Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis

Lactococcus lactis strains are important components in industrial starter cultures for cheese manufacturing. They have many strain-dependent properties, which affect the final product. Here, we explored the use of machine learning to create systematic, high-throughput screening methods for these properties. Fast acidification of milk is such a strain-dependent property. To predict the maximum hourly acidification rate (Vmax), we trained Random Forest (RF) models on four different genomic representations: Presence/absence of gene families, counts of Pfam domains, the 8 nucleotide long subsequences of their DNA (8-mers), and the 9 nucleotide long subsequences of their DNA (9-mers). Vmax was measured at different temperatures, volumes, and in the presence or absence of yeast extract. These conditions were added as features in each RF model. The four models were trained on 257 strains, and the correlation between the measured Vmax and the predicted Vmax was evaluated with Pearson Correlation Coefficients (PC) on a separate dataset of 85 strains. The models all had high PC scores: 0.83 (gene presence/absence model), 0.84 (Pfam domain model), 0.76 (8-mer model), and 0.85 (9-mer model). The models all based their predictions on relevant genetic features and showed consensus on systems for lactose metabolism, degradation of casein, and pH stress response. Each model also predicted a set of features not found by the other models.

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.

Technological properties of indigenous Lactococcus lactis strains isolated from Lait caillé, a spontaneous fermented milk from Burkina Faso

The experiments reported in this research paper aimed to determine the technological properties of indigenous Lactococcus lactis strains isolated from Lait caillé, a spontaneous fermented milk, from the perspective of starter culture development. Fermentations were conducted to determine the acidification patterns. The ropy character, growth in 0.04 g/ml NaCl and citrate metabolism were additionally tested. Furthermore, the rheological properties of samples from selected strains and the impact of cold storage were evaluated. Based on the rate of acidification, the indigenous strains were divided into 2 groups depending on their fermentation time, i.e. 10-13 h (fast acidifier), and up to 72 h (slow acidifier), respectively. The physiological tests suggested that most of these strains produced exopolysaccharides but none could ferment citrate. The flow properties of the samples inoculated by the fast acidifier strains showed a time-dependent shear thinning behaviour, while their viscoelastic properties corresponded structurally to those of weak gels. Cold storage decreased the viscosity and CFU counts for most of the indigenous strains tested. This study is a step towards the definition of starter cultures for African spontaneous fermented milks such as Lait caillé.

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

Lactic Acid Bacteria (LAB) are extensively employed in the production of various fermented foods, due to their safe status, ability to affect texture and flavor and finally due to the beneficial effect they have on shelf-life. More recently, LAB have also gained interest as production hosts for various useful compounds, particularly compounds with sensitive applications, such as food ingredients and therapeutics. As for all industrial microorganisms, it is important to have a good understanding of the physiology and metabolism of LAB in order to fully exploit their potential, and for this purpose, many systems biology approaches are available. Systems metabolic engineering, an approach that combines optimization of metabolic enzymes/pathways at the systems level, synthetic biology as well as in silico model simulation, has been used to build microbial cell factories for production of biofuels, food ingredients and biochemicals. When developing LAB for use in foods, genetic engineering is in general not an accepted approach. An alternative is to screen mutant libraries for candidates with desirable traits using high-throughput screening technologies or to use adaptive laboratory evolution to select for mutants with special properties. In both cases, by using omics data and data-driven technologies to scrutinize these, it is possible to find the underlying cause for the desired attributes of such mutants. This review aims to describe how systems biology tools can be used for obtaining both engineered as well as non-engineered LAB with novel and desired properties.

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.

Changes in oxidation-reduction potential during milk fermentation by wild lactic acid bacteria

Oxidation-reduction potential (E h) is a fundamental physicochemical property of lactic acid bacteria that determines the microenvironment during the cheese manufacture and ripening. For this reason the E h is of growing interest in dairy research and the dairy industry. The objective of the study was to perform a comprehensive study on the reduction activity of wild lactic acid bacteria strains collected in different periods (from 1960 to 2012) from Italian dairy products. A total of 709 strains belonging to Lactococcus lactis, Enterococcus durans, E. faecium, E. faecalis and Streptococcus thermophilus species were studied for their reduction activity in milk. Kinetics of milk reduction were characterised by the minimum redox potential (E h7) and time of reaching E h7 (t min), the maximum difference between two measures (Δmax) and the time at which these maximum differences occurred (t*). Broad diversity in kinetic parameters was observed at both species and strain levels. E. faecalis and L. lactis resulted to be the most reducing species, while S. thermophilus was characterised by the lowest reducing power while the greatest heterogeneity was pointed out among E. durans and E. faecium strains. Considering the period of collection (1960-2012) we observed that the more recently isolated strains generally showed less reducing activity. This trend was particularly evident for the species E. durans, E. faecium and L. lactis while an opposite trend was observed in E. faecalis species. Data reported in this research provide new information for a deeper understanding of redox potential changes during milk fermentation due to bacterial growth. Gain knowledge of the redox potential of the LAB cultures could allow a better control and standardisation of cheesemaking process.

ESTABILIDADE DO LEITE AO ÁLCOOL AINDA PODE SER UM INDICADOR CONFIÁVEL?

Resumo As provas de estabilidade alcoólica e acidez Dornic ainda são amplamente utilizadas em diversos países, mensurando indiretamente a qualidade microbiológica do leite. Porém, outros fatores além da contagem de micro-organismos alteram essa relação, causando um efeito confundidor nesses testes de triagem. O objetivo deste estudo foi relacionar o pH, a contagem bacteriana total, a acidez Dornic e a porcentagem de lactose em leites estáveis e instáveis ao álcool. Foram analisadas 322 amostras de leite, sendo classificadas em ácidas, normais ou instáveis não ácidas, segundo os testes de resistência alcoólica e acidez titulável. Diferentemente de leites normais ou ácidos, não existe relação entre pH, CBT e acidez Dornic em amostras de leite que possuem instabilidade alcoólica sem acidez adquirida. Nesse tipo de leite, valores de pH entre 6,6 e 6,8 são acompanhados de contagens bacterianas mais baixas, de até 105 bac.mL-1, e porcentagens de lactose mais altas, de até 4,5%. Conforme a CBT aumenta, a porcentagem de lactose ou o pH tendem a diminuir, porém não necessariamente juntos. Esse comportamento faz com que o teste do álcool não seja um indicador confiável para a qualidade do leite, devendo ser aplicado sempre em conjunto com outras provas que auxiliem no diagnóstico de acidez bacteriana e/ou resistência térmica, como titulação do ácido lático, mensuração de pH e teste da fervura.

Transcriptome analysis of Lactococcus lactis subsp. lactis during milk acidification as affected by dissolved oxygen and the redox potential

Performance of Lactococcus lactis as a starter culture in dairy fermentations depends on the levels of dissolved oxygen and the redox state of milk. In this study the microarray analysis was used to investigate the global gene expression of L. lactis subsp. lactis DSM20481(T) during milk acidification as affected by oxygen depletion and the decrease of redox potential. Fermentations were carried out at different initial levels of dissolved oxygen (dO2) obtained by milk sparging with oxygen (high dO2, 63%) or nitrogen (low dO2, 6%). Bacterial exposure to high initial oxygen resulted in overexpression of genes involved in detoxification of reactive oxygen species (ROS), oxidation-reduction processes, biosynthesis of trehalose and down-regulation of genes involved in purine nucleotide biosynthesis, indicating that several factors, among them trehalose and GTP, were implicated in bacterial adaptation to oxidative stress. Generally, transcriptional changes were more pronounced during fermentation of oxygen sparged milk. Genes up-regulated in response to oxygen depletion were implicated in biosynthesis and transport of pyrimidine nucleotides, branched chain amino acids and in arginine catabolic pathways; whereas genes involved in salvage of nucleotides and cysteine pathways were repressed. Expression pattern of genes involved in pyruvate metabolism indicated shifts towards mixed acid fermentation after oxygen depletion with production of specific end-products, depending on milk treatment. Differential expression of genes, involved in amino acid and pyruvate pathways, suggested that initial oxygen might influence the release of flavor compounds and, thereby, flavor development in dairy fermentations. The knowledge of molecular responses involved in adaptation of L. lactis to the shifts of redox state and pH during milk fermentations is important for the dairy industry to ensure better control of cheese production.