Microbiology in Dairy Processing

List of contributors xv Foreword xix Preface xxi Acknowledgements xxiii 1 Milk fat components and milk quality 1 Iolanda Altomonte, Federica Salari and Mina Martini 1.1 Introduction 1 1.1.1 Milk fat globules 2 1.1.2 Milk fat and fatty acid composition 4 1.2 Conclusions 7 References 7 2 Spore]forming bacteria in dairy products 11 Sonia Garde Lopez]Brea, Natalia Gomez]Torres and Marta Avila Arribas 2.1 Introduction 11 2.2 The bacterial spore 13 2.2.1 Structure and chemical composition of bacterial spores 14 2.2.1.1 Exosporium 14 2.2.1.2 Spore coat 14 2.2.1.3 Outer spore membrane 15 2.2.1.4 Cortex and germ cell wall 15 2.2.1.5 Inner spore membrane 15 2.2.1.6 The core spore 15 2.2.2 Spore resistance 16 2.2.3 Life cycle of spore]forming bacteria 17 2.3 Spore]forming bacteria important for the dairy industry 18 2.3.1 Class Bacilli 18 2.3.1.1 Bacillus genus 19 2.3.1.1.1 Bacillus cereus 19 2.3.1.1.2 Other Bacillus species 20 2.3.1.1.3 Importance of Bacillus spp. in the dairy industry 21 2.3.1.2 Geobacillus and Anoxybacillus genera 24 2.3.1.3 Paenibacillus genus 25 2.3.2 Class Clostridia 25 2.3.2.1 Clostridium botulinum 26 2.3.2.2 Clostridium perfringens 28 2.3.2.3 Clostridium tyrobutyricum and related species 28 2.4 Control strategies to prevent poisoning and spoilage of milk and dairy products by spore]forming bacteria 30 2.5 Conclusions 31 References 32 3 Psychrotrophic bacteria 37 Milena Brasca, Marilu Decimo, Stefano Morandi, Solimar Goncalves Machado, Francois Bagliniere and Maria Cristina Dantas Vanetti 3.1 Introduction 37 3.2 Sources of psychrotrophic bacteria contamination of milk 38 3.3 Important spoilage psychrotrophic bacteria in milk 42 3.4 Molecular tools to characterize psychrotrophic bacteria 43 3.5 Influence of psychrotrophic contamination of raw milk on dairy product quality 45 3.5.1 Bacterial proteases and proteolytic changes in milk 46 3.5.2 Bacterial lipases and phospholipases and their significance in milk 49 3.6 Regulation of extracellular enzymes 52 3.7 Control of psychrotrophic bacteria and related enzymes 53 3.8 Conclusions 54 References 54 4 Stabilization of milk quality by heat treatments 63 Palmiro Poltronieri and Franca Rossi 4.1 Introduction 63 4.2 Thermal treatments of milk 63 4.2.1 Thermization 63 4.2.2 Pasteurization 64 4.2.3 Grade A pasteurized milk 66 4.3 Milk sterilization 67 4.3.1 Control of proper time/temperature setting for safety of milk and milk products 67 4.4 Diseases associated with unpasteurized milk, or post]pasteurization dairy]processing contamination 68 4.5 Conclusions 68 References 68 5 Genomics of LAB and dairy]associated species 71 Palmiro Poltronieri, Franca Rossi, Cesare Camma, Francesco Pomilio and Cinzia Randazzo 5.1 Introduction 71 5.2 Genomics of lab and dairy]associated species 71 5.2.1 Next]generation sequencing of strains, dairy starter genomics and metagenomics 72 5.2.2 Pacific Bioscience single]molecule real]time sequencing technology 73 5.2.3 Illumina MySeq and HiSeq 2000 73 5.2.4 Ion Torrent platform 73 5.3 NGS platform applied to sequencing of microbial communities 74 5.3.1 Pangenomics 74 5.3.2 Omic technologies: transcriptomics, proteomics, functional genomics, systems biology 75 5.4 Metabolomics and proteomics 76 5.4.1 Subcellular localisation (SLC): secretion systems for secreted proteins 77 5.4.2 Interactome for cell adhesion and pathogen exclusion 78 5.4.3 Lab peptidome 79 5.5 Comparative genomics of dairy]associated bacteria: the lactobacillus genus complex, streptococci/lactococci, enterococci, propionibacteria and bifidobacteria 79 5.5.1 Comparative genomics of Lb. rhamnosus and Lb. casei 83 5.5.2 Lb. casei core genome and ecotype differences in dairy adapted strains 84 5.6 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in adaptive immunity 84 5.7 Regulation in carbon metabolism 85 5.7.1 Transcriptional and posttranscriptional regulation in carbon metabolism 85 5.7.2 Two]component systems and phosphorylation in sugar substrate regulation 86 5.7.3 Regulatory RNAs and alternative sigma factors in gene expression 87 5.8 Conclusions 88 References 88 6 Metabolism and biochemistry of LAB and dairy]associated species 97 Palmiro Poltronieri, Giovanna Battelli and Nicoletta Pasqualina Mangia 6.1 Introduction 97 6.2 Carbohydrate substrates, glycolysis and energy production 98 6.2.1 Pentose phosphate pathway 99 6.2.2 Citrate fermentation 99 6.3 Proteolysis, protein substrates and amino acid availability influencing gene expression 100 6.3.1 Cell]envelope proteinases: the Prt system 101 6.3.2 Oligopeptide permeases and other transporters for peptides and amino acids 101 6.3.3 Peptidolysis and free amino acids 102 6.3.4 Peptidolysis and catabolite repression 105 6.3.5 Amino acid biosynthesis and auxotrophy 105 6.4 Lipolysis, lipases, esterases 106 6.5 Aroma and flavour products of metabolism 107 6.5.1 Aldehydes, alcohols and carboxylic acids 110 6.5.2 Amino acids as precursor flavour compounds 112 6.6 Nonenzymatic production of flavours 113 6.7 Methods of analysis of flavours in dairy products: HPLC, gas chromatography/ mass analysis (GC/MS) 114 6.8 Natural biodiversity of strains in dairy productions 115 6.9 Conclusions 116 References 117 7 Growth needs and culture media for LAB and dairy]associated species 123 Giuseppe Blaiotta, Maria Aponte and Palmiro Poltronieri 7.1 Introduction 123 7.2 Established culture media for lactobacilli 123 7.2.1 Rogosa agar 124 7.2.2 MRS medium 125 7.2.3 Skim milk and whey agar 125 7.3 M17 medium for selection and enumeration of lactococci and streptococci 126 7.3.1 St. thermophilus agar 126 7.4 Selective media for lactobacilli 127 7.4.1 MRS vancomycin 127 7.4.2 Additional selective agents 128 7.4.3 MRSV plus selective agents for Lb. casei group enumeration 129 7.4.4 MRS]salicin, MRS]sorbitol, MRS]ribose, MRS gluconate agar 129 7.4.5 MRS]clindamycin]ciprofloxacin agar 129 7.4.6 MMV medium for Lb. casei group enumeration 130 7.4.7 MRS containing fructose (MRSF) 130 7.4.8 mMRS]BPB 131 7.4.9 MRS]NNLP agar and chromogenic agars for complex communities 131 7.4.10 Homofermentative]heterofermentative differential medium 131 7.5 Media for the isolation of bifidobacteria 132 7.5.1 MRS]NNLP agar 133 7.5.2 BSM, WSP, TOS]MUP 133 7.5.3 MRS]ABC 134 7.6 Phenotyping 134 7.7 Conclusions 135 References 135 8 LAB species and strain identification 139 Cinzia Randazzo, Alessandra Pino, Koenraad Van Hoorde and Cinzia Caggia 8.1 Introduction 139 8.2 Genotypic fingerprinting methods 140 8.3 Culture]dependent approaches 142 8.3.1 Random amplification of polymorphic DNA 142 8.3.2 ARDRA and RFLP 143 8.3.3 Ribotyping 143 8.3.4 Repetitive element sequence]based PCR 144 8.3.5 Amplified fragment length polymorphism 145 8.3.6 Pulsed field gel electrophoresis 145 8.4 Non]genotypic fingerprinting methods 146 8.5 Culture]independent approaches 147 8.5.1 Culture]independent methods for qualitative analysis of dairy foods microbiota 147 8.5.2 Culture]independent methods for quantitative analysis of dairy foods microbiota 150 8.6 Novel high]throughput techniques: sequencing and metagenomics 151 8.7 Conclusions 152 References 152 9 LAB strains with bacteriocin synthesis genes and their applications 161 Lorena Sacchini, Giacomo Migliorati, Elisabetta Di Giannatale, Francesco Pomilio and Franca Rossi 9.1 Introduction 161 9.2 Bacteriocins from lab 161 9.3 Potential for use of lab bacteriocins as food preservatives 164 9.4 Bacteriocins produced by dairy lab 165 9.5 Identification of lab]producing bacteriocins 168 9.6 A novel approach for screening lab bacteriocins 170 9.7 Biotechnological interventions for bacteriocin engineering 171 9.8 Conclusions 172 References 172 10 Starter strains and adjunct non]starter lactic acid bacteria (NSLAB) in dairy products 177 Paola Dolci and Luca Cocolin 10.1 Introduction 177 10.2 Controlled fermentation 177 10.2.1 Natural versus selected lactic acid bacteria starters 178 10.2.2 Starter strains: selection parameter approaches and strain concept 179 10.2.3 Starter culture formulation 180 10.3 Adjunct non]starter lactic acid bacteria 181 10.3.1 Biodiversity and adaptation to cheese environment 181 10.3.2 Prospective in industrial application 182 10.3.3 Biopreservation and health benefits 183 10.4 Conclusions 185 References 185 11 Milk Fat: stability, separation and technological transformation 191 Gianluigi Scolari 11.1 Introduction 191 11.1.1 Composition and physical state of milk fat 192 11.1.2 Melting point of milk fat 194 11.2 Physical instability of milk fat 194 11.3 Milk fat separation 195 11.3.1 Flocculation or natural creaming 195 11.3.2 Milk fat separation by centrifugation 197 11.4 Partial coalescence 199 11.4.1 General aspects 199 11.4.2 Barrier against coalescence 201 11.4.2.1 Low molecular mass surfactants 201 11.4.2.2 Large sized surfactants (casein micelle) 202 11.4.2.3 Polymeric surfactants (proteins and polysaccharides) 203 11.4.2.4 Mixed films 203 11.5 Foam in milk and cream 204 11.5.1 General aspects 204 11.5.1.1 Foam formation without surfactants 204 11.5.1.2 Foam formation with surfactants 205 11.5.1.3 Drainage of dispersion liquid in foam 206 11.5.2 Foam from cream containing more than 30% milk fat 207 11.6 Whipped cream and butter 209 11.6.1 Technological factors affecting whipped cream and butter production 209 11.7 Churning process 210 11.7.1 Type of cream 210 11.7.2 Physical (crystallization) and biological maturation of cream before churning 212 11.7.3 Churning technology 215 11.7.4 Continuous churning 216 11.7.5 Moulding and packaging 217 11.8 Conclusions 217 References 218 12 Biological traits of lactic acid bacteria: industrial relevance and new perspectives in dairy applications 219 Diego Mora, Fabio Dal Bello and Stefania Arioli 12.1 Introduction 219 12.2 Selecting fermenting bacteria for their ability to have a respiratory metabolism 220 12.3 Selecting galactose]positive yogurt cultures: working “against the natural evolution of the species” 221 12.4 Accelerating the milk acidification process by selecting proteinase]positive strains 222 12.5 Accelerating the milk acidification process by selecting urease]negative S. thermophilus strains 224 12.6 Protective cultures for dairy applications: “work but please do not grow and do not modify the sensory profile of the product” 225 12.7 Selection of starter culture free of transferable antibiotic]resistance mechanisms 227 12.8 Conclusions 228 References 229 13 Lactic acid bacteria bacteriophages in dairy products: problems and solutions 233 Giorgio Giraffa, Miriam Zago and Domenico Carminati 13.1 Introduction 233 13.2 Phage classification 234 13.3 Phage]host interactions 236 13.4 Sources of contamination 238 13.4.1 Milk and cheese whey 238 13.4.2 Dairy cultures 239 13.4.2.1 The lysogenic state 239 13.5 Phage detection and quantification 240 13.6 Methods to control phage contamination 242 13.6.1 Phage inactivation by physical treatments 242 13.6.2 Phage inactivation by chemical treatments 244 13.6.3 Phage control by biological approaches 245 13.7 Conclusions 246 14 Lactic acid bacteria: a cell factory for delivering functional biomolecules in dairy products 251 Tiziana Silvetti, Stefano Morandi and Milena Brasca 14.1 Introduction 251 14.2 Vitamins 253 14.2.1 Vitamin B2 or Riboflavin 254 14.2.2 Vitamin B9 or Folate 255 14.2.3 Vitamin B12 or cobalamin 256 14.2.4 Vitamin K: menaquinone 257 14.2.5 Other B]group vitamins 258 14.3 Minerals 258 14.4 Bioactive compounds 261 14.4.1 Anti]hypertensive peptides 262 14.4.2 Antioxidative peptides 263 14.4.3 Bioactive amines 265 14.4.4 Immune system affecting peptides 267 14.4.5 Opioid peptides 267 14.4.6 Metal]binding peptides 268 14.4.7 Conjugated linoleic acid and conjugated linolenic acid 268 14.5 Low]calorie sweeteners 269 14.6 Exopolysaccharides (EPS) 271 14.7 Conclusions 273 References 273 15 Dairy technologies in yogurt production 279 Panagiotis Sfakianakis and Constantina Tzia 15.1 Introduction 279 15.2 Yogurt types 280 15.3 Yogurt manufacturing process 281 15.3.1 Initial treatment of milk 281 15.3.2 Standardization of milk components – fat and SNF content 283 15.3.3 Homogenization 284 15.3.4 Heat treatment 286 15.3.5 Fermentation process 288 15.3.5.1 Monitoring of fermentation process – prediction of fermentation evolution 290 15.3.6 Post]fermentation processing 292 15.3.6.1 Cooling – addition of additives 292 15.3.6.2 Addition of fruit 292 15.3.6.3 Packaging 294 15.3.7 Quality control of yogurt production 294 15.4 Conclusions 295 References 295 16 Milk protein composition and sequence differences in milk and fermented dairy products affecting digestion and tolerance to dairy products 299 Maria Gabriella Giuffrida, Marzia Giribaldi, Laura Cavallarin and Palmiro Poltronieri 16.1 Introduction 299 16.2 Caseins 301 16.2.1 Gene polymorphisms in κ]casein genes 302 16.2.2 Gene polymorphisms in β]casein gene 303 16.3 Proteolytic release of bioactive peptides in fermented milk and cheese 304 16.4 Minor milk proteins 305 16.4.1 Lactoferrin 305 16.4.2 β]Lactoglobulin (β]LG) 306 16.4.3 α]Lactalbumin (α]LA) 306 16.5 Proteins with bioactive roles 307 16.6 MFGM-associated proteins 308 16.7 Cow’s milk protein allergy (CMPA) 308 16.8 Conclusions 309 References 309 Index 315