Microbiology (non-medical) Books

Book SynopsisRecent years have seen extensive research in the molecular underpinnings of symbiotic plant-fungal interactions. Molecular Mycorrhizal Symbiosis is a timely collection of work that will bridge the gap between molecular biology, fungal genomics, and ecology.Table of ContentsList of contributors vii Foreword xi Preface xiii Section 1: Structure and phylogeny of mycorrhizal symbioses 1 1 Origins of the mycorrhizal symbioses 3Christine Strullu‐Derrien Paul Kenrick and Marc‐André Selosse 2 Reappraising the origin of mycorrhizas 21William R Rimington, Silvia Pressel, Katie J Field, Christine Strullu‐Derrien, Jeffrey G Duckett, and Martin I Bidartondo 3 The structure of arbuscular mycorrhizas: A cell biologist’s view 33Andrea Genre and Paola Bonfante 4 Structure and development of ectomycorrhizal roots 47Raffaella Balestrini and Ingrid Kottke 5 Structure and development of orchid mycorrhizas 63John Dearnaley, Silvia Perotto and Marc‐André Selosse Section 2: Cellular genetic and molecular mechanisms in the establishment of mycorrhizal symbioses 87 6 The evolution of the mycorrhizal lifestyles – a genomic perspective 89Annegret Kohler and Francis Martin 7 Strigolactones and lipochitooligosaccharides as molecular communication signals in the arbuscular mycorrhizal symbiosis 107Clare Gough and Guillaume Bécard 8 Calcium signaling and transcriptional regulation in arbuscular mycorrhizal symbiosis 125Leonie Luginbuehl and Giles ED Oldroyd 9 Signaling pathways driving the development of ectomycorrhizal symbiosis 141Yohann Daguerre, Jonathan M Plett, and Claire Veneault‐Fourrey Section 3: Physiology including carbon and nutrient exchange between symbionts 159 10 Carbohydrate metabolism in ectomycorrhizal symbiosis 161Uwe Nehls Arpita Das and Dimitri Neb 11 Nitrogen acquisition in ectomycorrhizal symbiosis 179Rodica Pena 12 Phosphorus metabolism and transport in arbuscular mycorrhizal symbiosis 197Katsuharu Saito and Tatsuhiro Ezawa 13 Primary metabolism in arbuscular mycorrhizal symbiosis: Carbon nitrogen and sulfur 217Michael Bitterlich Jan Graefe and Philipp Franken 14 The transportome of mycorrhizal systems 239Pierre‐Emmanuel Courty, Joan Doidy, Kevin Garcia Daniel Wipf and Sabine Dagmar Zimmermann 15 Soil organic matter decomposition mechanisms in ectomycorrhizal fungi 257Anders Tunlid, Dimitrios Floudas Roger Koide and François Rineau 16 Homeostasis of trace elements in mycorrhizal fungi 277Joske Ruytinx, Elena Martino, Piotr Rozpądek, Stefania Daghino, Katarzyna Turnau, Jan Colpaert, and Silvia Perotto Section 4: Population and community ecology and environmental genomics 299 17 Molecular identification of fungi 301Leho Tedersoo and R Henrik Nilsson 18 Molecular technologies applied to the ecology of ectomycorrhizal communities 323Marc Buée, Erwin Sentausa, and Claude Murat 19 The biogeography of ectomycorrhizal fungi – a history of life in the subterranean 341Kabir G Peay and P Brandon Matheny 20 Spatial ecology of ectomycorrhizal fungal communities 363Brian J Pickles and Ian C Anderson 21 Fungal ecology in boreal forest ecosystems 387Björn D Lindahl and Karina E Clemmensen 22 Ecology of ericoid mycorrhizal fungi: What insight have we gained with molecular tools and what’s missing? 405Gwen Grelet, Elena Martino, Ian A Dickie, Rosnida Tajuddin, and Rebekka Artz 23 Evolutionary genomics of arbuscular mycorrhizal fungi 421Rohan Riley, Philippe Charron, Timea Marton, and Nicolas Corradi 24 Mycorrhiza helper bacteria 437Aurélie Deveau and Jessy Labbé 25 Mixotrophy in mycorrhizal plants: Extracting Carbon from mycorrhizal networks 451Marc‐André Selosse, Melissa Faust Bocayuva, Maria Catarina Megumi Kasuya, and Pierre‐Emmanuel Courty 26 Second‐generation molecular understanding of mycorrhizas in soil ecosystems 473Ian A Dickie and Mark G St John Index 493

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Book SynopsisAn authoritative guide to microbiological solutions to common challenges encountered in the industrial processing of milk and the production of milk products Microbiology in Dairy Processing offers a comprehensive introduction to the most current knowledge and research in dairy technologies and lactic acid bacteria (LAB) and dairy associated species in the fermentation of dairy products. The text deals with the industrial processing of milk, the problems solved in the industry, and those still affecting the processes. The authors explore culture methods and species selective growth media, to grow, separate, and characterize LAB and dairy associated species, molecular methods for species identification and strains characterization, Next Generation Sequencing for genome characterization, comparative genomics, phenotyping, and current applications in dairy and non-dairy productions. In addition, Microbiology in Dairy Processing covers the Lactic Acid Table of ContentsList of contributors xv Foreword xix Preface xxi Acknowledgements xxiii 1 Milk fat components and milk quality 1Iolanda 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 11Sonia 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 37Milena 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 63Palmiro 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 71Palmiro 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 97Palmiro 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 123Giuseppe 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 139Cinzia 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 161Lorena 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 177Paola 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 191Gianluigi 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 219Diego 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 233Giorgio 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 251Tiziana 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 279Panagiotis 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 299Maria 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

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Book SynopsisFood is an essential means for humans and other animals to acquire the necessary elements needed for survival. However, it is also a transport vehicle for foodborne pathogens, which can pose great threats to human health. Use of antibiotics has been enhanced in the human health system; however, selective pressure among bacteria allows the development for antibiotic resistance. Foodborne Pathogens and Antibiotic Resistance bridges technological gaps, focusing on critical aspects of foodborne pathogen detection and mechanisms regulating antibiotic resistance that are relevant to human health and foodborne illnesses This groundbreaking guide: Introduces the microbial presence on variety of food items for human and animal consumption. Provides the detection strategies to screen and identify the variety of food pathogens in addition to reviews the literature. Provides microbial molecular mechanism of food spoilage along with molecular mechanism of Table of ContentsList of Contributors xiii Preface xix Introduction 1 1 Diversity of Foodborne Bacterial Pathogens and Parasites in Produce and Animal Products and Limitations of Current Detection Practices 5Debabrata Biswas and Shirley A. Micallef 1.1 Introduction 5 1.2 Common Bacterial Pathogens and Parasites Found in Produce and Animal Products 6 1.3 Unusual Bacterial Pathogens and Parasites in Produce and Animal Products 7 1.4 Farming Systems and Mixed (Integrated) Crop‐Livestock Farming 8 1.5 Major Sources of Unusual/Under‐Researched Bacterial Pathogens and Parasites in Food 10 1.6 Diversity of Farming and Processing Practices and Possible Risks 11 1.7 Current Hygienic Practices and Their Effects on These Under‐Researched Pathogens 12 1.8 Current Detection Methods and Their Limitations 13 1.9 Recommendation to Improve the Detection Level 14 1.10 Conclusion 14 References 14 2 Characterization of Foodborne Pathogens and Spoilage Bacteria in Mediterranean Fish Species and Seafood Products 21A. Bolivar, J.C.C.P. Costa, G.D. Posada‐Izquierdo, F. Pérez‐Rodríguez, I. Bascón, G. Zurera, and A. Valero 2.1 Fish Quality Assurance 21 2.2 Microbiological Standards To Be Accomplished 21 2.3 Hazard Analysis and Critical Control Points (HACCP) Implemented in the Fishery Industry 22 2.4 Microbial Ecology of Mediterranean Fishery Products 24 2.5 Fish and Seafood Spoilage: Characterization of Spoilage Microorganisms During Capture, Manufacture, and Distribution of Fishery Products 28 2.6 Foodborne Pathogens in Mediterranean Fishery Products 30 2.7 Molecular Methods for Pathogen Detection in Fishery Products 33 References 34 3 Food Spoilage by Pseudomonas spp.—An Overview 41António Raposo, Esteban Pérez, Catarina Tinoco de Faria, María Antonia Ferrús, and Conrado Carrascosa 3.1 Introduction 41 3.2 Pseudomonas spp. in Milk and Dairy Products 44 3.3 Meat Spoilage by Pseudomonas spp. 47 3.4 Fish Spoilage by Pseudomonas spp. 50 3.5 Water Contamination by Pseudomonas spp. 51 3.6 Pseudomonas spp. in Fruit and Vegetables 55 3.7 Biochemical and Molecular Techniques for Pseudomonas spp. Detection 56 3.8 Conclusions 58 References 58 4 Arcobacter spp. in Food Chain—From Culture to Omics 73Susana Ferreira, Mónica Oleastro, and Fernanda Domingues 4.1 Introduction 73 4.2 Isolation and Detection of Arcobacter 86 References 102 5 Microbial Hazards and Their Implications in the Production of Table Olives 119A. Valero, E. Medina, and F.N. Arroyo‐López 5.1 Table Olives: Origin, Production, and Main Types of Elaborations 119 5.2 Importance of Microorganisms in Table Olives 121 5.3 Molecular Methods for the Study of Microbial Populations in Table Olives 122 5.4 Biological Hazards in Table Olives 124 5.5 Use of Starter Cultures to Reduce Biological Hazards in Table Olives 126 5.6 Hazard Analysis and Critical Control Point (HACCP) System As a Useful Tool to Improve Microbial Safety and Quality of Table Olives 127 5.7 Conclusions 132 References 133 6 The Problem of Spore‐Forming Bacteria in Food Preservation and Tentative Solutions 139Stève Olugu Voundi, Maximilienne Nyegue, Blaise Pascal Bougnom, and François‐Xavier Etoa 6.1 Introduction 139 6.2 Sporulation 139 6.3 Metabolic State of the Spore 140 6.4 Spore Structure and Associated Mechanisms of Resistance 140 6.5 Germination of Spore 142 6.6 Problems of Spore‐Forming Bacteria in Food Preservation 143 6.7 Techniques of Spore Inactivation 146 References 148 7 Insights into Detection and Identification of Foodborne Pathogens 153Jodi Woan‐Fei Law, Vengadesh Letchumanan, Kok‐Gan Chan, Bey‐Hing Goh, and Learn‐Han Lee 7.1 Introduction 153 7.2 Nucleic Acid‐Based Methods 157 7.3 Conclusion 183 References 183 8 Rapid, Alternative Methods for Salmonella Detection in Food 203Anna Zadernowska and Wioleta Chajęcka‐Wierzchowska 8.1 Introduction 203 8.2 Conventional Methods and Their Modifications 203 8.3 Alternative Methods—Definitions, Requirements 205 8.4 Conclusions 208 References 208 9 CRISPR‐Mediated Bacterial Genome Editing in Food Safety and Industry 211Michael Carroll and Xiaohui Zhou 9.1 Introduction 211 9.2 Application of CRISPR for Bacterial Genome Editing 215 9.3 Vaccination of Industrial Microbes 217 9.4 Application of CRISPR in the Development of Antimicrobials 218 9.5 CRISPR Delivery Systems 220 9.6 Concluding Remarks 221 References 222 10 Meat‐borne Pathogens and Use of Natural Antimicrobials for Food Safety 225Ashim Kumar Biswas and Prabhat Kumar Mandal 10.1 Introduction 225 10.2 Incidences of Some Important Foodborne Pathogens 226 10.3 Application of Natural Antimicrobials 230 10.4 Regulatory Aspects of Natural Antimicrobials 238 10.5 Health Benefits of Natural Antimicrobials 239 10.6 Summary 239 References 239 11 Foodborne Pathogens and Their Apparent Linkage with Antibiotic Resistance 247Mariah L. Cole and Om V. Singh 11.1 Introduction 247 11.2 Food Spoilage 248 11.3 Food Processing and Microbial Contamination 254 11.4 Foodborne Pathogens and Antibiotic Resistance 255 11.5 Antibiotics and Alternatives 266 11.6 Genomics and Proteomics of Foodborne Pathogens and Antibiotic Resistance 268 11.7 Conclusion 270 References 270 12 Antimicrobial Food Additives and Disinfectants: Mode of Action and Microbial Resistance Mechanisms 275Meera Surendran Nair, Indu Upadhyaya, Mary Anne Roshni Amalaradjou, and Kumar Venkitanarayanan 12.1 Introduction 275 12.2 Food Additives 275 12.3 Mode of Action and Resistance to Antimicrobial Food Preservatives 277 12.4 Disinfectants 284 12.5 Mode of Action and Resistance to Disinfectants 285 12.6 Plant‐Derived Antimicrobials as Alternatives 289 12.7 Conclusion 291 References 291 13 Molecular Biology of Multidrug Resistance Efflux Pumps of the Major Facilitator Superfamily from Bacterial Food Pathogens 303Ranjana K.C., Ugina Shrestha, Sanath Kumar, Indrika Ranaweera, Prathusha Kakarla, Mun Mun Mukherjee, Sharla R. Barr, Alberto J. Hernandez, T. Mark Willmon, Bailey C. Benham, and Manuel F. Varela 13.1 Foodborne Bacterial Pathogens 303 13.2 Major Classes of Clinically Important Antibacterial Agents 307 13.3 Antimicrobial Agents Used in Food Animals for Treatment of Infections 307 13.4 Antimicrobial Agents Used in Food Animals for Prophylaxis 309 13.5 Antimicrobial Agents Used in Food Animals for Growth Enhancement 309 13.6 Mechanisms of Bacterial Resistance to Antimicrobial Agents 310 13.7 The Major Facilitator Superfamily of Solute Transporters 314 13.8 Key Bacterial Multidrug Efflux Pump Systems of the Major Facilitator Superfamily 314 13.9 Future Directions 318 References 319 14 Prevalence, Evolution, and Dissemination of Antibiotic Resistance in Salmonella 331Brian W. Brunelle, Bradley L. Bearson, and Heather K. Allen 14.1 Introduction 331 14.2 Antibiotic Resistance Prevalence Among Salmonella Serotypes 332 14.3 Antibiotic Treatment of Salmonella 335 14.4 Antibiotics and Resistance Mechanisms 336 14.5 Evolution and Transfer of Antibiotic Resistance 339 14.6 Co‐Localization of Resistance Genes 342 14.7 Conclusions 343 References 343 15 Antibiotic Resistance of Coagulase‐Positive and Coagulase‐Negative Staphylococci Isolated From Food 349Wioleta Chajęcka‐Wierzchowska and Anna Zadernowska 15.1 Characteristics of the Genus Staphylococcus 349 15.2 Coagulase‐Positive Staphylococci 349 15.3 Coagulase‐Negative Staphylococci 350 15.4 Genetic Mechanisms Conditioning Antibiotic Resistance of Staphylococci 350 15.5 Food as a Source of Antibiotic‐Resistant Staphylococci 355 15.6 Summary 359 References 359 16 Antibiotic Resistance in Enterococcus spp. Friend or Foe? 365Vangelis Economou, Hercules Sakkas, Georgios Delis, and Panagiota Gousia 16.1 Introduction 365 16.2 Enterococcus Biology 365 16.3 Enterococcus as a Probiotic 366 16.4 Enterococcus in Food 367 16.5 Antibiotic Resistance 369 16.6 Enterococcus Infection 377 16.7 Enterococcus Epidemiology 380 References 382 17 Antibiotic Resistance in Seafood‐Borne Pathogens 397Sanath Kumar, Manjusha Lekshmi, Ammini Parvathi, Binaya Bhusan Nayak, and Manuel F. Varela 17.1 Human Pathogenic Bacteria in Seafood 397 17.2 An Overview of Bacterial Antimicrobial Resistance Mechanisms 401 17.3 Antibiotic‐Resistant Bacteria in the Aquatic Environment 402 17.4 Antimicrobial Resistance in Seafood‐Borne Pathogens 403 17.5 Antimicrobials in Aquaculture and their Human Health Consequences 407 17.6 Future Directions 410 References 410 18 Antimicrobial Resistance of Campylobacter sp. 417Tareq M. Osaili and Akram R. Alaboudi 18.1 Introduction 417 18.2 Antimicrobial Resistance 418 18.3 Consequences of Foodborne Antimicrobial Resistance on Humans 419 18.4 Antimicrobial Resistance Mechanisms 419 18.5 Antimicrobial Susceptibility Testing of Campylobacter 420 18.6 Campylobacter Antimicrobials Resistance: Global Overview 421 18.7 Antimicrobial Resistance of Campylobacter Isolates From the Middle East Region 423 18.8 Strategies to Prevent Future Emergences of Bacterial Resistance 423 References 425 19 Prevalence and Antibiogram of Pathogenic Foodborne Escherichia coli and Salmonella spp. in Developing African Countries 431Adeyanju Gladys Taiwo (DVM, MVPH) 19.1 Introduction 431 19.2 Factors that Play a Role in the Epidemiology of Foodborne Diseases 432 19.3 Food Poisoning and Food Vending 433 19.4 Foodborne Colibacillosis and Salmonellosis 434 19.5 Antibiotic Resistance 435 19.6 Reasons for Resistance Against Specific Antibiotics 436 19.7 Antibiotic Resistance of Salmonella 436 19.8 Antibiotic Resistance of Escherichia coli 437 19.9 How to Combat Foodborne Diseases And Antibiotic Resistance 437 References 437 20 Evolution and Prevalence of Multidrug Resistance Among Foodborne Pathogens 441Sinosh Skariyachan, Anagha S. Setlur, and Sujay Y. Naik 20.1 Introduction 441 20.2 Major Causes of the Evolution of Bacterial Drug Resistances 441 20.3 Food Poisoning and Foodborne Illness—An Overview 443 20.4 Factors that Influence the Growth of Foodborne Pathogens in Food Products 444 20.5 Food Poisoning and Foodborne Infections 445 20.6 An Illustration of Major Foodborne Gastroenteritis 446 20.7 Major Types of Antibiotics Used to Treat Foodborne Infections 448 20.8 Mechanisms of Evolution of Antibiotic Resistance in Food Products 449 20.9 Evolution of XDR and PDR Bacteria 456 20.10 Need for Caution and WHO/FDA Stands Toward the Development of MDR Pathogens in Foods 457 20.11 Possible Solutions and Recommendations for Prevention 458 20.12 Conclusion 458 References 458 Index 465

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Book SynopsisTable of Contents1 Scope and History of Microbiology 1 Why Study Microbiology? 2 Scope of Microbiology 4 Historical Roots 9 The Germ Theory of Disease 11 Emergence of Special Fields of Microbiology 15 Tomorrow’s History 19 2 the Microbiome 25 Introduction to the Microbiome 26 Fat or Lean 26 Diversity of Microbiomes 27 3 Fundamentals of Chemistry 31 Why Study Chemistry? 32 Chemical Building Blocks and Chemical Bonds 32 Water and Solutions 36 Complex Organic Molecules 40 4 Microscopy and Staining 53 Historical Microscopy 54 Principles of Microscopy 54 Light Microscopy 60 Electron Microscopy 64 Techniques of Light Microscopy 70 5 Characteristics of Prokaryotic and Eukaryotic Cells 77 Basic Cell Types 78 Prokaryotic Cells 78 Eukaryotic Cells 97 Evolution by Endosymbiosis 103 The Movement of Substances across Membranes 105 6 Essential Concepts of Metabolism 113 Metabolism: An Overview 114 Enzymes 116 Enzyme Inhibition 118 Anaerobic Metabolism: Glycolysis and Fermentation 122 Aerobic Metabolism: Respiration 126 The Metabolism of Fats and Proteins 132 Other Metabolic Processes 133 The Uses of Energy 136 7 Growth and Culturing of Bacteria 142 Growth and Cell Division 143 Factors Affecting Bacterial Growth 152 Sporulation 161 Culturing Bacteria 163 Living, But Nonculturable, Organisms 170 8 Microbial Genetics 173 An Overview of Genetic Processes 174 DNA Replication 178 Protein Synthesis 179 The Regulation of Metabolism 187 Mutations 191 9 Gene Transfer and Genetic Engineering 205 The Types and Significance of Gene Transfer 206 Transformation 206 Transduction 208 Conjugation 212 Gene Transfer Mechanisms Compared 216 Plasmids 216 Genetic Engineering 220 10 An Introduction to Taxonomy: The Bacteria 232 Taxonomy: The Science of Classification 233 Using A Taxonomic Key 235 The Five-Kingdom Classification System 236 The Three-Domain Classification System 240 Classification of Viruses 244 The Search for Evolutionary Relationships 246 Bacterial Taxonomy and Nomenclature 249 11 Viruses 258 General Characteristics of Viruses 260 Classification of Viruses 263 Emerging Viruses 271 Viral Replication 274 Culturing of Animal Viruses 285 Viruses and Teratogenesis 287 Viruslike Agents: Satellites, Virophages, Viroids, and Prions 288 Viruses and Cancer 292 Human Cancer Viruses 292 12 Eukaryotic Microorganisms and Parasites 297 Principles of Parasitology 298 Protists 300 Fungi 307 Helminths 315 Arthropods 323 13 Sterilization and Disinfection 329 Principles of Sterilization and Disinfection 330 Chemical Antimicrobial Agents 331 Physical Antimicrobial Agents 341 14 Antimicrobial Therapy 353 Antimicrobial Chemotherapy 354 The History of Chemotherapy 355 General Properties of Antimicrobial Agents 356 Determining Microbial Sensitivities to Antimicrobial Agents 364 Attributes of An Ideal Antimicrobial Agent 367 Antibacterial Agents 367 Antifungal Agents 373 Antiviral Agents 376 Antiprotozoan Agents 378 Antihelminthic Agents 379 Special Problems with Drug-Resistant Hospital Infections 379 15 Host-Microbe Relationships and Disease Processes 385 Host–Microbe Relationships 386 Koch’s Postulates 391 Kinds of Diseases 392 The Disease Process 393 Infectious Diseases—Past, Present, and Future 405 16 Epidemiology and Nosocomial Infections 409 Epidemiology 410 Nosocomial Infections 431 Bioterrorism 439 17 Innate Host Defenses 445 Innate and Adaptive Host Defenses 446 Physical Barriers 446 Chemical Barriers 447 Cellular Defenses 447 Inflammation 456 Fever 458 Molecular Defenses 459 Development of the Immune System: Who Has One? 465 18 Basic Principles of Adaptive Immunity and Immunization 469 Immunology and Immunity 470 Types of Immunity 470 Characteristics of the Immune System 472 Humoral Immunity 478 Monoclonal Antibodies 484 Cell-Mediated Immunity 486 Mucosal Immune System 490 Immunization 492 Immunity to Various Kinds of Pathogens 501 19 Immune Disorders 508 Overview of Immunological Disorders 509 Immediate (Type I) Hypersensitivity 510 Cytotoxic (Type II) Hypersensitivity 514 Immune Complex (Type III) Hypersensitivity 518 Cell-Mediated (Type IV) Hypersensitivity 521 Autoimmune Disorders 523 Transplantation 527 Drug Reactions 530 Immunodeficiency Diseases 531 Immunological Tests 540 20 Diseases of the Skin and Eyes; Wounds and Bites 551 The Skin, Mucous Membranes, and Eyes 552 Diseases of the Skin 555 Diseases of the Eyes 569 Wounds and Bites 573 21 Urogenital and Sexually Transmitted Diseases 581 Components of the Urogenital System 582 Urogenital Diseases Usually Not Transmitted Sexually 585 Sexually Transmitted Diseases 591 22 Diseases of the Respiratory System 613 Components of the Respiratory System 614 Diseases of the Upper Respiratory Tract 617 Diseases of the Lower Respiratory Tract 624 23 Oral and Gastrointestinal Diseases 650 Components of the Digestive System 651 Diseases of the Oral Cavity 653 Gastrointestinal Diseases Caused By Bacteria 658 Gastrointestinal Diseases Caused By Other Pathogens 669 24 Cardiovascular, Lymphatic, and Systemic Diseases 690 The Cardiovascular System 691 Cardiovascular and Lymphatic Diseases 692 Systemic Diseases 697 25 Diseases of the Nervous System 727 Components of the Nervous System 728 Diseases of the Brain and Meninges 728 Other Diseases of the Nervous System 737 26 Environmental Microbiology 754 Fundamentals of Ecology 755 Biogeochemical Cycles 755 Air 765 Soil 766 Water 770 Marine Environments 771 Sewage Treatment 778 Bioremediation 780 27 Applied Microbiology 785 Microorganisms Found in Food 786 Preventing Disease Transmission and Food Spoilage 793 Microorganisms as Food and in Food Production 799 Beer, Wine, and Spirits 804 Industrial and Pharmaceutical Microbiology 806 Useful Organic Products 808 Microbiological Mining 811 Microbiological Waste Disposal 812 Appendices A Metric System Measurements, Conversions, and Math Tools A-1 B Classification of Viruses B-1 C Word Roots Commonly Encountered in Microbiology C-1 D Safety Precautions in the Handling of Clinical Specimens D-1 E Metabolic Pathways E-1 F Diseases and the Organisms That Cause Them* G Pathogens and the Diseases They Cause* H parasites* Glossary G-1 Index I-1 *Appendices F through H can be found at the web site, www.wiley.com/college/black, and in WileyPLUS

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Book SynopsisLactic Acid Bacteria Biodiversity and Taxonomy Lactic Acid BacteriaBiodiversity and Taxonomy Edited by Wilhelm H. Holzapfel and Brian J.B. Wood The lactic acid bacteria (LAB) are a group of related microorganisms that are enormously important in the food and beverage industries. Generally regarded as safe for human consumption (and, in the case of probiotics, positively beneficial to human health), the LAB have been used for centuries, and continue to be used worldwide on an industrial scale, in food fermentation processes, including yoghurt, cheeses, fermented meats and vegetables, where they ferment carbohydrates in the foods, producing lactic acid and creating an environment unsuitable for the survival of food spoilage organisms and pathogens. The shelf life of the product is thereby extended, but of course these foods are also enjoyed around the world for their organoleptic qualities. They are also important to the brewing and winemaking industries, whTrade Review"the current book is a very useful benchmark 'comprising well-crafted overviews of current developments' in lactic acid bacterial biodiversity and taxonomy." (Beneficial Microbes 2016)Table of ContentsList of contributors xiii Acknowledgements xv List of abbreviations xvi Abbreviations for genera and note on pronunciations xix 1 Introduction to the LAB 1 Wilhelm H. Holzapfel and Brian J.B. Wood 1.1 The scope 1 1.2 A little history 7 1.3 Where are the boundaries? 9 2 Physiology of the LAB 13 Akihito Endo and Leon M.T. Dicks 2.1 Metabolism 13 2.2 Energy transduction and solute transport 20 3 Phylogenetics and systematics 31 Peter Vandamme, Katrien De Bruyne and Bruno Pot 3.1 Introduction 31 3.2 Phylogeny and polyphasic taxonomy of LAB 34 3.3 Conclusions and perspectives 39 4 Overview of the ecology and biodiversity of the LAB 45 Giorgio Giraffa 4.1 Introduction 45 4.2 LAB ecology, diversity and metabolism 45 4.3 Importance of LAB in food and feed ecology and biotechnology 46 4.4 LAB as functional cultures 48 4.5 LAB with health-promoting properties 50 4.6 Concluding remarks 51 5 Comparative genomics of Lactobacillus and other LAB 55 Trudy M. Wassenaar and Oksana Lukjancenko 5.1 Introduction 55 5.2 Selection of LAB genomes for comparative analysis 57 5.3 Numerical comparisons of the selected genomes 58 5.4 Phylogeny of the 16S rRNA gene extracted from the genomes 63 5.5 Pan-genome and core genome of protein genes 63 5.6 Comparison of gene function categories 66 5.7 Conclusions 68 Section I The family Aerococcaceae 71 Paul A. Lawson 6 The genus Abiotrophia 75 Paul A. Lawson 6.1 Introduction and historical background 75 6.2 Description of the genus Abiotrophia 76 6.3 Differentiation of Abiotrophia species from other genera 76 6.4 Isolation, cultivation, ecology and medical importance 76 6.5 Species descriptions 78 7 The genus Aerococcus 81 Paul A. Lawson 7.1 Introduction and historical background 81 7.2 Description of the genus Aerococccus 81 7.3 Differentiation of Aerococcus species from other genera 82 7.4 Differentiation of species of the genus Aerococcus from one another 83 7.5 Isolation, cultivation, ecology and medical importance 84 7.6 Species descriptions 86 8 The genus Facklamia 91 Lesley Hoyles 8.1 Introduction 91 8.2 Differentiation of Facklamia species from other genera 91 8.3 Ecological, medical and industrial relevance of Facklamia species 92 8.4 Antimicrobial susceptibilities of members of the genus Facklamia 94 8.5 Differentiation between species of the genus Facklamia 95 8.6 Descriptions of the genus Facklamia and its species 95 9 Minor genera of the Aerococcaceae (Dolosicoccus, Eremococcus, Globicatella, Ignavigranum) 99 Melanie Huch, Cho Gyu-Sung, Antonio Gálvez and Charles M.A.P. Franz 9.1 Historical background 99 9.2 Phenotypic differentiation of the minor genera of the Aerococcaceae from other genera 100 9.3 Genotypic delineation of the minor genera of the Aerococcaceae 101 9.4 Isolation, cultivation, ecology and medical importance 102 9.5 Description of the minor genera of the Aerococcaceae and list of species 102 Section II The family Carnobacteriaceae 107 Elena V. Pikuta 10 The genus Carnobacterium 109 Elena V. Pikuta and Richard B. Hoover 10.1 Historical background and chronology of nomenclature 109 10.2 Definition of the genus Carnobacterium 110 10.3 Relationship to other groups 111 10.4 Future perspectives for characterization 112 10.5 Techniques and growth requirements for cultivation 112 10.6 Biodiversity 112 10.7 Importance of the genus and particular species 113 10.8 Other applications and future perspectives 115 10.9 Description of species 115 11 The genus Marinilactibacillus 125 Morio Ishikawa and Kazuhide Yamasato 11.1 Introduction 125 11.2 General and taxonomic characters 125 11.3 Phylogenetic affiliation of Marinilactibacillus species 126 11.4 Physiological properties 127 11.5 Differentiation of Marinilactibacillus from other related species 127 11.6 Lactic acid fermentation and aerobic metabolism of glucose 127 11.7 Ecology and isolation methods 129 11.8 Description of the species of the genus Marinilactibacillus 132 12 The genus Trichococcus 135 Elena V. Pikuta and Richard B. Hoover 12.1 Historical background and chronology of nomenclature for the Trichococcus species 135 12.2 Definition of the genus Trichococcus 136 12.3 Relationship to other genera within the Carnobacteriaceae and other LAB families 136 12.4 Future taxonomic perspectives 139 12.5 Techniques and growth requirements for cultivation of Trichococcus species 139 12.6 Biodiversity 139 12.7 Importance of the genus and particular species 140 12.8 Species descriptions 141 13 The genus Alkalibacterium 147 Isao Yumoto, Kikue Hirota and Kenji Nakajima 13.1 Introduction 147 13.2 Taxonomy 148 13.3 Description of the genus 148 13.4 Enrichment and isolation procedures 148 13.5 Natural habitats 149 13.6 Acid production 150 13.7 Identification of Alkalibacterium species 150 13.8 Overview of the current situation for this genus 150 13.9 Description of species 153 13.10 Concluding remarks 156 14 Minor genera of the Carnobacteriaceae: Allofustis, Alloiococcus, Atopobacter, Atopococcus, Atopostipes, Bavariicoccus, Desemzia, Dolosigranulum, Granulicatella, Isobaculum and Lacticigenium 159 Ulrich Schillinger and Akihito Endo 14.1 Introduction 159 14.2 Taxonomy 159 14.3 Biodiversity of each genus 162 14.4 Practical importance 163 14.5 Species descriptions 164 Section III The family Enterococcaceae 171 Pavel Švec and Charles M.A.P. Franz 15 The genus Enterococcus 175 Pavel Švec and Charles M.A.P. Franz 15.1 Historical background and chronology of nomenclature 175 15.2 Phenotypic differentiation of the genus Enterococcus 178 15.3 Genotypic delineation of the genus Enterococcus 178 15.4 Phylogenetic structure within the genus Enterococcus 179 15.5 Isolation and cultivation 179 15.6 Identification of Enterococcus spp. 179 15.7 Importance of the genus and particular species 182 15.8 Species of the genus Enterococcus 186 16 The genus Tetragenococcus 213 Annelies Justè, Bart Lievens, Hans Rediers and Kris A. Willems 16.1 Introduction 213 16.2 Phenotypic characteristics of the genus Tetragenococcus 215 16.3 Genotypic characteristics of the genus Tetragenococcus 217 16.4 Industrial relevance of the genus Tetragenococcus 221 16.5 Description of species 222 17 The genus Vagococcus 229 Paul A. Lawson 17.1 Introduction and historical background 229 17.2 Description of the genus Vagococcus 229 17.3 Differentiation of Vagococcus species from other genera 230 17.4 Differentiation of species of the genus Vagococcus from one another 231 17.5 Isolation, cultivation, ecology and medical importance 231 17.6 Species descriptions 232 18 Minor genera of the Enterococcaceae (Catellicoccus, Melissococcus and Pilibacter) 239 Leon M.T. Dicks, Akihito Endo and Carol A. Van Reenen 18.1 Introduction 239 18.2 Phylogeny 239 18.3 Morphology 240 18.4 Growth characteristics 240 18.5 Practical importance 241 18.6 Description of species 241 Section IV The family Lactobacillaceae 245 Giovanna E. Felis and Bruno Pot 19 The genus Lactobacillus 249 Bruno Pot, Giovanna E. Felis, Katrien De Bruyne, Effie Tsakalidou, Konstantinos Papadimitriou, Jørgen Leisner and Peter Vandamme 19.1 Historical background 249 19.2 Lactobacillus metabolism 250 19.3 The taxonomy of the genus Lactobacillus 282 19.4 The current phylogenetic structure of the genus Lactobacillus 286 19.5 Food and health applications of the genus Lactobacillus 293 19.6 Short descriptions of the validly published species of the genus Lactobacillus 294 19.7 Lactobacillus species awaiting validation pending publication of the manuscript (March 2013) 327 19.8 Lactobacillus species and subspecies that have been renamed after their original description 329 19.9 Lactobacillus species that have never been validly named, but whose names nonetheless appear in the literature, and their current names 335 20 The genus Paralactobacillus 355 Jørgen J. Leisner and Bruno Pot 20.1 Introduction 355 20.2 Defining the genus as phenotype and genotype 355 20.3 Biodiversity within the genus and species based on phenotype 356 20.4 Importance of the genus and particular species 356 20.5 Description of species 357 21 The genus Pediococcus 359 Charles M.A.P. Franz, Akihito Endo, Hikmate Abriouel, Carol A. Van Reenen, Antonio Gálvez and Leon M.T. Dicks 21.1 Historical background and chronology of nomenclature 359 21.2 Phenotypic differentiation of the genus Pediococcus 360 21.3 Genotypic delineation of the genus Pediococcus 360 21.4 Phylogenetic structure within the genus Pediococcus 361 21.5 Isolation and cultivation 362 21.6 Identification of Pediococcus spp 362 21.7 Importance of the genus and particular species 365 21.8 Species of the genus Pediococcus 366 Section V The family Leuconostocaceae 377 Akihito Endo, Leon M.T. Dicks, Johanna Björkroth and Wilhelm H. Holzapfel 22 The genus Fructobacillus 381 Akihito Endo and Leon M.T. Dicks 22.1 Introduction 381 22.2 Phylogenetic relationships 381 22.3 Morphology 383 22.4 Biochemical characteristics 383 22.5 Physiological characteristics 386 22.6 Habitat 386 22.7 Species in the genus Fructobacillus 386 23 The genus Leuconostoc 391 Johanna Björkroth, Leon M.T. Dicks, Akihito Endo and Wilhelm H. Holzapfel 23.1 Historical background, chronology of nomenclature and relationship to other LAB 391 23.2 Definition of the genus as phenotype 392 23.3 Biodiversity within the genus based on phenotype 393 23.4 Genomic studies and genotyping of Leuconostoc 393 23.5 Importance of the genus and particular Leuconostoc species 394 23.6 Description of species of the genus Leuconostoc 395 24 The genus Oenococcus 405 Akihito Endo and Leon M.T. Dicks 24.1 Introduction 405 24.2 Phylogeny and evolution 405 24.3 Morphology 406 24.4 Growth characteristics 407 24.5 Intraspecies diversity 409 24.6 Practical importance 410 24.7 Stress response 410 24.8 Description of species in the genus Oenococcus 412 25 The genus Weissella 417 Johanna Björkroth, Leon M.T. Dicks and Akihito Endo 25.1 Historical background, chronology of nomenclature and relationship to other LAB 417 25.2 Defining the genus as phenotype and genotype 417 25.3 Biodiversity within the genus and within particular species based on phenotype 419 25.4 Importance of the genus and particular species 419 25.5 Descriptions of species in the genus Weisella 421 26 The genus Lactococcus 42 Wonyong Kim 26.1 Introduction 429 26.2 Defining the genus as phenotype and genotype 429 26.3 Biodiversity within the genus based on phenotype 433 26.4 Biodiversity within species based on phenotype 434 26.5 Importance of the genus Lactococcus and species 436 26.6 Description of species of the genus Lactococcus 437 Section VI The family Streptococcaceae 445 Maret du Toit, Melanie Huch, Gyu-Sung Cho and Charles M.A.P. Franz 27 The genus Lactovum 447 Harold L. Drake 27.1 Introduction 447 27.2 Phylogeny and taxonomy of Lactovum 447 27.3 Morphology of Lactovum 448 27.4 Soil: the origin of Lactovum 449 27.5 Growth properties and substrate range of Lactovum 449 27.6 Physiology of Lactovum 451 27.7 Genus description 452 27.8 Conclusion 453 28 The genus Streptococcus 457 Maret du Toit, Melanie Huch, Gyu-Sung Cho and Charles M.A.P. Franz 28.1 Historical background and chronology of nomenclature 457 28.2 Phenotypic differentiation of the genus Streptococcus 458 28.3 Genotypic delineation of the genus Streptococcus 458 28.4 Phylogenetic structure within the genus Streptococcus 459 28.5 Isolation and cultivation 465 28.6 Identification of Streptococcus spp. 466 28.7 Importance of the genus and particular species 475 28.8 Species of the genus Streptococcus 476 Section VII Physiologically ‘related’ genera 507 Wilhelm H. Holzapfel and Brian J.B. Wood 29 The genera Bifidobacterium, Parascardovia and Scardovia 509 Paola Mattarelli and Bruno Biavati 29.1 Historical background 509 29.2 Taxonomy of the bifidobacteria 514 29.3 Ecology 521 29.4 Health benefits 522 29.5 Industrial applications 523 29.6 Other applications 523 29.7 Description of species 524 29.8 Bifidobacterium: concluding remarks 534 29.9 The genera Parascardovia and Scardovia 534 30 The genus Sporolactobacillus 543 Stephanie Doores 30.1 Introduction 543 30.2 Defining the genus as phenotype and genotype 544 30.3 Importance of the genus and particular species 547 30.4 Description of species of the genus Sporolactobacillus 548 31 The genera Bacillus, Geobacillus and Halobacillus 555 Hikmate Abriouel, Nabil Benomar, Melanie Huch, Charles M.A.P. Franz and Antonio Gálvez 31.1 Introduction 555 31.2 The genus Bacillus 556 31.3 Related genera in the family Bacillaceae 563 31.4 Food, health and environmental applications 564 31.5 Concluding remarks 565 32 The genera Halolactibacillus and Paraliobacillus 571 Kazuhide Yamasato and Morio Ishikawa 32.1 Introduction 571 32.2 The genus Halolactibacillus 571 32.3 Paraliobacillus ryukyuensis 578 Appendix: Guidelines for characterizing LAB, bifidobacteria and related genera for taxonomic purposes 583 Paola Mattarelli, Bruno Biavati, Walter Hammes and Wilhelm H. Holzapfel A.1 Introduction 583 A.2 Phenotypic criteria 584 A.3 Genotypic criteria 588 A.4 Additional criteria 589 A.5 Concluding remarks 591 Index 593

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Book SynopsisFrom the Directors of the Award-Winning Documentary Microbirth At least two amazing events happen during childbirth. There’s the obvious main event, which is the emergence of a new human into the world. But there’s another event taking place simultaneously, a crucial event that is not visible to the naked eye, an event that could determine the lifelong health of the baby. This is the seeding of the baby’s microbiome, the community of “good” bacteria that we carry with us throughout our lives. The seeding of the microbiome, along with breastfeeding and skin-to-skin contact, kick-starts the baby’s immune system and helps protect the infant from disease across a lifetime. Researchers are discovering, however, that interventions such as the use of synthetic oxytocin, antibiotics, C-sections, and formula feeding interfere with, or bypass completely, the microbial transfer from mother to baby. These bacteria are vital for human health, and science has linked an imbalance in the human microbiome with multiple chronic diseases. Drawing on the extensive research they carried out for their documentary film Microbirth, authors Toni Harman and Alex Wakeford reveal a fascinating new view of birth and how microscopic happenings can have lifelong consequences, for ourselves, our children—and our species as a whole.Trade ReviewPublishers Weekly- Filmmaker couple Harman and Wakeford, who made the documentary Microbirth, share important information about infant health and the microbiome that they’ve learned from the “A-team of experts” interviewed for their movie. Each chapter title takes the form of a question, such as “What is the Human Microbiome?” and “What Do Bacteria Have to Do with Birth?” The human microbiome, the authors explain in the introduction, consists of the trillions of microorganisms (mostly bacteria) that live on and in the body, and its most critical period of formation is around childbirth. Chapter one further addresses where these bacteria reside and what they do, as well as their relationship with antibiotics. Subsequent chapters reveal that during vaginal birth, the baby is exposed to many beneficial microbes, that formula lacks key microbe-related ingredients in breast milk, and that babies born via C-section are often not exposed to the mother’s vaginal or intestinal microbes. Harman and Wakeford also delve into epigenetics, bacteria’s role in the immune system, and options for mothers who can’t breastfeed or have vaginal deliveries. This is a no-frills, easily comprehensible book that conveys the essentials of Harman and Wakeford’s research into childbirth.“You thought you were human. But you’re actually a multi-species ecosystem. We all cohabitate with bacteria, fungi, protists, and even microscopic animals, and scientists are discovering that the way we treat the microbial companions that live in us and on us has a lasting impact on our health. Exploring what we know about the role symbionts play in childbirth and the early days of a baby’s life, Your Baby’s Microbiome is a fascinating read for anyone interested in what it means to be human.”--Jennifer Margulis, PhD, award-winning journalist; author of Your Baby, Your Way; coauthor, with Paul Thomas, MD, of the bestselling The Vaccine-Friendly Plan“For expectant families, this is the must-read book of this generation. As an advocate for parents, focusing on how the maternal environment changes the long-term health outcomes for the baby, this book is adding a critical piece to the puzzle of health for our children. The ‘seeding and feeding’ of a child’s microbiome could potentially be one of the most important lessons for parents. This timely information should be included as part of every childbirth education and newborn care class. Your Baby’s Microbiome will help parents truly make informed decisions about how and where they give birth and how they feed and care for their baby. It is a must for every woman giving birth."--Laurel Wilson, IBCLC, CLE, CLD, CCCE, coauthor of The Attachment Pregnancy“A real life sci-fi with implications that touch each one of us and all future generations. My eyes opened wide at Toni Harman and Alex Wakeford’s documentary MicroBirth, and now their book invites you deeper into understanding the problem, the science, and the solutions calling us into action. “Your Baby’s Microbiome is essential reading for every expectant parent, grandparent, and anyone who works with or cares about childbirth, and the health and well-being of the next generations. It opens the door to what our intuition already knows—that disturbing nature’s well-orchestrated design in childbirth has short- and long-range health risks. You can make a difference and turn this potential health disaster around. Knowledge is power, and Toni and Alex have put the power into your hands. “It’s time to listen to Mother Nature and question whether we’ve strayed too far from our instincts and nature. In an effort to improve maternity care, we have tipped the scales too far and need to find balance again. The stakes are too high to ignore the science, wisdom, and intuition that Your Baby’s Microbiome shows us. Nature has a plan and disturbing it with overuse of surgery should be done with the greatest caution. When Cesarean section is needed, it must include care to seed a baby’s microbiome. “This book will give you the tools and insights to make sure you are prepared to provide a healthy microbiome in every situation to every baby. Written with great care and compassion, there is no need to feel guilty for what we have done in the past, but now that we know more, it’s time to change! “Your Baby’s Microbiome is a unique blend of text and film clips that takes you on a journey into the future of health, understanding that the day and way we are born does make a difference! You deserve to prepare to give birth to your baby with knowledge, power, and understanding of how birth choices and the care you receive matter on your baby’s short- and long-term health and well-being. I recommend Your Baby’s Microbiome to all who care about our future health.”--Debra Pascali-Bonaro, founder and president, Pain to Power; director of the award-winning documentary Orgasmic Birth: The Best-Kept Secret; cowriter of Orgasmic Birth: Your Guide to a Safe, Satisfying, and Pleasurable Birth Experience“Only in recent years has the ‘microbiome’ of the baby come to the attention of the obstetric and birthing communities. I believe that midwives and birth activists have come to be much more aware of its importance than doctors themselves because to acknowledge the essential need for the baby’s body to be colonized with its mother’s microflora rather than that of strangers entails making all efforts possible to avoid Cesarean section and to facilitate normal vaginal birth, immediate skin-to-skin contact of mother and newborn, and breastfeeding. While obstetricians have certainly come in recent decades to understand the importance of breastfeeding, they continue to perform Cesareans on 32 percent of American birthing women and appear to be making no efforts to reduce that extremely high rate. I believe that if parents come to understand the findings presented in this excellent and informative book, they themselves will make greater efforts to achieve vaginal birth and to insist on the mother’s hands to be the first to touch the newborn in order to bring him or her straight to the breast—or, even better, to allow the baby the chance to inch its own way up the mother’s body, thereby empowering itself at the very beginning of life and colonizing with her microflora all the way. I hope this extremely useful and informative book will be widely distributed and widely read, and that its findings will change birthing practice in this country and around the world!”--Robbie Davis-Floyd PhD, senior research fellow, Department of Anthropology, University of Texas Austin; author of Birth as an American Rite of Passage; lead editor of Birth Models That Work“Our expanding understanding of the roles of the microbiome and epigenetics in health and disease is profoundly changing maternity care and public health for the better. The conversational style and clear explanations in Your Baby’s Microbiome by some of the world’s leading scientists and maternity care providers make this new and complex information accessible and inspiring to the general public. We now know ways to support the role of healthy microbes in our bodies and in our environment to improve our lifelong health and well-being.”--Penny Simkin, author, doula, and birth educator“Toni Harman and Alex Wakeford shine the brightest of spotlights on the importance of birth and early infancy. Your Baby’s Microbiome is compelling and informative—a must read for parents-to-be.”--Dr. Rodney Dietert, professor of immunotoxicology, Cornell University; author of The Human Superorganism“How we give birth and feed our babies should be choices, not something for which we should have to fight for support. A huge ‘thank you’ to Toni Harman and Alex Wakeford for adding to a critical perspective on the individual and global impacts of some of those choices, in hopes that this conversation will keep going—pushing our maternity care systems to support physiological processes, as well as medicalized ones.”--Cristen Pascucci, founder, Birth Monopoly; cocreator, Exposing the Silence Project; vice president, Improving Birth (2012–2016)

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