Understand the function and basic principles of taxonomy
as complete description as possible
appropiate way of arranging and cataloguing units/species/strains/clones
=> classification, naming (nomenclature) and identification of organisms -> worldwide labeling for trackability based on evolutionary relatedness
Define the three termini of microbial taxonomy
Classification = organisation of organisms that share similar morphologic, physiologic and genetic traits into specific groups or taxa
Nomenclature = the naming of microorganisms according to established rules and guidelines provides accepted labels by which organisms are universally recognised
Identification = the practical use of classification criteria to distinguish certain organisms from others (e.g. to isolate and identify the organism that causes a disease)
Provide details on how the taxonomy classification system works
arranging objects into groups in relation to attributes possessed by those objects/bacteria
-> based on phenotypical and functional/causal attributes
-> familiar hierarchical system represented by family trees/dendograms with ranks
Provide details on dendograms and phylogenetic trees
dendograms
display of evolutionary relationships among various biological taxa
-> relatedness on gene content not (only) phenotype
=> length := evolutionary relatedness/distance
phylogenetic trees
property of relatedness
branches := distance reflection
claed := similar groupings
-> can be made from genes with distinct marker genes
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
rooted in tradition of (Carl) Linnaeus
mostly descriptive back in those days
Latin nomenclature
increasing similarity in more granular nomenclature
single names with characteristic endings in higher ranks
two-named basic unit: genus + particular species in latinized form (underlined/italic)
standardised by international agreement
now: genome for taxa naming in latinized form
different attributes including biochemical properties
Understand the differences between a bacterial species, strain and clone and what is meant by a ‘type strain’
species
strains of common origin
most similar to each other than to any other strain
strain
isolate or group of isolates
distinguished from other isolates of same genus and species
by phenotypic characteristics or genotypic characteristics or both
clone
genetically related isolates
indistinguishable from each other
by variety of genetic tests or similat to be persumed to be derived from a common parent
type strain
essentially definition of species
aka standard
for testing new methods
-> different no. for different countries
Provide basic details on identification methods (but this will be covered in more detail in the Identification lecture)
comparison of an unknown object with all similar and known objects
-> no match: considered a new species, variety or strain => adequately described then added to list of known objects
traditional identification methods: rely on phenotypic identification using staining, culturing and simple biochemical tests
modern identification methods: WGS best
Understand the principles of bacterial biodiversity and be able to discuss official vs. estimated bacterial ranks and numbers
2/3 of Earths bacteria
lots to discover in understudied environments
Provide details on some of the global efforts to catalogue bacteria including culture collections
DSMZ
NCTC
human microbiome projects
Meta HIT
HMP
Earth microbiome projects
Describe some of the different phenotypic methods that can be used in bacterial taxonomy and issues with only using these approaches (further details will be covered in the Identification lecture)
naming after someone -> not specific
naming after clinical syndromes -> sometimes more diverse syndromes (e. g. not only GIT but respiratory too)
List the different types of genomic methods used in bacterial taxonomy and associated advantages
DNA base content (GC ratio)
(digital) DNA-DNA hybridisation
16S rRNA
gene sequencing (house-keeping genes)
combination of gene targets in “multi-locus” analyses
WGS
Describe how some of the older genomic methods can be used in taxonomy including GC ratios and DNA-DNA hybridisations (and their limitations)
GC
guanine-cytosine content of biological sequence (melting temp/mol %)
btw. 25 - 75 % for bacterial genomes
conventional indirect methods
poor resultion
ratios difference >= 5 %
unrelatedness of similar/identical GC ratios
DNA-DNA hybridisation
denatured genomic DNA mixture
> 70 %: same species
gold standard for species definition
highly labor intensive
time consuming
error prone
poorly reproducible
Describe how molecular methods are used in bacterial taxonomy and their advantages
relatively quantitative way to view biodiversity in context of phylogenetic maps or evolutionary trees
fast-clock molecules for fine-structure
Understand how ribosomal genes (e.g. 16S rRNA) can be used as molecular clocks
found in all living creatures
culture-independ means of investigation by cell component analysis
excellent descriptors of organism’s evolutionary history
no detectable horizontal gene transfer
large and growing db
reconstruction of phylogenies
OTU (Operational Taxonomic Unit): classification of groups of closely related individuals by similarity (97% same genus, 98 - 99 % same species)
AVR (Amplicon Sequence Variant): single-nucleotide differenciation level over sequenced gene regions, introduction of amplification and sequencing errors, higher sensitivity and specificity than OTUs
Provide information on whole genome based comparison methods for bacterial taxonomy and their advantages over other methods (including basic overview of sequencing bacterial strains)
misleading results due to single/small numbers of genes
most objective and accurate comparison btw. whole genomes
cost effective
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)
genome relatedness indices
ANI (average nucleotide identity): average nucleotide identity of all orthologous genes shared btw. any two genomes
AAI (average amino acid identity): btw two genomic datasets of proteins, for more distantly related genomes
digital DDH: genomic in-silico method for genome-to-genome comparison, calibration of 70 % threshold
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
for providing relations or taxonomy WGS of bacteria
reconstruction form pure monoclonal cultures
MAGs (Metagenome Assembled Genomes): shotgun metagenomics
circumventing isolation and pure culture limitations
further refinement, correction and revolution of understanding tree of life
limiting values of these genomes
gaps
local assembly errors
chimeras
contamination by fragments from other genomes
UHGG (Unified Human Gastrointestinal Genome): 70 % lack cultured representatives
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