MICRB 265 LECTURE 1-3
Naming & Classifying Microbes
Lecture Overview
Introduction to the methods used for grouping, classifying, and naming microbes.
The use of DNA sequences for inferring evolutionary relationships between microbes and constructing phylogenetic trees.
Reference Textbook: Chapter 13, Sections I and II.
Key Terms for Systematics
Taxonomy
Definition: The science of classifying and naming biological organisms.
Phylogeny
Definition: The study of the evolutionary relationships among various organisms.
Taxonomists employ a mix of genotype, phenotype, and phylogenetic information to classify organisms.
Notably, over time, phylogeny has taken precedence over phenotype in guiding the taxonomic groupings of microbes.
Taxonomy Reminder
Organisms that share similar characteristics are classified together into taxa.
The organization of these groupings follows a hierarchical structure:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Mnemonic to remember these levels: "Did King Phillip Come Over For Great Soup?"
Taxonomic Hierarchy
Example: Humans
Domain: Eukarya
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primates
Family: Hominidae
Genus: Homo
Species: Homo sapiens
Example: Bacteria
Domain: Bacteria (or Eubacteria)
Phylum: Proteobacteria
Class: Gammaproteobacteria
Order: Enterobacteriales
Family: Enterobacteriaceae
Genus: Escherichia
Species: Escherichia coli
Naming Microorganisms: Taxonomy
Established by Carl Linnaeus in the 1700s.
Purpose: To create a system for classification that minimizes chaos and provides a structure for new species discoveries.
Each organism is given a two-part name:
Genus: Broad classification.
Species: Specific classification.
Example: Homo sapiens (humans).
Scientific names differ from common names (e.g., "Cat" versus Felis domesticus).
Scientific Names of Microbes
Scientific names are typically in Latin.
Names may describe characteristics, honor a scientist, or refer to physical properties.
Examples:
Deinococcus radiodurans: Named for its radiation resistance.
Escherichia coli: Named after the scientist Theodor Escherich.
Staphylococcus aureus: “Grapes-like” refers to its spherical cell arrangement, and “golden” corresponds to the colony color.
Formatting of Scientific Names
Species names (combination of species and genus) are italicized (or underlined if handwritten).
The genus is capitalized, while the species is lowercased.
Higher taxa (family, class, order, phylum, kingdom) are also capitalized but not italicized.
After the first mention in texts, scientific names are abbreviated to the first letter of the genus followed by the species name.
Examples:
Staphylococcus aureus → S. aureus
Escherichia coli → E. coli
Scientific Names: Specific Classifications Beyond Species
For some microbes, classifications more specific than species are used:
Subspecies: The next finer classification after species.
Biovar or Biotype: Grouping based on physiological or biochemical differences from other members of the species.
Serovar or Serotype: Grouping based on surface antigens.
Strain: A genetic variant or subtype, often referring to specific isolates. An example is STEC (Shiga toxin-producing E. coli).
Example of Species Classification
Escherichia coli, serotype O157:H7: This serotype serves as an example of a “STEC.”
Importance of Taxonomy
Taxonomy provides a means to impose order on the vast diversity of organisms.
Example: Mammalia (class of animals)
Allows for effective communication and educated guesses about newly discovered organisms.
Example: If a new pathogenic bacterium is identified, recognizing it as part of the genus Salmonella can yield important knowledge about its potential biology, virulence, and metabolism based on existing data about other Salmonella species.
Phylogenetic Trees – The Basics
Defined as a visual representation of predicted evolutionary relationships among organisms.
Key features include:
Lineages show both ancestors and modern-day organisms.
The most recent common ancestor, often hypothetical, appears at the center of branches.
Evolutionary time progresses from left (root) to right (modern lineages).
Branches illustrate unique evolutionary histories tied to connecting lineages.
Branch length indicates evolutionary distance between nodes (not always to scale).
Determining Phylogenetic Relationships
Comparing DNA sequences is a primary method for establishing how closely related organisms are.
Over time, DNA sequences undergo mutations during replication.
Comparison of conserved sequences across organisms highlights genetic similarities or differences—more differences indicate more evolutionary distance.
Ideal sequences for comparison are highly conserved genes with stable functions that mutate slowly over time.
Small Subunit rRNA (SSU rRNA) Sequencing
The ribosome is universally conserved among all organisms on Earth.
The small subunit ribosomal RNA (SSU rRNA) is frequently sequenced to infer phylogenetic relationships.
Variable regions of SSU rRNA are useful for identifying relationships, while conserved regions are beneficial for Polymerase Chain Reaction (PCR).
The sequencing method was pioneered by Carl Woese and George Fox in the 1970s.
The Woese Tree of Life
This universal tree of life is derived from nucleotides' sequence similarities in ribosomal RNA (rRNA).
The Woese tree illustrates the genealogy of all life on Earth.
Established three domains of life:
Bacteria
Archaea
Eukarya
Utilizing 16S rDNA for Bacterial Identification and Classification
Steps:
Isolate genomic DNA from pure cultures, environmental, or clinical samples.
Use PCR primers that bind to highly conserved regions of 16S rDNA to amplify and sequence 16S rDNA.
Align and analyze the sequences obtained.
Helpful resource: PCR reminder link available in the transcript.
Building Phylogenetic Trees from Sequences
Methodology: To enhance this approach, multiple conserved genes or even full genomes can be compared to analyze closely related organisms.
Limitations of Phylogenetic Trees
Phylogenetic trees represent predictions of evolutionary relationships; confidence may be high, but actual relationships are inferred.
Horizontal gene transfer (HGT) is a significant confounding factor; microbes can acquire foreign DNA that complicates evolutionary interpretations.
Acquired DNA may integrate via homologous recombination, potentially replacing host DNA sequences.
The mutation rates of the DNA being examined can vary due to selective pressures operating differently in distinct species, impacting phylogenetic analyses.
LEARNING OUTCOMES
Lecture Overview
Introduction to the methods used for grouping, classifying, and naming microbes.
The use of DNA sequences for inferring evolutionary relationships between microbes and constructing phylogenetic trees.
Reference Textbook: Chapter 13, Sections I and II.
Key Terms for Systematics
Taxonomy
Definition: The science of classifying and naming biological organisms.
Role of Carl Linnaeus: Established a system for classification in the 1700s to minimize chaos and structure new species discoveries.
Phylogeny
Definition: The study of the evolutionary relationships among various organisms.
Taxonomists employ a mix of genotype, phenotype, and phylogenetic information to classify organisms, with phylogeny increasingly taking precedence over phenotype.
Taxonomy Reminder
Organisms with similar characteristics are classified together into taxa following a hierarchical structure:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Mnemonic: "Did King Phillip Come Over For Great Soup?"
Example: Bacteria
Domain: Bacteria (or Eubacteria)
Phylum: Proteobacteria
Class: Gammaproteobacteria
Order: Enterobacteriales
Family: Enterobacteriaceae
Genus: Escherichia
Species: Escherichia coli
Naming Microorganisms: Taxonomy
Each organism is given a two-part name (binomial nomenclature):
Genus: Broad classification.
Species: Specific classification.
Example: Homo sapiens (humans).
Scientific Names of Microbes
Scientific names are typically in Latin.
Names may describe characteristics, honor a scientist, or refer to physical properties.
Examples of Naming:
Deinococcus radiodurans: Named for its radiation resistance.
Escherichia coli: Named after the scientist Theodor Escherich.
Staphylococcus aureus: “Grapes-like” refers to its spherical cell arrangement, and “golden” corresponds to the colony color.
Formatting of Scientific Names
Species names (combination of genus and species) are italicized (or underlined if handwritten).
The genus is capitalized, while the species is lowercased.
Higher taxa (family, class, order, phylum, kingdom) are also capitalized but not italicized.
After the first mention in texts, scientific names are abbreviated (e.g., Staphylococcus aureus → S. aureus; Escherichia coli → E. coli).
Scientific Names: Specific Classifications Beyond Species
For some microbes, classifications more specific than species are used to separate out lineages:
Subspecies: The next finer classification after species.
Biovar or Biotype: Grouping based on physiological or biochemical differences.
Serovar or Serotype: Grouping based on surface antigens (e.g., Escherichia coli, serotype O157:H7).
Strain: A genetic variant or subtype, often referring to specific isolates (e.g., STEC).
Importance of Taxonomy
Provides a means to impose order on the vast diversity of organisms.
Allows for effective communication and educated guesses about newly discovered organisms.
Example: Recognizing a new bacterium as part of the genus Salmonella can provide knowledge about its potential biology, virulence, and metabolism based on existing data.
Phylogenetic Trees – The Basics
Defined as a visual representation of predicted evolutionary relationships among organisms.
Key features:
Lineages show both ancestors and modern-day organisms.
The most recent common ancestor appears at the center of branches.
Evolutionary time progresses from left (root) to right (modern lineages).
Branches illustrate unique evolutionary histories.
Branch length indicates evolutionary distance between nodes (not always to scale).
Determining Phylogenetic Relationships
Comparing DNA sequences is a primary method for establishing relationships.
DNA sequences undergo mutations over time.
Comparison of conserved sequences across organisms highlights genetic similarities or differences; more differences indicate more evolutionary distance.
Ideal sequences for comparison are highly conserved genes with stable functions that mutate slowly over time.
Small Subunit rRNA (SSU rRNA) Sequencing
Pioneered by Carl Woese and George Fox in the 1970s.
The ribosome is universally conserved, making its RNA suitable for phylogenetic inference.
The small subunit ribosomal RNA (SSU rRNA) is frequently sequenced.
Variable regions of SSU rRNA are useful for identifying relationships between organisms.
Conserved regions are beneficial for Polymerase Chain Reaction (PCR) primer binding.
The Woese Tree of Life, based on rRNA sequence similarities, established three domains: Bacteria, Archaea, and Eukarya.
Utilizing 16S rDNA for Bacterial Identification and Classification
Steps:
Isolate genomic DNA from samples.
Use PCR primers that bind to highly conserved regions of 16S rDNA to amplify and sequence it.
Align and analyze the obtained sequences.
Limitations of Phylogenetic Trees
Phylogenetic trees represent predictions; actual relationships are inferred.
Horizontal gene transfer (HGT) is a significant confounding factor, as microbes can acquire foreign DNA that complicates evolutionary interpretations.
Mutation rates can vary due to selective pressures, impacting phylogenetic analyses.