Note: Intro -- BERGEY'S MANUAL® OFSystematic Bacteriology -- Preface to Volume Two of the Second Edition of Bergey's Manual® of Systematic Bacteriology -- Preface to the First Edition of Bergey's Manual® ofSystematic Bacteriology -- Preface to the First Edition of Bergey's Manual® of Determinative Bacteriology -- Contents -- Contributors -- Class I. Alphaproteobacteria class. nov. -- Class II. Betaproteobacteria class. nov. -- Class IV. Deltaproteobacteria class nov. -- Class V. Epsilonproteobacteria class. nov. -- Bibliography -- Index of Scientific Names of Archaea and Bacteria.

Note: Front Cover -- New Approaches to Prokaryotic Systematics -- Copyright -- Dedication -- Contents -- Contributors -- Preface -- Chapter 1: The Need for Change: Embracing the Genome -- 1. A brief history of genomic sequencing of prokaryotes -- 2. Why Sequence the Genomes of Prokaryotes? -- 3. The State-of-the-Art -- 4. Where We Are Going -- Acknowledgement -- References -- Chapter 2: An Introduction to Phylogenetics and the Tree of Life -- 1. Introduction -- 2. Step 1: Posing a question -- 3. Step 2: Choosing Relevant Sequences -- 3.1. Obtaining 16S rRNA Sequences for Bacteria, Archaea and Eukarya -- 3.2. A note on the availability and use of data and methods -- 4. Step 3: Aligning Sequences and Editing the Alignment -- 5. Step 4: The theory of Fitting and Selecting a Phylogenetic Model -- 5.1. Markov nucleotide substitution models -- 5.2. Inferring phylogenies under Markov substitution models -- 5.3. Frequentist inference -- 5.4. Bayesian inference -- 5.5. Model comparison and assessment -- 5.6. Frequentist methods -- 5.7. Bayesian model choice -- 6. Step 5: Inferring Trees-Practical Guidelines for fitting and comparing Markov substitution models -- 6.1. Alignment formats for phylogeny programs -- 6.2. Inferring maximum likelihood phylogenies using RAxML -- 6.3. Bayesian analyses with PhyloBayes -- 6.4. Posterior predictive checks -- 7. Step 6: Interpreting the Phylogenetic Tree -- Conclusions -- Acknowledgements -- References -- Chapter 3: The All-Species Living Tree Project -- 1. Introduction -- 2. Sources of Information -- 2.1. Classification of microbial databases -- 2.1.1. Taxonomy (LPSN and Bergey's Manual) -- 2.1.2. Type-strain information (StrainInfo database) -- 2.1.3. Sequences and alignments (ARB and SILVA) -- 3. Database creation and updating -- 4. Features of the Database -- 4.1. Optimized SSU and LSU alignments. , 4.2. Curated hierarchical classification -- 4.3. Risk-group classification -- 4.4. Taxonomic thresholds -- 5. Phylogenetic trees -- 6. LTP as a Taxonomic Tool -- Acknowledgements -- References -- Chapter 4: 16S rRNA Gene-Based Identification of Bacteria and Archaea using the EzTaxon Server -- 1. Introduction -- 2. Use of 16S rRNA gene sequences in prokaryotic systematics -- 2.1. Sequencing of 16S rRNA genes -- 2.2. Calculation of nucleotide sequence similarity values of 16S rRNA gene sequences -- 3. Identification of Bacteria Using the EzTaxon Database -- 3.1. EzTaxon database -- 3.2. Algorithm for ``EzTaxon search´´ -- 3.3. Overall workflow from Sanger DNA sequence data -- 3.4. Assembly and trimming of sequences -- 3.5. Manual editing of sequences using the secondary structure information -- 3.5.1. Manual editing of sequences with EzEditor -- 3.6. Identification of strains using the EzTaxon server -- 3.7. Phylogenetic analysis -- Concluding remarks -- Acknowledgement -- References -- Chapter 5: Revolutionizing Prokaryotic Systematics Through Next-Generation Sequencing -- 1. Introduction -- 2. Sequencing Approaches -- 3. Bioinformatic Analyses -- 3.1. De novo assembly and mapping -- 3.2. Annotation -- 3.3. Comparative genomic analysis -- 3.4. SNP extraction and functional characteristics -- 3.5. Phylogenetic analyses -- 4. Applications of Next-Generation Sequencing Technology -- 4.1. Prokaryotic systematics -- 4.2. Pathogen evolution, transmission and adaptation -- 4.3. Genetic basis of phenotypic characteristics -- 4.4. Metagenomics -- 4.5. Target resequencing -- 4.6. RNA-Seq and transcriptomics -- Conclusions -- Acknowledgements -- References -- Chapter 6: Whole-Genome Analyses: Average Nucleotide Identity -- 1. Introduction -- 1.1. Calculation of average nucleotide identity -- 1.2. Theoretical background: BLAST/MUMmer software. , 2. Preparation and DNA Sequencing -- 2.1. Strain cultivation -- 2.2. DNA extraction and quantification -- 2.3. Whole-genome sequencing -- 3. ANI Calculations Using JSpecies -- 3.1. Installation -- 3.2. Operation -- 3.3. Calculations on-line -- 4. Interpretation and publication of results -- 5. Application to Prokaryotic Classification: Case Studies -- Concluding remarks -- Acknowledgements -- References -- Chapter 7: Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways -- 1. Introduction -- 2. The Sequencing Revolution -- 2.1. Second-generation sequencing technologies -- 2.1.1. 454 pyrosequencing -- 2.1.2. Illumina sequencing technology -- 2.1.3. Ion Torrent -- 3. Bacterial typing with next-generation sequencing -- 4. Identifying transmission pathways using whole-genome sequencing - The toolkit -- 4.1. Mapping and alignment of whole genomes -- 4.1.1. Indexing -- 4.1.1.1. Hash tables -- 4.1.1.2. The Burrows-Wheeler transform -- 4.1.2. Realigning indels -- 4.1.3. The SAM format -- 4.1.4. Identifying variation from mapped reads -- 4.2. De novo assembly and genome alignment -- 4.2.1. Read correction -- 4.2.2. Assemblers -- 4.2.2.1. Overlap-layout-consensus -- 4.2.2.2. de Bruijn graphs -- 4.2.2.3. Platform-specific assemblers -- 4.2.3. Scaffolding and gap filling -- 4.2.4. Identifying variation using co-assembly -- 4.3. Identifying variation from whole-genome assemblies -- 4.3.1. Whole-genome alignment -- 4.3.1.1. BLAT -- 4.3.1.2. MUMmer -- 4.3.1.3. Mauve -- 4.3.1.4. Mugsy -- 4.4. Identifying transmissions using whole-genome variation -- 4.4.1. SNP distances - Defining a cutoff -- 4.4.2. Phylogenetic evidence -- 4.4.3. Phylodynamics -- 5. Combining genomic and epidemiological evidence -- 6. Future Directions -- References. , Chapter 8: Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies -- 1. Limitations of the phylogenetic trees for understanding microbial classification -- 2. Characteristics that are well-suited for classification -- 3. Conserved signature indels and Their usefulness for classification and evolutionary studies -- 4. Identification of Conserved Signature Indels in Protein Sequences -- 4.1. Creation of multiple sequence alignments -- 4.2. Identification of potential conserved indels in the sequence alignments -- 4.3. Blast searches on potential conserved indels to identify useful conserved indels -- 4.4. Formatting of the conserved indels -- 5. Interpreting the Significance of Conserved Indels -- 6. Correspondence of the Results Obtained from CSIs with rRNA and Other Phylogenetic Approaches -- 7. Importance of the discovered CSIs for understanding microbial classification and phylogeny -- Acknowledgements -- References -- Chapter 9: Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees -- 1. Introduction -- 2. Bacterial species tree -- 3. Gene Family -- 4. Evolution of Genes in Bacterial Genomes -- 5. Gene Tree/Species Tree Reconciliation -- 5.1. Protocol for running AnGST -- 5.2. Interpreting the results of AnGST analyses -- 6. Analysis at the Genome Scale -- 6.1. Protocol for running COUNT -- Concluding Remarks -- Acknowledgements -- References -- Chapter 10: Multi-Locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population -- 1. Introduction -- 1.1. Historical perspective -- 1.2. Multi-locus population analyses -- 2. Multi-locus sequence typing -- 3. Whole-Genome Data Analyses -- 3.1. Gene-by-gene analysis of WGS data -- 3.2. The Bacterial Isolate Genome Sequence Database -- 3.3. Isolate and sequence databases. , 3.4. Reference sequence and profile definitions database -- 3.5. Database Integrity -- 3.6. Gene nomenclature -- 3.7. Typing and analysis schemes -- 4. Examples of Gene-by-Gene Analysis: Neisseria -- 4.1. Ribosomal multi-locus sequence typing -- 4.2. Neisseria rplF assay -- 5. Examples of Gene-by-Gene Analysis: Campylobacter -- 5.1. Core genome multi-locus sequence typing -- 5.2. Whole-genome multi-locus sequence typing -- Conclusions -- References -- Chapter 11: Multi-locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level -- 1. Introduction -- 2. Multi-Locus Sequence Analysis -- 2.1. Underlying concepts -- 2.2. Selection of gene loci -- 2.3. Generating sequences -- 2.4. Data analysis -- 2.4.1. Properties of loci -- 2.4.1.1. Sequence alignments -- 2.4.1.2. Loci statistics -- 2.4.1.3. Establishing STs -- 2.4.2. Phylogenetic analysis -- 2.4.2.1. Models of evolution -- 2.4.2.2. Evaluating phylogenetic congruence -- 2.4.2.3. Construction of phylogenetic trees -- 2.5. Comparison with other taxonomic methods -- 2.6. MLSAs: Advantages and disadvantages -- 2.7. MLSA databases -- 3. Application of MLSAs in Prokaryotic Systematics -- 3.1. The genus Streptomyces -- 3.1.1. The Streptomyces MLSA scheme -- 3.1.2. DNA:DNA hybridization and MLSAs -- 3.2. Classification of the S. pratensis phylogroup -- 3.3. MLSA of phytopathogenic Streptomyces species -- 3.4. MLSA: Actinobacteria -- 4. Detection of Ecotypes Based on MLSAs -- 5. MLSA Based on Whole Genome Sequences -- References -- Chapter 12: Bacterial Typing and Identification By Genomic Analysis of 16S-23S rRNA Intergenic Transcribed Spacer (ITS) Seque -- 1. Introduction -- 2. Methods -- 2.1. Search and download bacterial whole-genome sequences -- 2.2. Annotation of rrn alleles. , 2.3. Extraction of the gene components (16S, 23S and 5S) and extra genic regions (ITS1, ITS2, pre-16S and post-5S) that make.

Note: Intro -- Bergey's Manual® of Systematic Bacteriology -- Preface to volume 5 of the second edition of Bergey's Manual ® of Systematic Bacteriology -- Contents -- Contributors -- On using the Manual -- Citation -- Arrangement of the Manual -- Articles -- a. Name of the genus. -- b. Name of author(s). -- c. Synonyms. -- d. Etymology of the name. -- e. Salient features. -- f. Type species. -- g. Further descriptive information. -- h. Enrichment and isolation. -- i. Maintenance procedures. -- j. Procedures for testing special characters. -- k. Differentiation of the genus from other genera. -- l. Taxonomic comments. -- m. Further reading. -- n. Differentiation of the species of the genus. -- o. List of species of the genus. -- p. Species incertae sedis. -- q. References. -- Tables -- Use of the Manual for determinative purposes -- Errors, comments, and suggestions -- Road map of the phylum Actinobacteria -- References -- Data analysis -- Taxonomic interpretation -- Phylum " Actinobacteria " -- Class " Actinobacteria " -- Order Actinomycetales and family Actinomycetaceae -- Order " Actinopolysporales " and family Actinopolysporaceae -- Order Bifidobacteriales and family Bifidobacteriaceae -- Order " Catenulisporales " and families Catenulisporaceae and Actinospicaceae -- Order " Corynebacteriales " -- Family Corynebacteriaceae -- Family Dietziaceae -- Family Mycobacteriaceae -- Family Nocardiaceae -- Family Segniliparaceae -- Family Tsukamurellaceae -- Order " Frankiales " -- Family Frankiaceae -- Family Acidothermaceae -- Family Cryptosporangiaceae -- Family Geodermatophilaceae -- Family Nakamurellaceae -- Family Sporichthyaceae -- Order " Glycomycetales " and family Glycomycetaceae -- Order " Jiangellales " and family Jiangellaceae -- Order " Kineosporiales " and family Kineosporiaceae -- Order Micrococcales -- Family Micrococcaceae. , Family Beutenbergiaceae -- Family Bogoriellaceae -- Family Brevibacteriaceae -- Family Cellulomonadaceae -- Family Dermabacteraceae -- Family Dermacoccaceae -- Family Dermatophilaceae -- Family Intrasporangiaceae -- Family Jonesiaceae -- Family Microbacteriaceae -- Family Promicromonosporaceae -- Family Rarobacteraceae -- Family Ruaniaceae -- Family Sanguibacteraceae -- Order " Micromonosporales " and family Micromonosporaceae -- Order " Propionibacteriales " -- Family Propionibacteriaceae -- Family Nocardioidaceae -- Order " Pseudonocardiales " and family Pseudonocardiaceae -- Order " Streptomycetales " and family Streptomycetaceae -- Order " Streptosporangiales " -- Family Streptosporangiaceae -- Family Nocardiopsaceae -- Family Thermomonosporaceae -- Order incertae sedis and the genus Thermobispora -- Class " Acidimicrobiia " and order Acidimicrobiales -- Class " Coriobacteriia " and order Coriobacteriales -- Class " Nitriliruptoria " -- Class " Rubrobacteria " and order Rubrobacterales -- Class " Thermoleophilia " -- Taxonomic outline of the phylum Actinobacteria -- Phylum XXVI. Actinobacteria phyl. nov. -- Taxonomic comments -- Class I. Actinobacteria Stackebrandt, Rainey and Ward-Rainey 1997, 483 -- Order I. Actinomycetales Buchanan 1917, 162 AL emend. Zhi, Li and Stackebrandt 2009, 594 -- Family I. Actinomycetaceae Buchanan 1918, 403 (emend. Stackebrandt, Rainey and Ward-Rainey 1997, 484), emend. Zhi, Li and Stackebrandt 2009, 594 VP -- Genus I. Actinomyces Harz 1877 , 133 AL emend. Georg, Pine and Gerencser 1969 , 292 VP -- Further descriptive information -- Phylogeny. -- Cell morphology. -- Cell-wall composition. -- Other chemotaxonomic characteristics. -- Fine structure. -- Cultural characteristics. -- Life cycle. -- Nutrition and growth conditions. -- Metabolism and metabolic pathways. -- Adherence mechanisms. , 16S rRNA gene sequence and other molecular data. -- Mutants, plasmids, phages, and bacteriocins. -- Antigenic structure. -- Susceptibility to antibiotics and various chemical compounds. -- Trace element requirements. -- Pathogenicity. -- Human diseases and impairments. -- Animal diseases. -- Ecology. -- Enrichment and isolation procedures -- Maintenance procedures -- Procedures for testing of special characters -- Differentiation of the genus Actinomyces from other genera -- Taxonomic comments -- Further reading -- Identification and descriptive characteristics of Actinomyces species -- Genus II. Actinobaculum Lawson, Falsen, Åkervall, Vandamme and Collins 1997, 902 VP -- Further descriptive information -- Isolation procedures -- Maintenance procedures -- Taxonomic comments -- Differentiation of the genus Actinobaculum from other genera -- Differentiation of species of the genus Actinobaculum -- Genus III. Arcanobacterium Collins, Jones and Schofield 1983, 438 VP (Effective publication: Collins, Jones and Schofield 1982b, 1280.), emend. Lehnen, Busse, Frölich, Krasinska, Kämpfer and Speck 2006, 864 VP -- Further descriptive information -- Phylogeny. -- Cell morphology. -- Cell-wall composition. -- Menaquinone composition. -- Polar lipids. -- Fatty acid composition. -- Peptidoglycan composition. -- Metabolism and metabolic pathways. -- Pathogenicity. -- Human infections. -- Animal infections. -- Antigenic structure. -- Virulence factors. -- Susceptibility to antibiotics. -- Habitat and ecology. -- Isolation, enrichment and maintenance procedures -- Differentiation of the genus Arcanobacterium from other genera -- Taxonomic comments -- Further reading -- Identification and descriptive characteristics of Arcanobacterium species -- Genus IV. Mobiluncus Spiegel and Roberts 1984a, 180 VP emend. Hoyles, Collins, Falsen, Nikolaitchouk and McCartney 2004. , Further descriptive information -- Phylogeny. -- Cell-wall composition. -- Fatty acids. -- Flagella. -- Colonial and cultural characteristics. -- Nutrition and growth conditions. -- Antibodies. -- Antibiotic sensitivity. -- Ecology -- Association with BV. -- Prevalence in healthy women. -- Role in pre-term delivery. -- Presence in men. -- Extragenital infections. -- Hosts other than humans. -- Pathogenicity. -- Potential virulence factors. -- Enrichment and isolation procedures -- Differentiation of the genus Mobiluncus from other genera -- Taxonomic comments -- Further reading -- Differentiation of the species of the genus Mobiluncus -- Genus V. Varibaculum Hall, Collins, Lawson, Hutson, Falsen, Inganas and Duerden 2003e, 644 VP -- Further descriptive information -- Isolation procedures -- Maintenance procedures -- Procedures for testing special characters -- Commercially available identification systems. -- Amplified 16S rDNA restriction analysis (ARDRA). -- Differentiation of the genus Varibaculum from other genera -- Taxonomic comments -- References -- Further descriptive information -- Key to the genera of the family Actinomycetaceae -- List of species of the genus Actinomyces -- Species incertae sedis -- List of species of the genus Actinobaculum -- List of species of the genus Arcanobacterium -- List of species of the genus Mobiluncus -- List of species of the genus Varibaculum -- Order II. Actinopolysporales ord. nov. -- References -- Family I. Actinopolysporaceae Zhi, Li and Stackebrandt 2009, 595 VP -- Genus I. Actinopolyspora Gochnauer, Leppard, Komaratat, Kates, Novitsky and Kushner 1975 , 1510 AL -- Further descriptive information -- Phylogeny. -- Cell morphology. -- Fine structure. -- Colony morphology. -- Chemotaxonomy. -- Nutrition and growth conditions. -- Metabolism and genetics. -- Antibiotic sensitivity. -- Ecology. , Isolation procedures -- Maintenance procedures -- Differentiation of the genus Actinopolyspora from other genera -- Taxonomic comments -- Differentiation of the species of the genus Actinopolyspora -- List of species of the genus Actinopolyspora -- Species incertae sedis -- References -- Order III. Bifidobacteriales Stackebrandt, Rainey and Ward-Rainey 1997, 487 VP -- References -- Family I. Bifidobacteriaceae Stackebrandt, Rainey and Ward-Rainey 1997, 487 VP -- Genus I. Bifidobacterium Orla-Jensen 1924 , 472 AL -- Further descriptive information -- Phylogeny. -- Cell morphology. -- Cell-wall composition. -- Fine structure. -- Nutrition and growth conditions. -- Anaerobiosis. -- Metabolism and metabolic pathways. -- Urease activity. -- Nitrate reduction. -- Genetics. -- Plasmids. -- Antibiotic or drug sensitivity. -- Bacteriocins. -- Pathogenicity. -- Ecology. -- Bifidobacteria as health-promoting agents: probiotic, prebiotic, and symbiotic substances. -- Isolation procedures -- Maintenance procedures -- Enzymes used for species and group differentiation -- Transaldolases. -- 6-Phosphogluconate dehydrogenases (6PGD). -- Procedures for testing special identification characteristics -- F6PPK test. -- Classical procedure. -- Modified procedure. -- Differentiation of the species of the genus Bifidobacterium -- List of species of the genus Bifidobacterium -- Genus II. Aeriscardovia Simpson, Ross, Fitzgerald and Stanton 2004 , 405 VP -- Further descriptive information -- Phylogeny. -- Anaerobiosis. -- Maintenance procedures -- List of species of the genus Aeriscardovia -- Genus III. Alloscardovia Huys, Vancanneyt, D'Haene, Falsen, Wauters and Vandamme 2007 , 1445 VP -- Further descriptive information -- Maintenance procedures -- List of species of the genus Alloscardovia -- Genus IV. Gardnerella Greenwood and Pickett 1980 , 176 VP. , Further descriptive information.