Microbial Taxonomy Overview
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Questions and Answers

What defines bacterial species according to modern definitions?

Bacterial species are defined by shared genome sequences that are at least 95% identical (ANI: average nucleotide identity).

How does horizontal gene transfer (HGT) impact bacterial species definition?

HGT can lead to significant genetic differences within bacterial species, complicating traditional classification based on shared traits.

What is the significance of molecular methods in microbial taxonomy?

Molecular methods have revolutionized microbial taxonomy by providing precise evolutionary relationships through DNA sequence analysis.

What is a clade in the context of cladistics?

<p>A clade is a group of organisms that share a common ancestor and possess similar characteristics.</p> Signup and view all the answers

Why are genes encoding key functions often used in sequence comparisons for classification?

<p>These genes are critical for basic cellular functions and are expected to be conserved across closely related organisms.</p> Signup and view all the answers

What is the primary focus of modern phylogenetics?

<p>The primary focus is on studying evolutionary relationships among groups of organisms using molecular sequencing data.</p> Signup and view all the answers

How do molecular approaches affect the classification of organisms like Streptomyces?

<p>Molecular approaches challenge traditional classifications, questioning whether certain organisms like Streptomyces are fungi or bacteria.</p> Signup and view all the answers

What role do phenotypic features play in the historical context of bacterial species definition?

<p>Phenotypic features were traditionally used to define bacterial species before modern genomic methods emerged.</p> Signup and view all the answers

What are the primary genetic characteristics used in bacterial taxonomy?

<p>The primary genetic characteristics include gene presence/absence, gene sequences, and the analysis of mutations such as SNPs.</p> Signup and view all the answers

Name and briefly describe the three major mechanisms of horizontal gene transfer in bacteria.

<p>The three major mechanisms are transformation (uptake of free DNA), transduction (transfer via bacteriophages), and conjugative transfer (direct transfer via plasmids).</p> Signup and view all the answers

Define 'biovar' and explain how it differs from a 'strain' in bacterial taxonomy.

<p>A 'biovar' is a strain differentiated by physiological or biochemical characteristics, while a 'strain' is a population descended from a single microbe differing in minor ways.</p> Signup and view all the answers

What are the key phenotypic features used in microbial species classification?

<p>Key phenotypic features include morphological characteristics, physiological and metabolic characteristics, and genetic characteristics.</p> Signup and view all the answers

What is the significance of the 16S rRNA gene in bacterial classification?

<p>The 16S rRNA gene is significant because it provides limited information content that is essential for understanding phylogenetic relationships among bacteria.</p> Signup and view all the answers

How can horizontal gene transfer complicate taxonomy based on genetics?

<p>Horizontal gene transfer can complicate taxonomy because it allows for the exchange of genetic material between unrelated species, blurring the lines of evolutionary relationships.</p> Signup and view all the answers

What defines a 'serovar' in bacterial classification?

<p>A 'serovar' is a strain of bacteria differentiated by serological methods, indicating distinct antigenic properties.</p> Signup and view all the answers

Why is it important to analyze the physiological and metabolic characteristics of bacteria?

<p>Analyzing physiological and metabolic characteristics is important because it provides indirect genomic comparisons, revealing functional differences among bacteria.</p> Signup and view all the answers

What are single nucleotide polymorphisms (SNPs) and how do they influence genetic diversity?

<p>SNPs are variations at a single nucleotide position in a DNA sequence that can lead to differences in traits among individuals, contributing to genetic diversity.</p> Signup and view all the answers

In the context of sequence comparisons, what are the implications of deletions and insertions?

<p>Deletions remove segments of a gene sequence while insertions add extra sequences, both leading to potential changes in the resulting protein.</p> Signup and view all the answers

Explain the difference between simple and complex sequence alignments.

<p>Simple alignments involve direct comparison with few mutations, while complex alignments require the insertion of gaps to accommodate larger differences.</p> Signup and view all the answers

What is the purpose of multiple sequence alignment (MSA) in phylogenetic studies?

<p>MSA helps compare multiple gene sequences to determine evolutionary relationships and construct phylogenetic trees.</p> Signup and view all the answers

Describe how a distance matrix is created from MSA and its significance.

<p>A distance matrix summarizes the genetic distances between sequences based on percent similarity, indicating how closely related they are.</p> Signup and view all the answers

What role does phenotypic variation play in the definition of microbial species?

<p>Phenotypic variation helps distinguish between microbial species based on observable traits, aiding in classification and identification.</p> Signup and view all the answers

How does horizontal gene transfer influence genetic characteristics in microbial populations?

<p>Horizontal gene transfer allows for the exchange of genetic material between organisms, increasing genetic diversity and adaptability in microbial populations.</p> Signup and view all the answers

What are the taxonomic ranks commonly used in biology, and why are they important?

<p>Taxonomic ranks include domain, kingdom, phylum, class, order, family, genus, and species; they provide a hierarchical classification system for organizing and identifying living organisms.</p> Signup and view all the answers

Study Notes

Microbial Taxonomy

  • Microbial taxonomy is the science of classifying and naming microorganisms.
  • Systematics is the study of the diversity of life and its evolutionary relationships.
  • Taxonomy includes the science of biological classification:
    • Biological classification arranges organisms into groups or taxa.
    • Nomenclature is the branch of systematics, assigning names to organisms.

Taxonomic Ranks

  • Domain
  • Kingdom
  • Phylum
  • Class
  • Order
  • Family
  • Genus
  • Species
  • Species names are generally written in italics.

Important Bacterial Phyla

  • Common Gram-negative bacterial pathogens mostly belong to the phylum Pseudomonadota (synonym Proteobacteria).
  • Common Gram-positive bacterial pathogens mostly belong to the phylum Bacillota (synonym Firmicutes).

Eukaryotic Kingdoms

  • Eukaryotes are now divided into six kingdoms/divisions:
    • Excavata (e.g., Giardia, Trichomonas)
    • Rhizaria
    • Chromalveolata
    • Plantae
    • Opisthokonta (e.g., Candida, Homo)
    • Amoebozoa (e.g., Entamoeba)

Virus Types: DNA Viruses

  • Nonenveloped:
    • ssDNA: Parvovirus
    • dsDNA: Papovavirus, Adenovirus, Iridovirus
  • Enveloped:
    • Partially dsDNA: Hepadnavirus
    • dsDNA: Poxvirus, Herpesvirus

Virus Types: RNA Viruses

  • Nonenveloped:
    • ssRNA: Norovirus
    • dsRNA: Reovirus
  • Enveloped:
    • ssRNA: Togavirus, Rhabdovirus, Orthomyxovirus, Paramyxovirus, Retrovirus
    • Other: Coronavirus, Bunyavirus, Arenavirus

Virus Taxonomy: Baltimore Scheme

  • Classification is based on genome type and replication strategy.
    • dsDNA viruses (e.g., Adenoviruses, Herpesviruses, Poxviruses)
    • ssDNA viruses (+)sense DNA (e.g., Parvoviruses)
    • dsRNA viruses (e.g., Reoviruses)
    • (+)ssRNA viruses (+)sense RNA (e.g., Norovirus)
    • (-)ssRNA viruses (-)sense RNA (e.g., Orthomyxoviruses, Rhabdoviruses)
    • ssRNA-RT viruses (+sense RNA with DNA intermediate) (e.g., Retroviruses)
    • dsDNA-RT viruses RNA intermediate (e.g., Hepadnaviruses)

Virus Taxonomy: ICTV

  • International Committee on Taxonomy of Viruses (ICTV)
  • Taxon suffixes:
    • Order: -virales
    • Family: -viridae
    • Subfamily: -virinae
    • Genus: -virus
    • Species: -virus

Taxonomic Mnemonics

  • One way to remember the taxonomic ranks is through the mnemonic "Dear King Philip Came Over For Good Soup."

Species Definition (Sexually-Reproducing Organisms)

  • Initial taxonomy was based on appearance (morphology).
  • Closely related organisms have more similar appearances.
  • Species is defined as groups of interbreeding (or potentially interbreeding) natural populations reproductively isolated from other groups.

Microbial Species Definition

  • Organisms are assigned to species based on phenotypic (appearance) and genotypic (genetic) features.
  • Microbial species is a collection of bacteria sharing many stable properties but differing from other groups of bacteria.

Sub-Species Ranks

  • Strain: population of microbes descending from a single microbe or culture isolate differing (in minor ways) from other bacteria of the same species.
  • Biovar: strain distinguishable via physiology or biochemistry.
  • Pathovar: strain differentiated by pathogenicity.
  • Serovar: strain differentiated by serological means.
  • Morphovar: strain differentiated by morphology.

Characteristics Used in Taxonomy:

  • Morphological characteristics (appearance)
  • Physiological and metabolic characteristics
  • Genetic characteristics
  • Other molecular characteristics

Physiological and Metabolic Characteristics

  • Biochemical testing (e.g., enzyme or transport protein activity) provides an indirect genomic comparison.

Genetic Characteristics

  • Gene presence/absence
  • Gene sequences (DNA, RNA)
  • Point mutations (SNPs)
  • Insertions/Deletions
  • Genome sequences (genomics, WGS)

Horizontal Gene Transfer

  • A significant factor that needs to be considered in evaluating taxonomy based on genetics.

Phylogenetics and Cladistics

  • Making clusters of similar organisms.
  • Clustered (similar) organisms share a common ancestor (= clade)
  • Taxonomic groups are (ideally) clades.
  • Cladistics is based on comparison of DNA or protein sequences.
  • Sequence(s) have to be found in all organisms being classified.

Sequence Comparisons

  • Closely related organisms have less divergent genes and protein sequences.
  • Differences can consist of point mutations, insertions, or deletions.

Sequence Alignment

  • Alignment of sequences via pairwise or multiple sequence alignment(MSA) methods to find similar sequences.
  • Gaps can be inserted for more complex alignments.

Multiple Sequence Alignment (MSA)

  • Complex computational method for comparing multiple sequences and constructing family trees.
  • Often starts by aligning the most similar pairs and then adding the next most similar sequences.

Genetic Distance

  • Calculate relationships between organisms via distance methods using sequence alignments.
  • Summarizes genetic distances/similarities between pairs of sequences in order to find relatedness through the use of a matrix.

Phylogenetic Trees

  • Tree diagrams showing evolutionary relationships graphically.

Interpreting Phylogenetic Trees

  • Clade: Organisms sharing a common ancestor.
  • Dendrogram: A distance tree showing existing (sampled) organisms.
  • Root: The ancestor/oldest point of the tree.
  • Outgroup: Organisms outside the group being studied that serves as a reference for evolutionary relationships.
  • Nodes: Formation of new species or type.
  • Branch length: The changes that occur during speciation (genetic distance between organisms).

Cladograms

  • Some trees only show groupings (clades) with fixed branch lengths.

Types of Trees

  • Rectangular and radial trees can display various relationships and data in visual form.
  • The diagrams can display relationships effectively for example, by including lengths of branches, which can denote genetic distance.

Phylogenetics Questions

  • Includes questions on outgroups, root position, most closely and distantly related sequences, and other questions based on phylogenetic data that can be derived from the phylogenetic diagrams.

Recent Developments

  • Dominance of molecular methods (including DNA sequences) in microbial systematics.
  • Taxonomy based on phylogenetic information, the study of evolutionary relationships between organisms.
  • Modern phylogenetics uses molecular sequences (data from genes) to provide information on evolutionary relationships. Construct phylogeny charts (family trees) based on family members.

Impacts of Molecular Approach

  • Existence of a large portion of the tree of life is now known (1/3)
  • Changed classifications of related species or organisms.

Bacterial Species Definition

  • For sexually-reproducing organisms: Species defined by potential for interbreeding.
  • For bacteria: Originally defined by shared phenotypic traits.
  • Modern approach: Sharing genome sequences with at least 95% identity.

Phylogenetic Trees Domain Bacteria

  • Trees that include phylum Proteobacteria and Firmicutes, Spirochaetes, and Actinobacteria are demonstrated to provide specific information on the taxonomic classifications of organisms (using scientific classification techniques).

Phylogenetic Trees: SARS-like Coronavirus

  • Trees that illustrate relationships between SARS-like coronaviruses based on their genetic divergence.

Homework

  • Identify two important pathogens from each of the following bacterial phyla:
    • Pseudomonadota (Proteobacteria)
    • Bacillota (Firmicutes)
    • Spirochaetes
    • Actinobacteria

Microbes Dominate the Tree of Life

  • Bacteria and Archaea significantly outweigh eukaryotes in numbers and influence.

Learning Outcomes

  • Describe the major taxonomic groups of microorganisms.
  • Describe the characteristics of each group.
  • Explain how microbes are classified.

Discussion Question

  • How would you investigate the taxonomy of a newly isolated bacterium, potentially a new species?

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HCS228 Microbial Taxonomy 2024-25 PDF

Description

Explore the classification and naming of microorganisms in this quiz about microbial taxonomy. Learn about the hierarchical taxonomic ranks and the major bacterial phyla, as well as the different kingdoms of eukaryotes. Test your knowledge on the diversity of life forms and their evolutionary relationships.

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