"Methods in microbial systematics have developed and changed significantly in the last 40 years. This book will provide an overview of new methodologies and wider information sources to provide accurate identifications, in the context of current microbial systematic concepts"--.

• Cover
• Trends in the Systematics of Bacteria and Fungi
• Copyright
• Contents
• List of Figures
• List of Tables
• List of Authors
• Preface
• 1 Bridging 200 Years of Bacterial Classification
  • Introduction
  • The Historical Perspective
    • The changing consideration of bacterial taxonomic assessment
      • The early era
      • A witness of scientific progress: Bergey’s Manual of Determinative Bacteriology
    • The dawn of unravelling the evolution of Prokaryotes
    • Reconciliation of bacterial taxonomy
    • Changing gear: Bergey’s Manual of Systematic Bacteriology
  • Some Considerations on Taxonomy and the Misunderstandings
  • The Paramount Relevance of the Genomic Data
  • Recent Innovations
  • Taxonomy Needs to Change Its Path
  • Conclusions: Reconciliation or Divorce
  • Acknowledgements
  • References
• 2 Identification of Fungi: Background, Challenges and Prospects
  • Introduction
  • Fungi and Fungi
  • The Identification Process
  • Challenges of Identifying Fungi
  • Prospects for Addressing Challenges
  • Conclusion
  • References
• 3 Names of Microorganisms and Data Resources to Retrieve Information About Published Names
  • Introduction
  • The International Code of Nomenclature of Prokaryotes (the Prokaryotic Code)
  • Resources from Which Information About Names of Prokaryotic Taxa Can Be Retrieved
    • The ‘official’ sources of information: articles and lists in the IJSB/IJSEM
  • Online Resources that Provide Information on Validly Published Names of Taxa of Prokaryotes
    • List of Prokaryotic names with Standing in Nomenclature (LPSN) (Euzéby, 1997; Parte, 2014, 2018)
    • Prokaryotic Nomenclature Up-to-Date (Leibniz Institute DSMZ, 2019)
    • NamesforLife (Garrity, 2010)
  • Names of Prokaryotes Effectively but not Validly Published
  • Names of Candidatus Taxa of Prokaryotes
  • The Special Status of the Cyanobacteria/Cyanophyta
  • Names of Fungi and Related Digital Resources
  • Effective Publication Under the ICN
    • Chapter F of the ICN
    • Typification
    • Priority, starting-point dates and hemihomonyms
    • Registration of nomenclatural acts
    • Pleomorphic life cycles – One fungus: one name
    • Lists of approved and rejected names
    • Naming cryptic diversity
    • eDNA
    • Linking names to DNA, and DNA to names
  • Data Standards and Databases
  • Digital Resources
    • Names
    • Taxa
    • Descriptive data
    • Sequence-related databases
  • Conclusion
  • References
• 4 Preserving the Reference Strains
  • Rationale
  • Introduction
  • Handling Samples from the Environment to the Laboratory
  • DNA Sample Preparation and Storing
  • Sample Acquisition and Authentication
  • Preservation Techniques
  • Approaches to Testing Stability in Storage
  • mBRC Management: Adopting an Appropriate Standard
  • Conclusion
  • References
• 5 Can Older Fungal Sequence Data be Useful?
  • Introduction
  • Data Available
  • Placing mOTUs in Beauveria
  • ‘Fishing’ for New Sequences
  • ‘Clustering’ for New Sequences
  • Outcome
  • Mislabelled Sequences
  • Limitations in the Methodology
    • ITS
    • Cut-off values
      • Duplicated sequences
    • Limitations of names and labels
  • Species Complexes
  • Conclusion
  • References
• 6 Data Resources: Role and Services of Culture Collections
  • Introduction
  • The Importance of Reliable Data
  • Desired Function of a Modern Culture Collections Management System
  • Reliable and Useful Data
  • Supporting Fungal Taxonomy
  • Standards and Open Access
  • Conclusion
  • References
• 7 MALDI-TOF MS and Currently Related Proteomic Technologies in Reconciling Bacterial Systematics
  • Introduction
  • Proteins in Microbial Systematics
  • Arrival of MALDI-TOF MS in Microbiology
  • Establishing MALDI-TOF MS in Clinical Microbiology
  • MALDI-TOF MS in the Non-clinical Laboratory and its Role in Searching for New Diversity
  • MALDI-TOF MS in Subspecies Identification, Typing and Screening for Genetic Variants: Implication for Systematics
  • MALDI-TOF MS in Microbial Systematics; a Case Study Involving Cutibacterium acnes
    • Brief biology of Cutibacterium acnes
    • MALDI-TOF MS delineates three proteotypes
    • Correlation of proteotypes with whole-genome sequencing
  • MALDI-TOF MS and the Future Interest of MS Companies
  • Use of MALDI-TOF MS in a Clinical Laboratory
    • Limitations of MALDI-TOF MS as currently used
  • Retaining the Interest of Mass Spectrometry Companies
  • Potential to Identify the Biomarker Peaks in a MALDI-TOF MS Spectrum: Towards a MALDI-TOF MS Global Database
    • High-resolution forms of MS that may be used to deduce peptide/protein taxon-specific signatures
    • From linear MALDI-TOF MS to tandem LC-MS/MS: unravelling the proteome of microbial species and future implications for bacterial systematics
    • Case study: use of tandem LC-MS/MS during a major disease outbreak of pathogenic E. coli and taxonomic implications
      • Nature of the outbreak
      • Proteomics and systematics in a high-containment laboratory
  • Conclusion
  • References
• 8 MALDI-TOF MS and its Requirements for Fungal Identification
  • Introduction
  • Principles of MALDI-TOF MS and its Application in Fungal Taxonomy
  • Examples of the Use of MALDI-TOF MS Technique in Fungal Identification
  • Limitations to the Use of MALDI-TOF MS Technique in Fungal Identification
  • MALDI-TOF MS for Cryptic and Dimorphic Fungal Identification
  • MALDI-TOF MS Databases and Data Analysis in Fungal Identification
    • Current situation of each different commercial database dedicated to fungal identification
    • In-house MALDI-TOF MS databases for fungal identification
  • Conclusion
  • Acknowledgements
  • References
• 9 The Strength of Chemotaxonomy
  • Introduction
  • Background and History of Chemotaxonomic Biomarkers
    • Cell wall components
    • Lipids
    • Polyamines
  • Applications of Chemotaxonomy to Bacterial Systematics
    • Winds of Change: Chemotaxonomy in the Era of Omics
  • Conclusion: Chemotaxonomy and What Lies Ahead
  • References
• 10 Microbial Genomic Taxonomy
  • Introduction
  • Genomic Microbial Taxonomy
  • In silico Phenotyping
  • Suggestions for a Genome-based Taxonomy
  • Challenges Ahead for Microbial Taxonomy in the Context of Microbial Ecology
  • Challenges in the Taxonomy of the Cyanobacteria Phylum
  • Conclusion
  • References
• 11 Navigating Bacterial Taxonomy in a World of Unchartered Microbial Organisms
  • Introduction
  • Determining Taxonomy in Metabarcoding Experiments
  • Approaches for Assigning OTUs to Amplicon Sequences
  • Emergence of Amplicon Sequence Variants (ASVs)
  • Assigning Taxonomy to MAGS
  • The Disconnect Between MAGs and Metabarcoding Approaches
  • Conclusion
  • References
• 12 Sequence-based Identification and Classification of Fungi
  • Introduction
  • The ITS Region as a Universal Barcode for Fungal Identification: Advantages and Limitations
  • Secondary DNA Barcode Regions as Adjuncts to (or Replacements for) ITS
  • Quality of Reference Sequence Libraries
  • The Problem of Sequences Without Names: ‘Dark Taxa’
  • Implications for Fungal Taxonomy and Nomenclature
  • Conclusion
  • References
• 13 Identification and Classification of Prokaryotes Using Whole-genome Sequences
  • Introduction
  • Genome-based Classification: Advantages
  • What Did Whole-genome Sequencing Reveal About Traditional Taxonomic Practices?
  • Genome-based Classification: Limitations
  • Genome Classification Resources Available
  • Unculturable Taxa: Genome-based Classification is the Only Way Forward
  • Tips for Genome-based Classification of an Unknown Query Genome
  • Acknowledgements
  • References
• 14 Genomic Sequences for Fungi
  • Introduction
  • The Species Concept in the Next-generation Sequencing (NGS) Era
  • Methodology
    • Sequencing technologies
      • De novo, resequencing and targeted sequencing
      • RNA sequencing (RNA-Seq)
      • Epigenetics
      • Genomic variation and mutation detection
    • Data analysis and interpretation
      • Experimental design and generation of data
      • Analysis
      • Interpretation
      • Visualization and reporting
  • Techniques
    • Comparative genomics
    • Genome sequences to link genetics with biological traits
      • From biochemistry to genomics
    • Metagenomics
  • Technology and Fungal Systematics
    • Saccharomyces
    • Penicillium
    • Aspergillus
    • Fusarium
    • Colletotrichum
  • Discussion and Conclusion
  • Acknowledgements
  • References
• 15 What can Genome Analysis Offer for Bacteria?
  • Introduction
  • Schools of Taxonomic Thought and Associated Methods of Analysis
  • Methodological Issues in Polyphasic Taxonomy
  • Causes of Conflict Between Taxonomic Classifications and Genome-scale Analyses
  • Assigning Taxonomic Ranks Using Genome-scale or Other Data
  • Conclusion
  • References
• 16 Genomes Reveal the Cohesiveness of Bacterial Species Taxa And Provide a Path Towards Describing All of Bacterial Diversity
  • Introduction
  • How Taxonomy Demarcates Bacterial Species
  • A Genome-based Species Taxonomy
    • Substituting a type genome sequence for a type strain
    • Demarcating genomes into new species
    • Describing the phenotype of novel species
  • Is There Something Real About Species?
  • Recombination Does Not Prevent Ecological Divergence Between Bacterial Populations
  • Periodic Selection as a Force of Cohesion in Bacterial Species
  • Ecotypes as Species-like Lineages
  • Enriching Bacterial Systematics with Ecotypes
  • Recombination as a Force of Cohesion Among Ecologically Distinct Lineages
  • A Force of Cohesion That is Limited to Species Taxa Across Much of Life
  • Conclusion
  • References
• 17 Are Species Concepts Outdated for Fungi? Intraspecific Variation in Plant-pathogenic Fungi Illustrates the Need for Subspecific Categorization
  • Introduction
  • Difficulties in Applying Species Concepts in Fungi
  • Phylogenetic Species Concept and Molecular Data
  • Structured Case Summaries
    • Rhizoctonia solani
    • Colletotrichum
    • Fusarium oxysporum
    • Verticillium
      • Redefinition of species in Verticillium
      • Intraspecific diversity in Verticillium species and its phytopathological relevance
  • Conclusion
  • References
• 18 Where to Now?
  • Introduction
  • Progress in Mycological Systematics
  • Species Concepts
  • Diverging Developments in Bacterial Classification
  • Bacterial Nomenclature in the Future
  • Reference Materials for Mycology
    • Herbarium resources
    • Curating the names
  • Networking Microbial Strain Information
  • Systematics in the Post-Nagoya Era
  • Conclusion
  • References
• Appendix Abbreviations and Acronyms List
  • Abbreviations and Acronyms List
    • Chapters 1–10
    • Chapters 11–17
• Index
• Back Cover