Describe the function and basic principles of taxonomy
taxonomy provides a uniform / consistent means to classify, name and identify organisms
consistency allows scientists worldwide to use a common label for each organism
it has 2 main functions:
describe as completely as possible the basic taxonomic units
devise an appropriate way of arranging and cataloguing these units
How does the taxonomy classification system work?
classification = arranging objects (i.e. bacteria) into groups (taxa) in relation to attributes posses by those objects (based on how they look / what they can do)
Hierarchy represented by a dendogram (display evolutionary relationships)
units at each level (taxonomic rank) are given distinctive names —> nomenclature
What are phylogenetic trees?
capture major events in a species existence
composed of leaved, branches and inner nodes
branch lenght can also reflect distance
clades represent similar grouping
Provide details on how the taxonomy naming (nomenclature) system works including the history, hierarchies, latinized binomials and the international standards for naming new bacterial taxa
History
Carl Linnaeus (1707-1778): “You have to name your bacteria”
Hierarchy:
Superkinkdom: Bakteria
Phylum: Firmicutes
Class: Clostridia
Order: Clostridiales
Family: Clostridiaceae
Genus: Clostridium
Species: Clostridium perfringens
Naming: latinized
species is give two names
generic name (genus)
specific name (particular species)
Higher rank only one name with charactersitic ending
What is the differences between a bacterial species, strain and clone and what is meant by a ‘type strain’?
Species: ‘A species consists of strains of common origin which are more similar to each other than they are to any other strain’
Strain: ‘… an isolate or group of isolates that can be distinguished from other isolates of the same genus and species by phenotypic characteristics or genotypic characteristics or both’
Clone: ‘Genetically related isolates (clones) are isolates that are indistinguishable from each other by a variety of genetic tests, or that are so similar that they are presumed to be derived from a common parent’
Provide basic details on identification methods
Compare unkown object whith all knwon similar objects
if there is a match -> object has been identfied
no match -> new species, variety or strain and can be added to the list of know objects
Traditionally relies on phenotypic identification (tests on staining, culturing and simple biochemical tests)
Newer are molecular, immunological, and biochemical analytical methods
What are the principles of bacterial biodiversity and discuss official vs. estimated bacterial ranks and numbers
2/3 of Earths biodiversity is bacteria
Still lots to discover (e.g. bacteria from understudied environmets)
Current numbers in published taxonomic literature vs. 16S rRNA databases vs estimated numbers:
Kingdom – 1 (Bacteria or eubacteria)
Phylum - ~50 vs. ~120 vs. ~1,500
Class - ~200 vs. ~2500 vs. ~5,000
Family - ~400 vs. ~6,000 vs. ~25,000
Order - ~800 vs. ~15,000 vs. ~70,000
Genus - ~3,500 vs. ~60,000 vs. ~200,000
Species ~20,000 vs. ~200,000 vs. ~1 mil - 1 tril
Provide details on some of the global efforts to catalogue bacteria including culture collections
Human micobiome project
Earth micorbiome project
Describe some of the different phenotypic methods that can be used in bacterial taxonomy and issues with only using these approaches
Taxonomic phenotypic methods:
classical
biochemical
fatty acid analysis
Whole cell protein analyses
Differences in cell wall structure/components
Other factors (e.g. pigments, pathogenicity, antibiotic sensitivities)
Spctroscopy methods (e.g. M/S)
Problems: labor intensive, leasves uncertainties, results can be difficult to interpret, poorreproducibility
List the different types of genomic methods used in bacterial taxonomy and associated advantages
Advantages: highest level of resolution, rapid, relieable, reproduceable
Methods:
DNA base content (GC ratio)
DNA-DNA hybridisation
targeted sequencing of
ribosomal RNA
house-keeping genes (i.e. conserved essetial enzymes)
multi-locus
whole genome sequencing
Describe how some of the older genomic methods can be used in taxonomy including GC ratios and DNA-DNA hybridisations (and their limitations)
G + C content describes the guanine and cytosine content of a biological sequence
between 25% and 75% for bacterial genomes
frequently used in taxonomic descriptions of species and genera
determined using conventional, indirect methods (e.g. melting profiles)
More common to now calculate the DNA G+C content directly from genomes
poor resolution: even if similar GC ratios, may be unrelated
Denature genomic DNA (gDNA) mixture for organisms A and B
allow gDNA to anneal; hybrids result
Re-association of gDNA ≈ sequence similarity
Considered the gold standard for species definition
new species must be shown to have <70% DDH similarity to existing species to be recognised
Describe how molecular methods are used in bacterial taxonomy and their advantages
A relatively quantitative way to view biodiversity
Slowly evolving molecules (e.g. rRNA) used for large-scale structure; "fastclock" molecules for fine-structure
How can ribosomal genes (e.g. 16S rRNA) be used as molecular clocks?
Found in all living organisms (for 3.8 of the last 4.5 billion years)
Cell component analyses provide culture-independent means of investigating questions in microbial ecology
rRNAs offer a type of sequence information that makes them excellent descriptors of an organism's evolutionary history
No detectable horizontal gene transfer -> important for bacteria
Large and growing databases
16s rRNA has slow rates of evolution
Provide information on whole genome based comparison methods for bacterial taxonomy and their advantages over other methods (including basic overview of sequencing bacterial strains)
Whole gennome sequencing (WGS)
Single or small numbers of genes may provide misleading results (vulnerable to selection bias)
Most objective and accurate comparison would be between whole genomes
Describe the basic principles of WGS taxonomic methods including average nucleotide identity (ANI), amino acid identity (AAI), and digital DDH (and cut-offs for species identify)
ANI
average nucleotide identity of all orthologous genes shared between any two genomes
robust resolution between strains of the same or closely related species
does not strictly represent core genome evolutionary relatedness
similar concept to DNA–DNA hybridization
AAI
estimates average amino acid identity between two genomic datasets of proteins
for more distantly related genomes
dDDH
in silico method for genome-to-genome comparison
Provide detail on new methods that do not involve isolation and cultivation of pure bacterial strains (i.e. MAGs) and how these can be used to uncover novel bacterial taxa
Shotgun metagenomics-> Metagenome-assembled genomes (MAGs)
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