.5M with enhanced acidic pH tolerance were selected and confirmed, of which 3.5M grew better than ZM4 but worse than 3.6M in acidic-pH conditions that is served as a reference strain between 3.6M and ZM4 to help unravel the acidic-pH tolerance mechanism. Mutant strains 3.5M and 3.6M exhibited 50 ~ 130% enhancement on growth rate, 4 ~ 9 h reduction on fermentation time to consume glucose, and 20 ~ 63% improvement on ethanol productivity than wild-type ZM4 at pH 3.8. Next-generation sequencing (NGS)-based whole-genome resequencing (WGR) and RNA-Seq technologies were applied to unravel the acidic-pH tolerance mechanism of mutant strains. WGR result indicated that compared to wild-type ZM4, 3.5M and 3.6M have seven and five single nucleotide polymorphisms (SNPs), respectively, among which four are shared in common. Additionally, RNA-Seq result showed that the upregulation of genes involved in glycolysis and the downregulation of flagellar and mobility related genes would help generate and redistribute cellular energy to resist acidic pH while keeping normal biological processes in Z. mobilis. Moreover, genes involved in RND efflux pump, ATP-binding cassette (ABC) transporter, proton consumption, and alkaline metabolite production were significantly upregulated in mutants under the acidic-pH condition compared with ZM4, which could help maintain the pH homeostasis in mutant strains for acidic-pH resistance. Furthermore, our results demonstrated that in mutant 3.6M, genes encoding F₁F₀ ATPase to pump excess protons out of cells were upregulated under pH 3.8 compared to pH 6.2. This difference might help mutant 3.6M manage acidic conditions better than ZM4 and 3.5M. A few gene targets were then selected for genetics study to explore their role in acidic pH tolerance, and our results demonstrated that the expression of two operons in the shuttle plasmids, ZMO0956-ZMO0958 encoding cytochrome bc1 complex and ZMO1428-ZMO1432 encoding RND efflux pump, could help Z. mobilis tolerate acidic-pH conditions.

CONCLUSION

An acidic-pH-tolerant mutant 3.6M obtained through this study can be used for commercial bioethanol production under acidic fermentation conditions. In addition, the molecular mechanism of acidic pH tolerance of Z. mobilis was further proposed, which can facilitate future research on rational design of synthetic microorganisms with enhanced tolerance against acidic-pH conditions. Moreover, the strategy developed in this study combining approaches of ALE, genome resequencing, RNA-Seq, and classical genetics study for mutant evolution and characterization can be applied in other industrial microorganisms.

Microbial response to acid stress: mechanisms and applications

Microorganisms encounter acid stress during multiple bioprocesses. Microbial species have therefore developed a variety of resistance mechanisms. The damage caused by acidic environments is mitigated through the maintenance of pH homeostasis, cell membrane integrity and fluidity, metabolic regulation, and macromolecule repair. The acid tolerance mechanisms can be used to protect probiotics against gastric acids during the process of food intake, and can enhance the biosynthesis of organic acids. The combination of systems and synthetic biology technologies offers new and wide prospects for the industrial applications of microbial acid tolerance mechanisms. In this review, we summarize acid stress response mechanisms of microbial cells, illustrate the application of microbial acid tolerance in industry, and prospect the introduction of systems and synthetic biology to further explore the acid tolerance mechanisms and construct a microbial cell factory for valuable chemicals.

Use of Natural Selection and Evolution to Develop New Starter Cultures for Fermented Foods

The fermented foods industry is constantly seeking new starter cultures to deal with changing consumer preferences and new fermentation processes. New cultures can either be composed of strains isolated from nature or improved derivatives of existing isolates. A variety of techniques involving natural selection and evolution are available to enhance the performance of existing strains, including the isolation of mutants with desired properties, adaptive laboratory evolution, genome shuffling, and genome editing. Numerous examples of traits that can be improved are provided. These include resistance to bacteriophages; the secretion of glucose to increase sweetness; the production of vitamins, antifungal compounds, bacteriocins, texture, or aroma; enhancement of acidification rates and acid tolerance; and elimination of biofilm formation. Careful consideration is required to ensure the developed strains are suitable for the desired purpose, as some approaches may lead to regulatory concerns.

The Microbiome of an Active Meat Curing Brine

Traditional food products are important to our culture and heritage, and to the continued success of the food industry. Many of the production processes associated with these products have not been subjected to an in-depth microbial compositional analysis. The traditional process of curing meat, both preserves a natural protein source, as well as increasing its organoleptic qualities. One of the most important salting processes is known as Wiltshire curing. The Wiltshire process involves injecting pork with a curing solution and immersing the meat into microbial-rich brine which promotes the development of the distinct organoleptic characteristics. The important microbial component of Wiltshire brine has not been extensively characterized. We analyzed the key microbial component of Wiltshire brine by performing microbiome analysis using Next Generation Sequencing (NGS) technologies. This analysis identified the genera, Marinilactibacillus, Carnobacterium, Leuconostoc, and Vibrio as the core microflora present in Wiltshire curing brine. The important food industrial applications of these bacteria were also assessed. The bacterial diversity of the brine was investigated, and the community composition of the brine was demonstrated to change over time. New knowledge on the characterization of key microbiota associated with a productive Wiltshire brine is an important development linked to promoting enhanced quality and safety of meat processing in the food industry.

Adaptive laboratory evolution of cadmium tolerance in Synechocystis sp. PCC 6803

BACKGROUND

Cadmium has been a significant threat to environment and human health due to its high toxicity and wide application in fossil-fuel burning and battery industry. Cyanobacteria are one of the most dominant prokaryotes, and the previous studies suggested that they could be valuable in removing Cd2+ from waste water. However, currently, the tolerance to cadmium is very low in cyanobacteria. To further engineer cyanobacteria for the environmental application, it is thus necessary to determine the mechanism that they respond to high concentration of cadmium.

RESULTS

In this study, a robust strain of Synechocystis PCC 6803 (named ALE-9.0) tolerant to CdSO4 with a concentration up to 9.0 µM was successfully isolated via adaptive laboratory evolution over 802-day continuous passages under cadmium stress. Whole-genome re-sequencing was then performed and nine mutations were identified for the evolved strain compared to the wild-type strain. Among these mutations, a large fragment deletion in slr0454 encoding a cation or drug efflux system protein was found to contribute directly to the resistance to Cd2+ stress. In addition, five other mutations were also demonstrated related to the improved Cd2+ tolerance in ALE-9.0. Moreover, the evolved ALE-9.0 strain was found to obtain cross tolerance to some other heavy metals like zinc and cobalt as well as higher resistance to high light.

CONCLUSIONS

The work here identified six genes and their mutations related to Cd2+ tolerance in Synechocystis PCC 6803, and demonstrated the feasibility of adaptive laboratory evolution in tolerance modifications. This work also provided valuable information regarding the cadmium tolerance mechanism in Synechocystis PCC 6803, and useful insights for cyanobacterial robustness and tolerance engineering.

Resistance to bacteriocin Lcn972 improves oxygen tolerance of Lactococcus lactis IPLA947 without compromising its performance as a dairy starter

Background

Lactococcus lactis is the main component of the mesophilic starters used in cheese manufacture. The success of milk fermentation relies on the viability and metabolic activity of the starter bacteria. Therefore, robust strains able to withstand the harsh conditions encountered during cheese manufacture and starter production are demanded. In this work, we have applied adaptive evolution under cell envelope stress imposed by the cell wall active bacteriocin Lcn972 to evolve strains with more robust phenotypes.

Results

Consecutive exposure of the starter strain L. lactis IPLA947 to Lcn972 yielded a stable mutant, L. lactis R5, with enhanced survival when challenged with hydrogen peroxide. L. lactis R5 exhibited faster growth rates in aerobic fermentations in broth and was able to acidify milk to a lower pH in aerated milk cultures. The improved behavior of L. lactis R5 in the presence of oxygen did not translate into a better performance in the presence of heme (i.e. respiration metabolism) or into higher survival during storage at cold temperatures or after freeze-drying compared to the wild type L. lactis IPLA947. L. lactis R5 retained the same milk acidification rate and no changes in the consumption of lactose and production of organic acids were noticed. However, the profile of volatile compounds revealed a significant increase in 3-hydroxy-2-butanone (acetoin) in curds manufactured with L. lactis R5.

Conclusions

Based on our results, L. lactis R5 can be proposed as a suitable dairy starter with improved survival under oxidative stress and enhanced metabolic traits. The results support the notion that adaptive evolution under cell envelope stress might be useful to generate strain diversity within industrial L. lactis strains.