لایب سان

• SIN ‏ : ‎ B08L6WPHJ7
• Publisher ‏ : ‎ CRC Press; 2nd edition (November 11, 2014)
• Publication date ‏ : ‎ November 11, 2014
• Language ‏ : ‎ English
• File size ‏ : ‎ 31428 KB
• Simultaneous device usage ‏ : ‎ Up to 4 simultaneous devices, per publisher limits
• Text-to-Speech ‏ : ‎ Not enabled
• Enhanced typesetting ‏ : ‎ Not Enabled
• X-Ray ‏ : ‎ Not Enabled
• Word Wise ‏ : ‎ Not Enabled
• Sticky notes ‏ : ‎ Not Enabled
• Print length ‏ : ‎ 300 pages

Preface...............................................................................................................xiii About the Authors............................................................................................xv Chapter 1 Laboratory animal bacteriology: The past, the present, and the future...............................................................1 1.1 Foundation of the discipline of bacteriology........................................1 1.2 The need for securing the absence of zoonoses...................................2 1.3 Eradication of bacterial pathogens.........................................................2 1.3.1 The early age of laboratory animal pathology.......................2 1.3.2 Specific pathogen-free animal breeding and health monitoring...................................................................................3 1.3.3 New agents with a research-interfering potential.................4 1.3.4 The development of health monitoring...................................4 1.4 The impact of the symbiotic microbiota................................................5 1.4.1 The development of gnotobiotechnology...............................5 1.4.2 Schaedler’s flora..........................................................................6 1.4.3 Microbiome studies....................................................................7 1.5 The future of laboratory animal bacteriology......................................8 References..........................................................................................................10 Chapter 2 Sampling animals for bacteriological examination...........15 2.1 Examining healthy animals..................................................................15 2.1.1 Sampling strategies..................................................................17 2.1.1.1 Random sampling....................................................17 2.1.1.2 Calculation of the sample size...............................17 2.1.2 Sampling frequency.................................................................19 2.1.3 Defining the microbiological entity.......................................19 2.2 Characterization of the commensal microbiota.................................20 2.3 Sampling procedures.............................................................................21 2.3.1 Planning the work....................................................................21 2.3.2 Euthanasia.................................................................................21 2.3.3 Blood sampling.........................................................................24 2.3.4 Instruments and sterilizing procedures during sampling....26 2.3.5 Opening and inspecting the carcass.....................................27 2.3.6 Sampling from various organs...............................................27 2.3.7 Sampling from diseased animals...........................................34 2.3.8 Sampling from live animals....................................................36 2.3.8.1 Sampling from the gut............................................36 2.3.8.2 Sampling from the respiratory pathways............39 References..........................................................................................................45 Chapter 3 Cultivation and identification of bacteria.............................49 3.1 The basic steps in cultivation................................................................49 3.2 The choice of media................................................................................50 3.3 Incubation of media...............................................................................51 3.4 Isolation of bacteria................................................................................52 3.5 Initial characterization of the isolates..................................................52 3.6 Conclusive identification.......................................................................55 3.6.1 Specific techniques used for identification of bacteria........59 3.6.1.1 Gram-stainability tests............................................59 3.6.1.2 Other methods used for describing the shape of bacteria.......................................................61 3.6.1.3 Motility tests.............................................................61 3.6.1.4 Test for aerobic and anaerobic growth.................62 3.6.1.5 Catalase test..............................................................62 3.6.1.6 Cytochrome oxidase test.........................................62 3.6.1.7 Acid-fast or spore staining.....................................63 3.6.1.8 Carbohydrate fermentation and utilization assays.........................................................................63 3.6.1.9 Disk methods............................................................64 3.6.1.10 Commercial test kits................................................64 3.7 Molecular biology-based methods for rapid identification of microorganisms......................................................................................67 3.7.1 Extraction of DNA....................................................................67 3.7.2 Grouping by repetitive DNA element PCR..........................67 3.7.3 Identification by ribosomal RNA gene sequencing.............68 References..........................................................................................................69 Chapter 4 Immunological methods..........................................................71 4.1 Antigens and antibodies.......................................................................71 4.2 Agglutination..........................................................................................72 4.3 Immunofluorescence techniques.........................................................73 4.3.1 Diagnosing the presence of bacteria in a sample.................73 4.3.2 The immunofluorescence assay..............................................75 4.4 Immunoenzymatic staining..................................................................77 4.5 Enzyme-linked immunosorbent assay...............................................79 4.5.1 Principles...................................................................................79 4.5.2 The microtiter plates................................................................79 4.5.3 The antigen................................................................................82 4.5.4 Antibodies, enzymes, and substrates....................................82 4.5.5 Coating the wells......................................................................84 4.5.6 Blocking the wells.....................................................................85 4.5.7 Performing the assay................................................................86 4.5.8 Control sera...............................................................................87 4.5.9 Interpretation of the OD value................................................87 4.6 Immunoblotting......................................................................................87 4.7 Multiplex..................................................................................................89 References..........................................................................................................90 Chapter 5 Molecular biology-based methods for microbiota characterization..........................................................................91 5.1 Why molecular biology-based methods?............................................91 5.2 RNA and DNA storage and extraction................................................92 5.3 Denaturing and temperature gradient gel electrophoresis..............92 5.4 Terminal restriction fragment length polymorphism analysis.......95 5.5 Clone library analysis............................................................................95 5.6 High-throughput sequencing...............................................................97 5.7 Quantitative real-time PCR...................................................................99 References........................................................................................................100 Chapter 6 Mechanisms behind bacterial impact on animal models........................................................................................103 6.1 Mechanisms of pathogenicity and research interference from specific bacteria.....................................................................................103 6.1.1 Pathogenicity versus research interference........................103 6.1.2 Epidemiological terms...........................................................104 6.1.3 Host–bacterial interaction influencing pathogenicity and research interference......................................................104 6.1.3.1 Adhesins and receptors........................................106 6.1.3.2 Toxins.......................................................................108 6.1.4 Host–environment interaction influencing pathogenicity and research interference.............................109 6.2 Mechanisms of pathogenicity and research interference from the commensal gut microbiota............................................................110 6.2.1 Host–microbial interactions within immunity...................110 6.2.1.1 Interactions within acquired immunity..............110 6.2.1.2 Interactions within innate immunity..................113 6.2.2 Host–microbial interactions within metabolism................115 References.........................................................................................................116 Chapter 7 Systematic classification of bacteria....................................127 7.1 Domains of life......................................................................................127 7.1.1 Operational taxonomic units................................................127 7.1.2 Members of the mice and rat microbiome..........................128 References........................................................................................................131 Chapter 8 Firmicutes..................................................................................133 8.1 Introduction...........................................................................................134 8.2 Streptococcaceae...................................................................................134 8.2.1 Impact on the host..................................................................136 8.2.1.1 Lancefield’s groups A, B, C, and G......................136 8.2.1.2 Streptococcus pneumoniae.......................................136 8.2.1.3 Lancefield’s group D..............................................137 8.2.1.4 Lactococcus spp........................................................137 8.2.1.5 Gemella.....................................................................137 8.2.2 Characteristics of the agent...................................................137 8.3 Enterococcaceae....................................................................................139 8.4 Aerococcaceae.......................................................................................140 8.5 Lactobacillaceae....................................................................................140 8.6 Leuconostaceae......................................................................................141 8.7 Staphylococcaceae..................................................................................141 8.7.1 Impact on the host...................................................................141 8.7.2 Characteristics of the agent....................................................141 8.8 Bacillaceae..............................................................................................144 8.8.1 Impact on the host..................................................................144 8.8.2 Characteristics of the agent...................................................144 8.9 Listeriaceae............................................................................................146 8.9.1 Impact on the host..................................................................146 8.9.2 Characteristics of the agent...................................................146 8.10 Erysipelotrichidae.................................................................................147 8.11 Clostridiaceae........................................................................................149 8.11.1 Impact on the host..................................................................149 8.11.1.1 Clostridium difficile and C. perfringens..................150 8.11.1.2 Clostridium spiroforme.............................................150 8.11.1.3 Clostridium piliforme...............................................150 8.11.1.4 Segmented filamentous bacteria (Candidatus savagella)...................................................................151 8.11.1.5 Faecalibacterium prausnitzii.....................................152 8.11.2 Characteristics of the agent...................................................153 8.11.2.1 Clostridium difficile and C. perfringens..................153 8.11.2.2 Clostridium spiroforme.............................................156 8.11.2.3 Clostridium piliforme...............................................156 8.11.2.4 Segmented filamentous bacteria (Candidatus savagella)...................................................................157 8.12 Lachnospiraceae....................................................................................158 8.13 Eubacteriaceae.......................................................................................158 8.14 Ruminococcaceae..................................................................................158 References........................................................................................................158 Chapter 9 Bacteroidetes.............................................................................167 9.1 Introduction............................................................................................167 9.2 Bacteroidales..........................................................................................168 9.2.1 Bacteroidaceae.........................................................................168 9.2.1.1 Impact on the host.................................................168 9.2.1.2 Characteristics of the agent..................................169 9.2.2 S24-7..........................................................................................169 9.2.3 Prevotellaceae..........................................................................169 9.2.3.1 Impact on the host.................................................169 9.2.3.2 Characteristics of the agent..................................170 9.2.4 Rikenellaceae...........................................................................170 9.2.5 Porphyromonadaceae............................................................170 9.3 Flavobacteriales.....................................................................................170 9.4 Sphingobacteriales................................................................................171 9.4.1 Cilia-associated respiratory bacillus....................................171 9.4.1.1 Impact on the host.................................................171 9.4.1.2 Characteristics of the agent..................................172 References........................................................................................................172 Chapter 10 Proteobacteria...........................................................................177 10.1 Gammaproteobacteria.........................................................................177 10.1.1 Enterobacteriaceae..................................................................177 10.1.1.1 Impact on the host.................................................178 10.1.1.2 Characteristics of the agent..................................180 10.1.2 Pasteurellaceae........................................................................186 10.1.2.1 Impact on the host.................................................186 10.1.2.2 Characteristics of the agent..................................188 10.1.3 Pseudomonadacea..................................................................191 10.1.3.1 Pseudomonas..........................................................191 10.1.4 Francisellaceae........................................................................192 10.1.4.1 Francisella...............................................................192 10.1.5 Aeromonadaceae, Xanthomonadaceae, Sphingomonadaceae, and Moraxcellaceae..........................194 10.2 Betaproteobacteria................................................................................195 10.2.1 Alcaligenaceae.........................................................................195 10.2.1.1 Bordetella................................................................195 10.2.2 Spirillaceae...............................................................................196 10.2.2.1 Spirillum minus........................................................196 10.3 Epsilonproteobacteria..........................................................................197 10.3.1 Campylobacteraceae...............................................................197 10.3.1.1 Campylobacter.......................................................197 10.3.2 Helicobacteraceae...................................................................199 10.3.2.1 Helicobacter............................................................199 10.3.2.2 Rabbit-associated cilia-associated respiratory bacillus................................................203 10.4 Alphaproteobacteria.............................................................................203 References........................................................................................................204 Chapter 11 Actinobacteria...........................................................................213 11.1 Introduction...........................................................................................213 11.2 Micrococcaceae.....................................................................................213 11.3 Corynebacteriaceae...............................................................................214 11.3.1 Characteristics of infection...................................................215 11.3.2 Characteristics of the agent....................................................216 11.4 Actinomycetaceae..................................................................................216 11.4.1 Actinomyces...............................................................................216 11.4.2 Arcanobacterium.......................................................................218 11.5 Mycobacteriaceae..................................................................................219 11.5.1 Characteristics of infection...................................................219 11.5.2 Characteristics of the agent...................................................219 11.6 Bifidobacteriaceae.................................................................................222 References........................................................................................................223 Chapter 12 Spirochaetae..............................................................................227 12.1 Introduction...........................................................................................227 12.2 Treponema...............................................................................................227 12.2.1 Impact on the host..................................................................227 12.2.2 Characteristics of the agent...................................................228 12.3 Brachyspira..............................................................................................229 12.4 Leptospira................................................................................................229 12.4.1 Impact on the host..................................................................229 12.4.2 Characteristics of the agent...................................................230 References........................................................................................................231 Chapter 13 Tenericutes................................................................................233 13.1 Introduction...........................................................................................233 13.2 Mycoplasma.............................................................................................233 13.2.1 Impact on the host..................................................................233 13.2.2 Characteristics of the agent...................................................235 13.3 Acholeplasma...........................................................................................238 References........................................................................................................239 Chapter 14 Verrucomicrobia, Deferribacteres, Fusobacterium, and TM7.....................................................................................243 14.1 Verrucomicrobia...................................................................................243 14.1.1 Akkermansia..............................................................................243 14.1.1.1 Impact on the host.................................................243 14.1.1.2 Characteristics of the agent..................................244 14.2 Deferribacteres......................................................................................244 14.2.1 Mucispirillum schaedleri...........................................................244 14.2.1.1 Impact on the host.................................................244 14.2.1.2 Characteristics of the agent..................................245 14.3 Fusobacteria...........................................................................................245 14.3.1 Fusobacterium necrophorum.....................................................245 14.3.1.1 Impact on the host.................................................245 14.3.1.2 Characteristics of the agent..................................246 14.3.2 Streptobacillus moniliformis......................................................247 14.3.2.1 Impact on the host.................................................247 14.3.2.2 Characteristics of the agent..................................248 14.4 Candidate phylum TM7.......................................................................248 References........................................................................................................249 Appendix A: Producers of reagents for laboratory animal bacteriology......................................................................................................253 Appendix B: Biosafety levels for microbiological laboratories.................255 References........................................................................................................260 Appendix C: Media buffers and reagents commonly applied in laboratory animal bacteriology.....................................................................261

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