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Brewing Microbiology Current Research, Omics and Microbial Ecology

PrefaceBrewing Yeast Physiology AbstractIntroductionThe brewing yeast cycleYeast physiological response to the brewing process, transitions between growth and nongrowthQuiescent yeast cellsTransition from quiescence to growthCellular signalling systemsAssimilation and metabolism of sugarsYeast growth and nitrogen assimilation during fermentationFermentation growth medium- induced pathwayResponse of yeast to oxygenRoles of mitochondriaCell wall plasticityFlocculationReserve metabolismYeast responses to stressFuture perspectiveReferencesYeast Stress and Brewing FermentationsThe origins of brewing yeastBrewing fermentationsThe general stress responseOxidative stressOxygen in the breweryDefending against oxygen using antioxidantsAntioxidants are not the only defenceHow much oxygen should be deployed during fermentation?Osmotic stressHyperosmotic stress in the breweryOsmotolerance and osmoadaptionpH downshiftAcid washingAnaerobic shift and carbon dioxide toxicityControl of gene expressionThe cell wall responses to anaerobiosisEthanol toxicityResponses to ethanolEthanol can permanently damage the cellCold shockLow-temperature environments in the breweryCold tolerance and brewingCold tolerance and membrane fluidityImpact of low temperature on genome-wide expressionResponding to coldConclusions and future perspectivesReferencesYeast Supply, Fermentation and q Handling - Insights, Best Practice and 3 Consequences of FailureYeast supplyBest practiceLong-term storage - cryopreservation versus freezedryingRecovery and supplyConsequences of failurePropagationBest practiceConsequences of failureYeast supply - active dried yeastBest practiceConsequences of failurePitchingMeasurement of pitching rateGeneration numberA word or two on yeast viabilityAcid washing - yes or no?Best practiceConsequences of failureFermentationOxygenOxygen and lipid synthesisGlycogenCapacityBest practiceConsequences of failureCroppingThe cropping processImpact of warm cropping on yeast qualityAutolysisBest practiceConsequences of failureStorageTime, temperature and mixingGrowth, metabolism, stress and quiescencePopulation heterogeneity and genetic instabilityBest practiceConsequences of failureReferencesTaxonomy, Diversity, and Typing of Brewing Yeasts Yeasts - significance and relevanceYeast taxonomyTaxonomy of the genus SaccharomycesBrewing yeastsSaccharomyces cerevisiaeSaccharomyces pastorianus and Saccharomyces carlsbergensisSaccharomyces eubayanus and Saccharomyces bayanusSaccharomyces kudriavzevii hybridsBrettanomyces and DekkeraThe microbiota of Belgian specialty beers and other non-conventional brewing yeastsTyping and differentiationPhenotypic methodsDNA-based methodsReferencesGenetic Manipulation of Brewing Yeasts: Challenges and Opportunities Life cycle of Saccharomyces yeasts; genomes, ploidy, aneuploidy, and interspecific hybridsMembers of the Saccharomyces genus; interspecific hybridizationGenetic traits of interest to brewersBreeding and hybridization strategies currently used with brewing yeastsDirect matingRare mating within or between Saccharomyces speciesCytoductionProtoplast fusionHO-induced switching and hybridizationFuture directions for breeding and genetic manipulation of brewing yeastsThe future of hybrid yeasts in brewingMass matingMass mating and genome shuffling in asexual strains via transient HO inductionMass protoplast fusionWhole-genome and high-throughput sequencingGenetic modification strategiesMetabolic engineering and synthetic biologySummaryReferencesGenomics and Evolution of Beer YeastsFrom phenotyping to whole- genome sequencingSaccharomyces cerevisiae - an alcohol producer tuned to perfectionNatural selection shaped the Saccharomyces genomeSaccharomyces cerevisiae as the first domesticated microbeBeer fermentations are a highly selective nicheSaccharomyces cerevisiae phylogenetics and population structureThe complex genome structure of S. cerevisiae ale yeastsAle yeasts: probably the oldest microbial pets known to mankindSaccharomyces pastorianus - the odd one out of the Saccharomyces genusHybrid nature of lager yeastLager yeasts can be divided into two genetically and phenotypically distinct lineagesGenetic differencesPhenotypic differencesFuture prospects of lager yeastsBrettanomyces bruxellensis - the locomotive of spontaneous beer fermentationBrettanomyces taxonomy and phylogenyA first glimpse at the peculiar genome and population structure of Brettanomyces bruxellensisBrettanomyces is a well-adapted fermentation scavengerBrettanomyces genomics: catching up with SaccharomycesConclusionsReferencesMicrobial Ecology of Traditional Beer — Fermentations Introduction to traditional and mixed-culture beer fermentationsThe use of culture-dependent and culture-independent techniques in microbial biodiversity studiesEcology of lambic beers produced in traditional and industrial lambic beer breweriesThe traditional lambic beer fermentation processThe industrial lambic beer fermentation processThe inoculation source of the spontaneous lambic beer fermentation processThe microbiota and metabolites of ageing gueuze beersEcology of lambic-style ACA beersEcology of red-brown acidic beersOther mixed beer fermentationsBerliner WeisseSorghum beersOther cereal-based beveragesChichaBozaFuture perspectivesReferencesFungal Contamination of Barley and MaltEcological considerations (microbial ecology)Routes of fungal colonization of cereal grains and maltThe microbial community of brewing barley and maltProblems related to fungal contamination of brewing cereals and maltYield reductionFungal enzymatic activityFungal secondary metabolitesAntimicrobialsPigmentsFungal hormonesMycotoxinsToxins of Aspergillus and Penicillium in beer productionAflatoxinsCitrininCyclopiazonic acidOchratoxin A (OTA)Patulin and penicillic acidSterigmatocystinFusarium toxins in beer productionTrichothecenesFumonisinsEmerging mycotoxins: moniliformin, fusaproliferin, enniatins and beauvericinGushingDetection and identification of fungi and fungal metabolites in cereals, malt, and beerPhysical, chemical, and affinity- based methodsAffinity-based detection of mycotoxins has relied mainly on the use of antibodies or fragmentsMicrobiological methodsMolecular biological methodsPCR-based methodsLAMP-based methodsControl of fungal contamination in brewing cerealsPrevention of fungal contamination of raw materialsPrevention of fungal growth during storage and malt productionConclusionsReferencesInvestigation of Beer Spoilage Lactic r~ Acid Bacteria Using Omic ApproachesIntroduction to lactic acid bacteria in beer: ‘The good, the bad and the ugly’The promise of omics for BSR LAB researchDiversity, relatedness and maintenance of BSR LABGeneral LAB characteristicsBSR LAB diversityTraditional and emerging methods for BSR LAB detection and identificationCulture-based methodsMolecular techniquesrDNA and RNA detectionPCR and qPCRMolecular techniquesMultilocus sequence typing (MLST)OmicsDeep sequencing of DNA and mRNAProteomics and metabolomicsMethods of controlPhysical meansBacteriocinsPhage therapyBSR LAB and the brewing environmentNiche adaptation and horizontal gene transferIncreased transcriptomic studies, in conjunctionOrigin of BSR LABHop resistance Antimicrobial effect of hopsHop tolerance mechanismsProposed hop tolerance genesHop tolerance genes and the brewing environmentUtility of BSR LAB hop tolerance genesStress tolerance and adaptation of BSR LABStress tolerance to ethanol and low pHStress tolerance to low nutrient availabilityStress tolerance to low O2 tension and dissolved CO2Viable, but not culturable, stateMaintenance of BSR LAB and importance of biofilmsScreening physiological capacities of BSR LAB: contaminant versus fermentor?Conclusions and the futureReferencesBrewery- and Beer Spoilage- related Gram-negative Bacteria: The Unpleasant, the Malodorous and the Outright FetidAerobic GNBEnterobacteriaAcetic acid bacteriaZymomonas mobilisAnaerobic GNBMegasphaera and PectinatusPropionispira (formerly Zymophilus) and SelenomonasLocation in the brewery: biofilms and microbial communitiesIsolation, detection and identificationCommon structural features, genes, and genomesConclusions and the futureGenome sequencing and transcriptional analysisMetagenomics and biofilmsReferencesBeer-spoiling Yeasts: Genomics, и Detection, and ControlTaxonomy of beer-spoiling yeast speciesThe physiology of beer-spoiling yeastVegetative growth, cell structure and sexual divisionCell size and colour in beer-spoiling yeastsOrigins and impacts of beer- spoiling yeastsAnaerobic (fermentative) beer- spoiling yeastsHanseniaspora (Kloeckera)KluyveromycesSaccharomycesSchizosaccharomycesTorulasporaZygosaccharomycesAerobic (non-fermentative) beer- spoiling yeastsBrettanomyces (Dekkera)CandidaDebaryomycesPichiaLindnera (previously Williopsis)Other yeast contaminantsGenomics and metabolomics of beer-spoiling yeastProduction of phenolic compoundsBeer-spoiling yeasts and killer toxinsBeer-spoiling yeasts and flocculationSugar uptake and metabolism of beer-spoiling yeastsThe Pasteur effectThe Custers effectThe Kluyver effectFrequency and control of beer- spoiling yeastsIncidences of beer-spoiling yeasts in breweriesControl of beer-spoiling yeastsDetection and identificationIsolating beer-spoiling yeastsTraditional methods for characterizing beer-spoiling yeastsTraditional methods for differentiation of production strains and variantsAlternative methods for yeast detection and identificationMolecular methods for identification of beer-spoiling yeast speciesD1/D2 sequencingITS/NTS PCRConclusionsReferences

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