dairy fermentation
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Streptococcus thermophilus is an important starter culture bacterium in global dairy fermentation processes, where it is used for the production of various cheeses and yogurt. Bacteriophage predation of the species can result in substandard product quality and, in rare cases, complete fermentation collapse.

Streptococcus thermophilus-infecting phages represent a major problem in the dairy fermentation industry, particularly in relation to thermophilic production systems. Consequently, numerous studies have been performed relating to the biodiversity of such phages in global dairy operations. In the current review, we provide an overview of the genetic and morphological diversity of these phages and highlight the source and extent of genetic mosaicism among phages infecting this species through comparative proteome analysis of the replication and morphogenesis modules of representative phages. The phylogeny of selected phage-encoded receptor binding proteins (RBPs) was assessed, indicating that in certain cases RBP-encoding genes have been acquired separately to the morphogenesis modules, thus highlighting the adaptability of these phages. This review further highlights the significant advances that have been made in defining emergent genetically diverse groups of these phages, while it additionally summarizes remaining knowledge gaps in this research area.

Bacteria of the genus Lactobacillus have been employed in food fermentation for decades. Fermented dairy products, such as cheese and yogurt, are products of high value known as functional food and widely consumed due to their positive health impact. Fermentation was originally based on conversion of carbohydrate into organic acids, mostly lactic acid, intended to preserve nutrient in milk, but then it develops in other disclosure of capabilities associates with health benefit. It is expected that during the manufacture of fermented dairy products, some bioactive peptides from milk protein are released through proteolysis. Lactobacilli have been recognized and received increasing attention as probiotics by balancing gut microbial population. Information of molecular mechanisms of genome sequence focusing on the microbial that normally inhabit gut may explain as to how these bacteria positively give impact on improving host health. Recent post-biotics concept revealed that health benefit can also be associated after bacterial lysis. This mini review focuses on the contribution of lactobacilli in dairy fermentation with health-promoting properties on human health.

Lactococcus lactis is a Gram-positive lactic acid bacterium commonly used in the dairy industry for the production of fermented foods such as buttermilk and a wide variety of cheeses. Here, we report the complete genome sequences of 28 bacteriophages infecting different L. lactis industrial starter strains isolated from dairy plants throughout the world.

Streptococcus thermophilus strains are among the most widely employed starter cultures in dairy fermentations, second only to those of Lactococcus lactis. The extensive application of this species provides considerable opportunity for the proliferation of its infecting (bacterio)phages. Until recently, dairy streptococcal phages were classified into two groups (cos and pac groups), while more recently, two additional groups have been identified (5093 and 987 groups). This highlights the requirement for consistent monitoring of phage populations in the industry. Here, we report a survey of 35 samples of whey derived from 27 dairy fermentation facilities in ten countries against a panel of S. thermophilus strains. This culminated in the identification of 172 plaque isolates, which were characterized by multiplex PCR, restriction fragment length polymorphism analysis, and host range profiling. Based on this characterisation, 39 distinct isolates representing all four phage groups were selected for genome sequencing. Genetic diversity was observed among the cos isolates and correlations between receptor binding protein phylogeny and host range were also clear within this phage group. The 987 phages isolated within this study shared high levels of sequence similarity, yet displayed reduced levels of similarity to those identified in previous studies, indicating that they are subject to ongoing genetic diversification.

Optimization of dairy fermentation processes often requires multiplexed pH measurements over several hours. The method developed here measures up to 90 samples simultaneously, where traditional electrode-based methods require a lot more time for handing the same number of samples. Moreover, the new method employs commonly used materials and can be used with a wider range of fluorescence readers than commercial 96-well plates with optical pH sensors. For this application, a milk-like transparent medium is developed that shows acidification properties with dairy starters that are similar to milk. Combination of this milk-like medium and 3 fluorescent indicators allow precise measurements of pH in a range of 4·0–7·0. The new method showed much higher throughput compared to the benchmark electrode systems while being as accurate, as shown by successful application for a comparison of various dairy starter cultures and for optimizing the inoculation rate.

ABSTRACTCRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here, we describe the extension of the Cas9 application toolbox to the industrially important dairy speciesLactococcus lactis. The Cas9 expression vector pLABTarget, encoding theStreptocccus pyogenesCas9 under the control of a constitutive promoter, was constructed, allowing plug and play introduction of short guide RNA (sgRNA) sequences to target specific genetic loci. Introduction of apepN-targeting derivative of pLABTarget intoL. lactisstrain MG1363 led to a strong reduction in the number of transformants obtained, which did not occur in apepNdeletion derivative of the same strain, demonstrating the specificity and lethality of the Cas9-mediated double-strand breaks in the lactococcal chromosome. Moreover, the same pLABTarget derivative allowed the selection of apepNdeletion subpopulation from its corresponding single-crossover plasmid integrant precursor, accelerating the construction and selection of gene-specific deletion derivatives inL. lactis. Finally, pLABTarget, which contained sgRNAs designed to target mobile genetic elements, allowed the effective curing of plasmids, prophages, and integrative conjugative elements (ICEs). These results establish that pLABTarget enables the effective exploitation of Cas9 targeting inL. lactis, while the broad-host-range vector used suggests that this toolbox could readily be expanded to other Gram-positive bacteria.IMPORTANCEMobile genetic elements inLactococcus lactisand other lactic acid bacteria (LAB) play an important role in dairy fermentation, having both positive and detrimental effects during the production of fermented dairy products. The pLABTarget vector offers an efficient cloning platform for Cas9 application in lactic acid bacteria. Targeting Cas9 toward mobile genetic elements enabled their effective curing, which is of particular interest in the context of potentially problematic prophages present in a strain. Moreover, Cas9 targeting of other mobile genetic elements enables the deciphering of their contribution to dairy fermentation processes and further establishment of their importance for product characteristics.

ABSTRACT We report the complete genome sequence of Lactobacillus plantarum CGMCC 8198, a novel probiotic strain isolated from fermented herbage. We have determined the complete genome sequence of strain L. plantarum CGMCC 8198, which consists of genes that are likely to be involved in dairy fermentation and that have probiotic qualities.

ABSTRACTLactococcal bacteriophages represent one of the leading causes of dairy fermentation failure and product inconsistencies. A new member of the lactococcal 949 phage group, named WRP3, was isolated from cheese whey from a Sicilian factory in 2011. The genome sequence of this phage was determined, and it constitutes the largest lactococcal phage genome currently known, at 130,008 bp. Detailed bioinformatic analysis of the genomic region encoding the presumed initiator complex and baseplate of WRP3 has aided in the functional assignment of several open reading frames (ORFs), particularly that for the receptor binding protein required for host recognition. Furthermore, we demonstrate that the 949 phages target cell wall phospho-polysaccharides as their receptors, accounting for the specificity of the interactions of these phages with their lactococcal hosts. Such information may ultimately aid in the identification of strains/strain blends that do not present the necessary saccharidic target for infection by these problematic phages.