Prokaryotic Diversity: Mechanisms and Significance (Society for General Microbiology Symposia)

0521869358......Page 1
SERIES-TITLE......Page 4
TITLE......Page 5
COPYRIGHT......Page 6
CONTENTS......Page 7
CONTRIBUTORS......Page 9
EDITORS’ PREFACE......Page 13
THE CONTINUING SAGA OF THE MICROBIAL SPECIES......Page 15
MICROBIAL BIOGEOGRAPHY – DOES IT EXIST?......Page 24
HABITAT DIVERSITY......Page 26
REFERENCES......Page 27
INTRODUCTION......Page 33
Estimating microbial biodiversity......Page 34
Fundamental patterns in diversity......Page 36
ARE MICROBES TOO DIFFERENT?......Page 37
Distance-decay relationships......Page 39
Phylogenetic patterns......Page 40
Richness–area relationships......Page 42
Richness–energy relationships......Page 45
Richness–disturbance relationships......Page 46
CONCLUSIONS......Page 48
REFERENCES......Page 49
INTRODUCTION......Page 53
IDENTIFICATION, CLASSIFICATION AND EVOLUTIONARY ANALYSIS OF cas GENES......Page 54
HYPOTHESIS: CRISPR-CASS IS A PROKARYOTIC DEFENCE SYSTEM THAT FUNCTIONS ON THE RNAi PRINCIPLE......Page 64
Genes loosely associated with CASS......Page 72
IMPLICATIONS AND CONCLUSIONS......Page 74
REFERENCES......Page 76
Diversity revealed by 16S rRNA gene sequences......Page 79
Culturability, oxygen sensitivity and syntrophy......Page 81
Utilization of dietary carbohydrates......Page 84
Non-carbohydrate, and host-derived, substrates......Page 88
CONTRIBUTIONS OF DIFFERENT BACTERIAL GROUPS TO GUT METABOLISM......Page 89
SCFA metabolism......Page 90
Potential impact of pH on bacterial populations and SCFA production......Page 92
Impact of diet......Page 94
Changes with disease states......Page 95
CONCLUSIONS AND PROSPECTS......Page 96
REFERENCES......Page 97
EVOLUTIONARY EMERGENCE OF DIVERSITY......Page 105
GENETICS OF ADAPTATION......Page 106
THE EVOLUTIONARY ORIGINS OF NEW PHENOTYPES......Page 107
NETWORKS, POWER-LAW DISTRIBUTIONS AND ROBUSTNESS......Page 109
MODULARITY AND THE EVOLUTION OF PHENOTYPIC NOVELTY......Page 111
THE ORIGINS OF ROBUSTNESS AND MODULARITY......Page 112
STUDIES WITH EXPERIMENTAL PSEUDOMONAS POPULATIONS PROVIDE INSIGHT INTO THE EVOLUTION OF PHENOTYPIC NOVELTY......Page 113
CONCLUDING COMMENTS......Page 114
REFERENCES......Page 115
INTRODUCTION......Page 119
THE MINIMAL GENOME CONCEPT: BACKGROUND AND HISTORY......Page 120
Comparative genomics......Page 121
Experimental approaches......Page 124
A combined approach......Page 125
GENOME MINIMIZATION......Page 127
Experimental genome minimization......Page 128
Genome minimization in nature......Page 129
CONCLUDING REMARKS......Page 131
REFERENCES......Page 132
An inventory......Page 137
The core of universal genes......Page 138
The ever-changing core......Page 139
Antique genes: authentic or forgery?......Page 140
The phylogenetic core......Page 141
REFERENCES......Page 142
Microbial biogeography......Page 145
Bacteriophage diversity and abundance......Page 146
Rudiviruses......Page 147
Fuselloviruses......Page 148
Culture-independent surveys of virus diversity......Page 152
SUMMARY AND CONCLUDING REMARKS......Page 154
REFERENCES......Page 155
CHLAMYDIAE......Page 159
SEROLOGICAL EVIDENCE OF AN ASSOCIATION OF C. PNEUMONIAE WITH ATHEROSCLEROSIS......Page 160
EVIDENCE OF C. PNEUMONIAE IN ATHEROSCLEROTIC LESIONS......Page 161
Atherosclerosis......Page 162
In vitro studies......Page 164
Animal models of C. pneumoniae infection and atherosclerosis......Page 165
CLINICAL TRIALS......Page 168
REFERENCES......Page 169
INTRODUCTION......Page 177
THE DIVERSITY OF THE ORAL MICROFLORA......Page 178
CULTURE-INDEPENDENT ANALYSIS OF THE ORAL MICROFLORA......Page 179
PHYLOGENETIC DISTRIBUTION OF UNCULTURABLE BACTERIA......Page 180
BIASES IN MOLECULAR CHARACTERIZATION OF COMPLEX BACTERIAL COMMUNITIES......Page 184
UNCULTURABLE BACTERIA ASSOCIATED WITH ORAL DISEASE......Page 185
REFERENCES......Page 186
THE EXAMPLE OF YERSINIA PESTIS......Page 189
Comparative genomics of Y. pestis and Y. pseudotuberculosis......Page 190
Y. pestis evolved from Y. pseudotuberculosis......Page 194
IS THIS PATTERN OF EVOLUTION APPARENT WITH OTHER KEY PATHOGENS?......Page 196
REFERENCES......Page 198
COMMON FEATURES OF GENOMIC ISLANDS......Page 201
THE PARADIGM: GENOMIC ISLANDS IN THE ENTEROBACTERIACEAE......Page 202
GEIs shared by clinical and environmental isolates......Page 203
Spread of GEIs among species......Page 207
CONCLUSIONS......Page 210
REFERENCES......Page 212
INTRODUCTION......Page 215
Defining gene clusters......Page 216
Origin of gene clusters – tandem duplication and divergence......Page 217
SECONDARY METABOLISM AND ANTIBIOTIC GENE CLUSTERS......Page 219
Selective pressures favouring gene clustering......Page 222
Origin of gene clusters – HGT......Page 224
The streptomycin cluster – ecological context......Page 225
INTEGRONS: CO-ORDINATELY REGULATED MOBILE GENE CLUSTERS......Page 228
CONCLUSIONS......Page 230
REFERENCES......Page 231
INTRODUCTION......Page 237
EXTREMELY HALOPHILIC ARCHAEA......Page 238
FROM ‘SQUARE BACTERIA’ TO ‘SQUARE HALOARCHAEA’......Page 243
SALINIBACTER AND OTHER EXTREMELY HALOPHILIC BACTERIA......Page 249
MODERATELY HALOPHILIC BACTERIA......Page 251
VIRUSES......Page 254
OTHER HALOPHILIC ORGANISMS......Page 256
REFERENCES......Page 258
INTRODUCTION......Page 269
GENOMIC ISLANDS......Page 270
STRUCTURE OF GENOMIC ISLANDS......Page 271
PECULIARITIES OF THE clc ELEMENT......Page 274
clc ELEMENT EXCISION AND INTEGRATION......Page 275
GENOMIC ISLANDS STRONGLY RELATED TO THE clc ELEMENT......Page 277
PUTATIVE DNA TRANSFER FUNCTIONS OF THE clc ELEMENT......Page 280
REFERENCES......Page 282
INTRODUCTION......Page 289
THE SIGNIFICANCE OF HORIZONTAL GENE TRANSFER IN PROKARYOTIC ADAPTATION AND EVOLUTION......Page 290
TRANSFORMATION, TRANSDUCTION AND CONJUGATION: DNA ON THE MOVE......Page 292
THE MOBILE GENETIC ELEMENTS: THE MOVERS AND SHAKERS OF HORIZONTAL GENE TRANSFER......Page 295
COMPARATIVE GENOMICS, METAGENOMICS AND HORIZONTAL GENE TRANSFER......Page 298
EMERGING PHENOTYPES CONVEYED BY HORIZONTAL GENE TRANSFER......Page 300
REFERENCES......Page 303
INDEX......Page 309