Systems Biology - A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria

Response and acclimation of cyanobacteria to acidification: A comprehensive review

Cyanobacteria, as vital components of aquatic ecosystems, face increasing challenges due to acidification driven by various anthropogenic and natural factors. Understanding how cyanobacteria adapt and respond to acidification is crucial for predicting their ecological dynamics and potential impacts on ecosystem health. This comprehensive review synthesizes current knowledge on the acclimation mechanisms and responses of cyanobacteria to acidification stress. Detailly, ecological roles of cyanobacteria were firstly briefly concluded, followed by the effects of acidification on aquatic ecosystems and cyanobacteria. Then the review focuses on the physiological, biochemical, and molecular strategies employed by cyanobacteria to cope with acidification stress, highlighting key adaptive mechanisms and their ecological implications. Finally, a summary of strategies to enhance acid resistance in cyanobacteria and future directions was discussed. Utilizing omics data and machine learning technology to build a cyanobacterial acid regulatory network allows for predicting the impact of acidification on cyanobacteria and inferring its broader effects on ecosystems. Additionally, acquiring acid-tolerant chassis cells of cyanobacteria through innovative techniques facilitates the advancement of environmentally friendly production of acidic chemicals. By synthesizing empirical evidence and theoretical frameworks, this review aims to elucidate the complex interplay between cyanobacteria and acidification stressors, providing insights for future research directions and ecosystem management strategies.

Hyperpolarized 13C NMR Reveals Pathway Regulation in Lactococcus lactis and Metabolic Similarities and Differences Across the Tree of Life

The control of metabolic networks is incompletely understood, even for glycolysis in highly studied model organisms. Direct real-time observations of metabolic pathways can be achieved in cellular systems with 13C NMR using dissolution Dynamic Nuclear Polarization (dDNP NMR). The method relies on a short-lived boost of NMR sensitivity using a redistribution of nuclear spin states to increase the alignment of the magnetic moments by more than four orders of magnitude. This temporary boost in sensitivity allows detection of metabolism with sub-second time resolution. Here, we hypothesized that dDNP NMR would be able to investigate molecular phenotypes that are not easily accessible with more conventional methods. The use of dDNP NMR allows real-time insight into carbohydrate metabolism in a Gram-positive bacterium (Lactoccocus lactis), and comparison to other bacterial, yeast and mammalian cells shows differences in the kinetic barriers of glycolysis across the kingdoms of life. Nevertheless, the accumulation of non-toxic precursors for biomass at kinetic barriers is found to be shared across the kingdoms of life. We further find that the visualization of glycolysis using dDNP NMR reveals kinetic characteristics in transgenic strains that are not evident when monitoring the overall glycolytic rate only. Finally, dDNP NMR reveals that resting Lactococcus lactis cells use the influx of carbohydrate substrate to produce acetoin rather than lactate during the start of glycolysis. This metabolic regime can be emulated using suitably designed substrate mixtures to enhance the formation of the C4 product acetoin more than 400-fold. Overall, we find that dDNP NMR provides analytical capabilities that may help to clarify the intertwined mechanistic determinants of metabolism and the optimal usage of biotechnologically important bacteria.

Unveiling the Potential of Lactic Acid Bacteria from Serbian Goat Cheese

This study aimed to unleash the potential of indigenous lactic acid bacteria (LAB) originating from traditionally made Serbian goat cheese. Following the isolation and identification of the LAB, the safety aspects of the isolates were evaluated through tests for hemolytic activity and antibiotic sensitivity. The selected isolates were then tested for various technological properties, including growth in methylene blue, proteolytic activity, acidification, curd formation ability in both pure and enriched goat milk, diacetyl production, antagonistic potential against other LAB, and biofilm formation ability. The results indicated that Lactococcus spp., Lacticaseibacillus spp., and Lactiplantibacillus spp. did not exhibit α or β hemolysis, while enterococci displayed α hemolysis. A higher number of isolates demonstrated sensitivity to ampicillin, tetracycline, and streptomycin, while sensitivity to gentamicin and vancomycin was strain-dependent. Based on the evaluation of technological properties, Lacticaseibacillus paracasei M-1 and Lactiplantibacillus plantarum C7-7, C7-8, and C14-5 showed promising characteristics. Additionally, Lactococcus lactis subsp. lactis strains C0-14 and C21-8 emerged as promising candidates with notable technological properties. Notably, certain indigenous strains LAB exhibit promising technological properties and safety profiles. These characteristics make them suitable candidates for use as starter or adjunct cultures in goat's milk cheese production, potentially enhancing the quality and safety of the cheese as well as hygiene practices among small-scale dairy producers.

Using bifidobacterium and propionibacterium strains in probiotic consortia to normalize the gastrointestinal tract

Abstract The gastrointestinal microflora regulates the body’s functions and plays an important role in its health. Dysbiosis leads to a number of chronic diseases such as diabetes, obesity, inflammation, atherosclerosis, etc. However, these diseases can be prevented by using probiotics – living microorganisms that benefit the microflora and, therefore, improve the host organism's health. The most common probiotics include lactic acid bacteria of the Bifidobacterium and Propionibacterium genera. We studied the probiotic properties of the following strains: Bifidobacterium adolescentis АС-1909, Bifidobacterium longum infantis АС-1912, Propionibacterium jensenii В-6085, Propionibacterium freudenreichii В-11921, Propionibacterium thoenii В-6082, and Propionibacterium acidipropionici В-5723. Antimicrobial activity was determined by the ‘agar blocks’ method against the following test cultures: Escherichia coli ATCC 25922, Salmonella enterica ATCC 14028, Staphylococcus aureus ATCC 25923, Pseudomonas aeruginosa B6643, Proteus vulgaris ATCC 63, and Listeria monocytogenes ATCC 7644. Moderate antimicrobial activity against all the test cultures was registered in Bifidobacterium adolescentis АС-1909, Propionibacterium jensenii В-6085, and Propionibacterium thoenii В-6082. Antioxidant activity was determined by the DPPH inhibition method in all the lactic acid strains. Our study indicated that some Propionibacterium and Bifidobacterium strains or, theoretically, their consortia could be used as probiotic cultures in dietary supplements or functional foods to prevent a number of chronic diseases.

Applicable Strains, Processing Techniques and Health Benefits of Fermented Oat Beverages: A Review

Based on the high nutrients of oat and the demand of health-conscious consumers for value-added and functional foods, fermented oat beverages have great market prospects. This review summarizes the applicable strains, processing techniques and health benefits of fermented oat beverages. Firstly, the fermentation characteristics and conditions of the applicable strains are systematically described. Secondly, the advantages of pre-treatment processes such as enzymatic hydrolysis, germination, milling and drying are summarized. Furthermore, fermented oat beverages can increase the nutrient content and reduce the content of anti-nutritional factors, thereby reducing some risk factors related to many diseases such as diabetes, high cholesterol and high blood pressure. This paper discusses the current research status of fermented oat beverages, which has academic significance for researchers interested in the application potential of oat. Future studies on fermenting oat beverages can focus on the development of special compound fermentation agents and the richness of their taste.

Transcriptome responses of lactic acid bacteria isolated from kimchi under hydrogen peroxide exposure

In this study, five species of lactic acid bacteria (LAB) isolated from kimchi were analyzed in terms of their potential antioxidant activity. Latilactobacillus curvatus WiKim38, Companilactobacillus allii WiKim39, and Lactococcus lactis WiKim0124 exhibited higher radical scavenging activity, reducing power, and lipid peroxidation inhibition than the reference strain and tolerated hydrogen peroxide (H₂O₂) exposure up to a concentration of 2.5 mM. To investigate the antioxidant mechanism of LAB strains, transcriptomic and proteomic signatures were compared between the H₂O₂-exposed and untreated group using RNA sequencing and two-dimensional protein gel electrophoresis. Across all LAB strains, cell membrane responses and metabolic processes were the most prominent in the main categories of gene ontology classification, indicating that cellular components and interactions play an important role in oxidative stress responses. Thus, LAB strains isolated from kimchi could be considered for potential use in functional food production and in antioxidant starter cultures.

A novel SfaNI-like restriction-modification system in Caldicellulosiruptor extents the genetic engineering toolbox for this genus

Caldicellulosiruptor is a genus of thermophilic to hyper-thermophilic microorganisms that express and secrete an arsenal of enzymes degrading lignocellulosic biomasses into fermentable sugars. Because of this distinguished feature, strains of Caldicellulosiruptor have been considered as promising candidates for consolidated bioprocessing. Although a few Caldicellulosiruptor strains with industrially relevant characteristics have been isolated to date, it is apparent that further improvement of the strains is essential for industrial application. The earlier identification of the HaeIII-like restriction-modification system in C. bescii strain DSM 6725 has formed the basis for genetic methods with the aim to improve the strain's lignocellulolytic activity and ethanol production. In this study, a novel SfaNI-like restriction-modification system was identified in Caldicellulosiruptor sp. strain BluCon085, consisting of an endonuclease and two methyltransferases that recognize the reverse-complement sequences 5'-GATGC-3' and 5'-GCATC-3'. Methylation of the adenine in both sequences leads to an asymmetric methylation pattern in the genomic DNA of strain BluCon085. Proteins with high percentage of identity to the endonuclease and two methyltransferases were identified in the genomes of C. saccharolyticus strain DSM 8903, C. naganoensis strain DSM 8991, C. changbaiensis strain DSM 26941 and Caldicellulosiruptor sp. strain F32, suggesting that a similar restriction-modification system may be active also in these strains and respective species. We show that methylation of plasmid and linear DNA by the identified methyltransferases, obtained by heterologous expression in Escherichia coli, is sufficient for successful transformation of Caldicellulosiruptor sp. strain DIB 104C. The genetic engineering toolbox developed in this study forms the basis for rational strain improvement of strain BluCon085, a derivative from strain DIB 104C with exceptionally high L-lactic acid production. The toolbox may also work for other species of the genus Caldicellulosiruptor that have so far not been genetically tractable.

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.

Assessment of Different Lactic Acid Bacteria Isolated from Agro-Industrial Residues: First Report of the Potential Role of Weissella soli for Lactic Acid Production from Milk Whey

The production of lactic acid (LA) through the microbial conversion of agro-industrial residuals is an important process in the biotechnology industry. The growth kinetics of 30 strains of lactic acid bacteria (LAB) isolated from agro-industrial residues were determined and nine strains were selected for microbioreactor fermentation. Lactiplantibacillus pentosus_70-1 (1.662) and L. pentosus_19-2 (1.563) showed the highest OD600 values, whereas the highest growth rates were observed for L. pentosus_19-2 (0.267 h−1) and Weissella soli_31 (0.256 h−1). The production of LA and acetic acid (AA), glucose consumption, and metabolic profiles were determined, without finding significant differences in the production of LA; however, W. soli_29 produced the highest amount of LA (20.833 gL−1) and was able to metabolize most of the studied carbohydrates. Based on these results, W. soli_29 was chosen for a 20 h fermentation in a 7 L bioreactor using both standard medium and milk whey supplemented medium. W. soli_29 produced 16.27 gL−1 and 7.21 gL−1 of LA in each of these mediums, respectively. These results show the underlying potential of Weissella strains for biotechnological applications. Additional analysis which should contemplate different agro-industrial residues and other conditions in bioreactors must be carried out.

Textural and Functional Properties of Skimmed and Whole Milk Fermented by Novel Lactiplantibacillus plantarum AG10 Strain Isolated from Silage

Milk fermentation by lactic acid bacteria both enhances its nutritional value and provides probiotic strains to correct the intestinal microflora. Here, we show the comparative analysis of milk fermented with the new strain, Lactiplantibacillus plantarum AG10, isolated from silage and the industrial strain Lactobacillus delbrukii subs. bulgaricus. While the milk acidification during fermentation with L. plantarum AG10 was lower compared with L. bulgaricus, milk fermented with L. plantarum AG10 after a 14-day storage period retained a high level of viable cells and was characterized by an increased content of exopolysaccharides and higher viscosity. The increased EPS production led to clot formation with higher density on microphotographs and increased firmness and cohesiveness of the product compared with L. bulgaricus-fermented milk. Furthermore, the L. plantarum AG10-fermented milk exhibited increased radical-scavenging activity assuming lower fat oxidation during storage. Taken together, these data suggest that L. plantarum AG10 seems to be a promising starter culture for dairy products with lowered levels of lactic acid, which is important for people with increased gastric acid formation.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Nutritional and Volatile Characterisation of Milk Inoculated with Thermo-Tolerant Lactobacillus bulgaricus through Adaptive Laboratory Evolution

In this study, thermo-tolerant strain of Lactobacillus bulgaricus (L. bulgaricus) was developed using gradual increase in temperature to induce Adaptive Laboratory Evolution (ALE). Viable colony count of 1.87 ± 0.98 log cfu/mL was achieved at 52 °C, using MRS agar supplemented with 2% lactose. Changes in bacteria morphology were discovered, from rod (control) to filament (52 °C) to cocci after frozen storage (−80 °C). When milk was inoculated with thermo-tolerant L. bulgaricus, lactic acid production was absent, leaving pH at 6.84 ± 0.13. This has caused weakening of the protein network, resulting in high whey separation and lower water-holding capacity (37.1 ± 0.35%) compared to the control (98.10 ± 0.60%). Significantly higher proteolytic activity was observed through free amino acids analysis by LC-MS. Arginine and methionine (237.24 ± 5.94 and 98.83 ± 1.78 µg/100 g, respectively) were found to be 115- and 275-fold higher than the control, contributing to changing the aroma similar to cheese. Further volatile analysis through SPME-GC-MS has confirmed significant increase in cheese-aroma volatiles compared to the control, with increase in diacetyl formation. Further work on DNA profiling, metabolomics and peptidomics will help to answer mechanisms behind the observed changes made in the study.

Antioxidant and Anti-Inflammatory Effect and Probiotic Properties of Lactic Acid Bacteria Isolated from Canine and Feline Feces

Oxidative stress is a phenomenon caused by an imbalance between the production of reactive oxygen species and antioxidant defenses. It plays an important role in numerous disease states, including chronic kidney disease, neurological disorders, cardiovascular diseases, diabetes, and cancer. Lactic acid bacteria (LAB) are known to have prominent antioxidant properties. Therefore, this study aimed to measure the antioxidant activity and anti-inflammatory potential of LAB isolated from animals for the efficient use of probiotics with host specificity. Antioxidant activity measurements of sixteen strains revealed that ABTS radical scavenging activities ranged from 26.3 to 57.4%, and DPPH free radical scavenging activities ranged from 4.7 to 13.5%. Based on the antioxidant activity assessment, five strains (Enterococcus faecium MG9003(YH9003), Enterococcus faecium MG9007(YH9007), Lactobacillus reuteri MG9012(YH9012), Lactobacillus fermentum MG9014(YH9014), and Pediococcus pentosaceus MG9015(YH9015)) were selected with the consideration of fermentation productivity (>1 × 10⁹ CFU/g). The selected strains exhibited nitric oxide inhibition and inhibited inducible nitric oxide synthase and cyclooxygenase expression. Furthermore, probiotic properties, including intestinal adhesion and stability, were identified. Our results show that the selected animal-derived strains can be effective probiotic candidates for potential effects on animal hosts.

Physicochemical Parameters and Bioaccessibility of Lactic Acid Bacteria Fermented Chayote Leaf (Sechium edule) and Pineapple (Ananas comosus) Smoothies

In this study, popularly consumed traditional chayote leaves and locally produced pineapple fruit were used to develop a fermented smoothie using lactic acid bacteria (LAB) strains: Lactobacillus plantarum (L75), Weissella cibaria (W64), and their combination (LW64 + 75). The physicochemical parameters [pH, total soluble solids (TSS), and color], total phenols, and carotenoid contents of the smoothies fermented for 48 h and stored for 7 days at 4°C were compared with the unfermented (control) smoothies. Results indicated that LAB fermentation reduced the pH from 3.56 to 2.50 after 48 h (day 2) compared with the non-fermented smoothie at day 2 (pH 3.37). LAB strain L75 significantly reduced the TSS content of the smoothies to 13.06°Bx after 2 days of fermentation. Smoothies fermented by L75 showed overall acceptability after 7 days of storage compared with the non-fermented puree on day 0. The LW64 + 75 significantly reduced the color change (ΔE), which was similar to the control. L75 increased the phenolic content, and W64 enhanced the total carotenoid content of the smoothies after 2 days of fermentation compared with other treatments. The use of an in vitro model simulating gastrointestinal (GI) digestion showed that fermentation with L75 improved the total phenol recovery by 65.96% during the intestinal phase compared with the control. The dialysis phase mimicked an epithelial barrier, and 53.58% of the recovered free soluble are bioavailable from the L75 fermented smoothies compared with the control. The antioxidant capacity of dialyzable fraction of the L75 fermented smoothie was significantly higher than that of the control and smoothies fermented with W64 or LW64 + 75.

Cell wall homeostasis in lactic acid bacteria: threats and defences

Lactic acid bacteria (LAB) encompasses industrially relevant bacteria involved in food fermentations as well as health-promoting members of our autochthonous microbiota. In the last years, we have witnessed major progresses in the knowledge of the biology of their cell wall, the outermost macrostructure of a Gram-positive cell, which is crucial for survival. Sophisticated biochemical analyses combined with mutation strategies have been applied to unravel biosynthetic routes that sustain the inter- and intra-species cell wall diversity within LAB. Interplay with global cell metabolism has been deciphered that improved our fundamental understanding of the plasticity of the cell wall during growth. The cell wall is also decisive for the antimicrobial activity of many bacteriocins, for bacteriophage infection and for the interactions with the external environment. Therefore, genetic circuits involved in monitoring cell wall damage have been described in LAB, together with a plethora of defence mechanisms that help them to cope with external threats and adapt to harsh conditions. Since the cell wall plays a pivotal role in several technological and health-promoting traits of LAB, we anticipate that this knowledge will pave the way for the future development and extended applications of LAB.

Lifestyle, metabolism and environmental adaptation in Lactococcus lactis

Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.

Engineering Lactococcus lactis as a multi-stress tolerant biosynthetic chassis by deleting the prophage-related fragment

Background

In bioengineering, growth of microorganisms is limited because of environmental and industrial stresses during fermentation. This study aimed to construct a nisin-producing chassis Lactococcus lactis strain with genome-streamlined, low metabolic burden, and multi-stress tolerance characteristics.

Results

The Cre-loxP recombination system was applied to reduce the genome and obtain the target chassis strain. A prophage-related fragment (PRF; 19,739 bp) in the L. lactis N8 genome was deleted, and the mutant strain L. lactis N8-1 was chosen for multi-stress tolerance studies. Nisin immunity of L. lactis N8-1 was increased to 6500 IU/mL, which was 44.44% higher than that of the wild-type L. lactis N8 (4500 IU/mL). The survival rates of L. lactis N8-1 treated with lysozyme for 2 h and lactic acid for 1 h were 1000- and 10,000-fold higher than that of the wild-type strain, respectively. At 39 ℃, the L. lactis N8-1 could still maintain its growth, whereas the growth of the wild-type strain dramatically dropped. Scanning electron microscopy showed that the cell wall integrity of L. lactis N8-1 was well maintained after lysozyme treatment. Tandem mass tags labeled quantitative proteomics revealed that 33 and 9 proteins were significantly upregulated and downregulated, respectively, in L. lactis N8-1. These differential proteins were involved in carbohydrate and energy transport/metabolism, biosynthesis of cell wall and cell surface proteins.

Conclusions

PRF deletion was proven to be an efficient strategy to achieve multi-stress tolerance and nisin immunity in L. lactis, thereby providing a new perspective for industrially obtaining engineered strains with multi-stress tolerance and expanding the application of lactic acid bacteria in biotechnology and synthetic biology. Besides, the importance of PRF, which can confer vital phenotypes to bacteria, was established.

From Waste to Taste-Efficient Production of the Butter Aroma Compound Acetoin from Low-Value Dairy Side Streams Using a Natural (Nonengineered) Lactococcus lactis Dairy Isolate

Lactococcus lactis subsp. lactis biovar diacetylactis is widely used in dairy fermentations as it can form the butter aroma compounds acetoin and diacetyl from citrate in milk. Here, we explore the possibility of producing acetoin from the more abundant lactose. Starting from a dairy isolate of L. lactis biovar diacetylactis, we obtained a series of mutants with low lactate dehydrogenase (ldh) activity. One isolate, RD1M5, only had a single insertion mutation in the ldh gene compared to its parental strain as revealed by whole genome resequencing. We tested the ability of RD1M5 to produce acetoin in milk. With aeration, all the lactose could be consumed, and the only product was acetoin. In a simulated cheese fermentation, a 50% increase in acetoin concentration could be achieved. RD1M5 turned out to be an excellent cell factory for acetoin and was able to convert lactose in dairy waste into acetoin with high titer (41 g/L) and high yield (above 90% of the theoretical yield). Summing up, RD1M5 was found to be highly robust and to grow excellently in milk or dairy waste. Being natural in origin opens up for applications within dairies as well as for safe production of food-grade acetoin from low-cost substrates.

No more cleaning up - Efficient lactic acid bacteria cell catalysts as a cost-efficient alternative to purified lactase enzymes

β-galactosidases, commonly referred to as lactases, are used for producing lactose-free dairy products. Lactases are usually purified from microbial sources, which is a costly process. Here, we explored the potential that lies in using whole cells of a food-grade dairy lactic acid bacterium, Streptococcus thermophilus, as a substitute for purified lactase. We found that S. thermophilus cells, when treated with the antimicrobial peptide nisin, were able to hydrolyze lactose efficiently. The rate of hydrolysis increased with temperature; however, above 50 °C, stability was compromised. Different S. thermophilus strains were tested, and the best candidate was able to hydrolyze 80% of the lactose in a 50 g/L solution in 4 h at 50 °C, using only 0.1 g/L cells (dry weight basis). We demonstrated that it was possible to grow the cell catalyst on dairy waste, and furthermore, that a cell-free supernatant of a culture of a nisin-producing Lactococcus lactis strain could be used instead of purified nisin, which reduced cost of use significantly. Finally, we tested the cell catalysts in milk, where lactose also was efficiently hydrolyzed. The method presented is natural and low-cost, and allows for production of clean-label and lactose-free dairy products without using commercial enzymes from recombinant microorganisms. KEY POINTS: • Nisin-permeabilized Streptococcus thermophilus cells can hydrolyze lactose efficiently. • A low-cost and more sustainable alternative to purified lactase enzymes. • Reduction of overall sugar content. • Clean-label production of lactose-free dairy products.

Calretinin is a novel candidate marker for adverse ovarian effects of early life exposure to mixtures of endocrine disruptors in the rat

Disruption of sensitive stages of ovary development during fetal and perinatal life can have severe and life-long consequences for a woman’s reproductive life. Exposure to endocrine disrupting chemicals may affect ovarian development, leading to subsequent reproductive disorders. Here, we investigated the effect of early life exposure to defined mixtures of human-relevant endocrine disrupting chemicals on the rat ovary. We aimed to identify molecular events involved in pathogenesis of ovarian dysgenesis syndrome that have potential for future adverse outcome pathway development. We therefore focused on the ovarian proteome. Rats were exposed to a mixture of phthalates, pesticides, UV-filters, bisphenol A, butyl-paraben, and paracetamol during gestation and lactation. The chemicals were tested together or in subgroups of chemicals with anti-androgenic or estrogenic potentials at doses 450-times human exposure. Paracetamol was tested separately, at a dose of 360 mg/kg. Using shotgun proteomics on ovaries from pup day 17 offspring, we observed exposure effects on the proteomes. Nine proteins were affected in more than one exposure group and of these, we conclude that calretinin is a potential key event biomarker of early endocrine disruption in the ovary.

Safety Aspects of Genetically Modified Lactic Acid Bacteria

Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of various systems for their engineering. Together with novel approaches such as CRISPR-Cas, the established systems for engineering now allow significant improvements to LAB strains. Nevertheless, genetically modified LAB (GM-LAB) still encounter disapproval and are under extensive regulatory requirements. This review presents data on the prospects for LAB to obtain 'generally recognized as safe' (GRAS) status. Genetic modification of LAB is discussed, together with problems that can arise from their engineering, including their dissemination into the environment and the spread of antibiotic resistance markers. Possible solutions that would allow the use of GM-LAB are described, such as biocontainment, alternative selection markers, and use of homologous DNA. The use of GM-LAB as cell factories in closed systems that prevent their environmental release is the least problematic aspect, and this is also discussed.

Investigation of genomic characteristics and carbohydrates' metabolic activity of Lactococcus lactis subsp. lactis during ripening of a Swiss-type cheese

Genetic diversity and metabolic properties of Lactococcus lactis subsp. lactis were explored using phylogenetic, pan-genomic and metatranscriptomic analysis. The genomes, used in the current study, were available and downloaded from the GenBank which were primarily related with microorganisms isolated from dairy products and secondarily from other foodstuffs. To study the genetic diversity of the microorganism, various bioinformatics tools were employed such as average nucleotide identity, digital DNA-DNA hybridization, phylogenetic analysis, clusters of orthologous groups analysis, KEGG orthology analysis and pan-genomic analysis. The results showed that Lc. lactis subsp. lactis strains cannot be sufficiently separated into phylogenetic lineages based on the 16S rRNA gene sequences and core genome-based phylogenetic analysis was more appropriate. Pan-genomic analysis of the strains indicated that the core, accessory and unique genome comprised of 1036, 3146 and 1296 genes, respectively. Considering the results of pan-genomic and KEGG orthology analyses, the metabolic network of Lc. lactis subsp. lactis was rebuild regarding its carbohydrates' metabolic capabilities. Based on the metatranscriptomic data during the ripening of the Swiss-type Maasdam cheese at 20 °C and 5 °C, it was shown that the microorganism performed mixed acid fermentation producing lactate, formate, acetate, ethanol and 2,3-butanediol. Mixed acid fermentation was more pronounced at higher ripening temperatures. At lower ripening temperatures, the genes involved in mixed acid fermentation were repressed while lactate production remained unaffected resembling to a homolactic fermentation. Comparative genomics and metatranscriptomic analysis are powerful tools to gain knowledge on the genomic diversity of the lactic acid bacteria used as starter cultures as well as on the metabolic activities occurring in fermented dairy products.

Harnessing biocompatible chemistry for developing improved and novel microbial cell factories

White biotechnology relies on the sophisticated chemical machinery inside living cells for producing a broad range of useful compounds in a sustainable and environmentally friendly way. However, despite the impressive repertoire of compounds that can be generated using white biotechnology, this approach cannot currently fully replace traditional chemical production, often relying on petroleum as a raw material. One challenge is the limited number of chemical transformations taking place in living organisms. Biocompatible chemistry, that is non‐enzymatic chemical reactions taking place under mild conditions compatible with living organisms, could provide a solution. Biocompatible chemistry is not a novel invention, and has since long been used by living organisms. Examples include Fenton chemistry, used by microorganisms for degrading plant materials, and manganese or ketoacids dependent chemistry used for detoxifying reactive oxygen species. However, harnessing biocompatible chemistry for expanding the chemical repertoire of living cells is a relatively novel approach within white biotechnology, and it could potentially be used for producing valuable compounds which living organisms otherwise are not able to generate. In this mini review, we discuss such applications of biocompatible chemistry, and clarify the potential that lies in using biocompatible chemistry in conjunction with metabolically engineered cell factories for cheap substrate utilization, improved cell physiology, efficient pathway construction and novel chemicals production.