1-3 - Naming and Classifying Microbes.pdf

1-3: Naming & Classifying Microbes Lecture Overview: • Introduction to the ways in which we group, classify and name microbes. Using DNA sequences to infer evolutionary relationships between microbes & building phylogenetic trees. • Textbook: Chapter 13, I/II Some key terms for systematics Taxonom...

1-3: Naming & Classifying Microbes Lecture Overview: • Introduction to the ways in which we group, classify and name microbes. Using DNA sequences to infer evolutionary relationships between microbes & building phylogenetic trees. • Textbook: Chapter 13, I/II Some key terms for systematics Taxonomy: Science of classifying/naming biological organisms Phylogeny: Study of the evolutionary relationships between different organisms Taxonomists use a combination of genotype, phenotype and phylogenetic information to make classifications. for microbes to , dictate over time , taxonomy guide groupings we've .... increasingly less and used less phylogeny phenotype to Taxonomy reminder • • Organisms with similar characteristics are grouped together into taxa The levels of similarity are hierarchical, from very broad to very similar Remember this?? Domain Kingdom Phylum Class Order Family Genus Species Did King Phillip Come Over For Great Soup? Taxonomy reminder Domain Kingdom Phylum Class Order Family Genus Species Subspecies Red fox E. coli, (Image: Wikipedia) (Image: BioCote) Eukarya Animalia Chordata Mammalia Carnivora Canidae Vulpes Vulpes Vulpes V. vulpes abietorum Bacteria N/A (or eubacteria) Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia Escherichia coli (see coming slides) Naming Microorganisms: Taxonomy o Carl Linnaeus, 1700s. o System for classification – minimize chaos, define structure to be used when new species are discovered o Each organism has two names: the genus (more broad) and species (more specific). Example: Homo sapiens Image: wikipedia o Different from common names (“Cat” vs. Felis domesticus) Scientific Names of Microbes • Latin • May be descriptive of Characteristics (e.g. Deinococcus radiodurans - radiation surviving) • Might honor a scientist (e.g. Escherichia coli - Theodor Escherich) • Might describe physical properties/appearance (Staphylococcus aureus = “Grapes-like”, spherical [cell appearance], golden [colony colour]. Scientific Names • Species names (species/genus) italicized (or underlined handwriting only) • The genus is capitalized and species is lower case • Higher taxa (family, class, order, phylum, kingdom) are not italicized. They are capitalized, through. • After the first use in a manuscript, paper, or report, scientific names are abbreviated with the first letter of the genus plus the species name • Staphylococcus aureus à S. aureus • Escherichia coli à E. coli Scientific Names: Zeroing in beyond species For some microbes, we often work with classifications more specific than species. This can include: ↳ mostly based on phylogenetics • Subspecies: Essentially just the next finer classification after species & biological characteristics • Biovar or biotype - grouping based on physiological or biochemical difference from other members of the species ~ microbes like to switch surface antigens - We can determine diff ones • Serovar or serotype - grouping based on surface antigens • Other naming systems. Sometimes strains can be lumped together based on an important feature. Example: STEC (Shiga toxinproducing E. coli) ~ Pathotypes • Strain “genetic variant or subtype”. Often used to refer to a specific isolate – isolate a new strain give it a name to identify it. ↳ identical genotype to other strain . Scientific Names - beyond species From: cbc.ca news Escherichia coli, serotype O157:H7 This serotype is an example of a “STEC” from previous slide Taxonomy: How does it help us?? • Incredible amount of diversity out there • Taxonomy brings order to chaos. Way to lump together similar organisms with similar traits. Example: Mammalia (a class of animals) - what comes to mind? • Can allow us to communicate more effectively and to make educated guesses about newly discovered organisms • Example – identify a new pathogenic bacterium - determine that is falls into the Salmonella genus. Can make predictions about its cell biology, virulence, metabolism, etc based on what we know about other Salmonella species. Phylogenetic trees – the basics Most recent ancestor common to 1,2 & 3 (usually hypothetical) o Visual means of showing predicted evolutionary relationships between different organisms o Evolutionary time goes from left (root) to right (modern lineages) Textbook Fig. 13.27 o Branches show evolutionary history unique to connecting lineages o Branch length (not always to scale) can show evolutionary distance between nodes Lineage Ancestors à Modern day Determining phylogenetic relationships: Comparing DNA sequences o Over evolutionary time, DNA sequences change (e.g. mutation during DNA replication) o To determine how closely related organisms are -- compare DNA sequences (e.g. specific genes) that are conserved amongst all organisms being compared o More differences in DNA sequence = more evolutionary distance o Certain DNA sequences are better choices than others. Typically looking for highly conserved genes with a highly conserved function that accumulate mutations slowly over time. Determining phylogenetic relationships: SSU rRNA sequencing The ribosome is a conserved feature of all organisms of earth The ribosomal RNA (rRNA, encoded by rDNA) of the small subunit (SSU) of ribosome is commonly sequenced to infer phylogenetic relationships Variable regions useful for identifying relationships, conserved regions useful for PCR Developed by Carl Woese & George Fox in the 1970s E. coli 16S rRNA Textbook Fig. 13.24 The Woese tree of life o Universal tree of life based on nucleotide sequence similarity in ribosomal RNA (rRNA) o Genealogy of all life on Earth o Established the presence of three domains of life: Bacteria, Archaea, Eukarya Textbook Fig. 13.9 16S rDNA to identify/classify bacteria - L What use we for PCR - Isolate genomic DNA (pure culture, environmental/clinical sample) Use PCR primers that bind highly conserved regions of 16S rDNA Generaa Encodes * PCR amplify & sequence 16S rDNA. Align/analyze sequences # Getting * enough DNA PCR allows to start in 1/2 copies ~ PCR reminder (https://www.youtube.com/watch?v=3XPAp6dgl14) Textbook Fig. 13.25 Using sequences to build phylogenetic trees Textbook Fig. 13.28 To increase power of this approach (e.g. analyze closelyrelated organisms) can compare sequences of multiple conserved genes (or even full genomes!) Phylogenetic trees: Limitations Phylogenetic trees are predictions. We can feel very confident in them, but we infer evolutionary relationships (we don’t know them) Horizontal gene transfer (HGT) can confuse things. Microbes can undergo significant HGT. Will have recently-acquired “foreign DNA” mixed in with ancestral DNA Acquired DNA can use undergo homologous recombination. DNA sequence of host genes can be replaced with that of homologous genes from another organism