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77 Cards in this Set
- Front
- Back
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how many microbial genomes?
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1x10^30 microbial genomes
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Described how many species to date? why?
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5000.
because most microbes are hard to grow |
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phenotypic classification likely possible? if not, what is?
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no.
DNA sequencing (genotype) |
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How many sequenced DNA on earth?
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1 x 10^-22%
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taxonomy
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tax = arrangement/order
nom = law law of arrangement/order |
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Taxonomy is composed of 3 parts. what are they?
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1.) Classification
2.) nomenclature 3.) identification |
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Define taxa
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organisms that are grouped together by mutual similarities
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What is natural classification? (2 points)
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1.) organisms arranged into groups based on similar characteristics
2.)evolutionary relationships was based on phenotypic comparisons |
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Who first developed natural classification?
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Carolus linnaeus,the botanist
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classical microbe taxation?
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microbes were originally names after the type of disease they caused
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what is polyphasic taxonomy?
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combines all three phenotypic (observable) classification, phyletic classification, genotypic
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Binomial system
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consists of genus and species names, italicized
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what is phenotypic classification? (4 points)
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1.) based only phenotypic characteristics
2.) does not show evolutionary relationships 3.) no weight/importance assigned to the phenotypic features 4.)taxa assigned based on a large number of different attributes |
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What is Phylogenetic classification?
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based on evolutionary relationships
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What did they use in early studies for phylogenetic classification?
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fossil records
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Would fossil records work for phylogenetically classifying microbes? why?
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no.
microbes are small and soft, so they won't be reserved |
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what did Woese and Fox establish?
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they established a relationship based on the sequence of small subunit rRNA
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What is a ribosome?
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RNA machine
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how many subunits does a ribosome have in e.coli?
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2.
30s and 50s |
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what does 30s subunit contain?
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16S rRNA and 21 ribosomal proteins
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What kind of rRNA do eukaryotes consist of?
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18S
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How many 16S and 18S sequences does the current database contain?
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exceeds 500,000
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What is genotypic classification?
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compares the similarity of different organisms genomes (entire sequence of DNA)
70% homologous were considered the same species (due to horizontal gene transfer) |
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What is the problem with genotypic classification?
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they came up with the 70% threshold from classical grouping of organisms
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How do you group animals?
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animals that can interbreed and create fertile offspring
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what does serotype mean?
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it is recognized by different antibodies
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What are the three domains?
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Bacteria, archae, eukarya
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suffix for order?
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-ales
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suffix for famile?
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-ceae
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define species
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group of strains that share stable properties that are different than those from other strains
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Strain
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descendants from an isolated, pure culture
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biovar
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strain that differ biochemically and physiologically
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morphovar
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strains that differ morphologically
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serovar
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strains that differ antigenically (immunulogically distinct)
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what is strain type?
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it holds the species name
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what is Candidatus?
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species that are provisional based on genetic information, but will never grow in a pure culture
ps. candidates names are not italicized |
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What are the four characteristics for determining hierarchy classical style?
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1.) morphological
2.) physiological and metabolic 3.) biochemical 4.) ecological |
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Classical characteristics:
Morphological |
based on structural features
specific features can determine genetic sequences |
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Classical characteristics:
Physiological and metabolic |
relates to microbial activities
eg. energy sources, motility, oxygen relationships etc indirectly compares genomes |
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Classical characteristics:
Biochemical |
FAME: fatty acid methyl ester
compares the composition of fatty acid chains (environmental conditions must be the same in order to do so) |
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Classical characteristics:
Ecological |
based on the ability to colonize in a specific environment
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Determining hierarchies molecular style
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does not require fossil records
direct analysis of DNA and RNA and protein |
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Nucleic acid base compostion
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look at the GC content
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what is the GC content in animals/plants and microbes?
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animals/plants - 30-50% avg. 40%
microbes - 25-80% |
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What has a higher melting temperature: AT base pair or GC base pair? why?
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GC, it has 3 bonds therefore its stronger
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Hybridization
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to determine 70% threshold
use ssDNA and a radiolabled ssDNA of a different species. if its 70% homologous and <5% melting temp, its considered the same species |
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sequencing
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preferred method for phylogeny
need to find genes that are conserved |
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Why is rRNA good to look at sequencing?
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horizontal gene transfer does not take place
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what is indels?
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insertions and deletions
random sequences of rRNA genes that are inserted or deleted between organisms |
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oligonucleotide signature sequences
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short conserved, sequences in the rRNA that are specific for phylogenetically defined organisms
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Geonomic fingering
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examine genes that evolve faster than rRNA or indels
MLSA - multilocus sequence analysis RFLP - restriction fragment length polymorphism SNP - single nucleotide polymorphism (refers to human genetic disease) |
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define orthologous species
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genes that are the same but in different species
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What do phylogenetic trees do?
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display evolutionary relationships
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OTUs
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operations taxonomic units
sequenced organisms on the tips of the branch |
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Is distance between organisms important?
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YES
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what does a node in the tree represent?
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a shared common ancestor that is now extinct
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To assemble a tree, why must there be a mix of random and matched positions?
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the matched positions are to line up the sequence and look up small changes
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phenetic tree
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distance between organisms is important
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cladistic tree
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character-based, starts with assumption of evolution
shows relatedness but not the time frame CANNOT rotate cladistic tree |
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rooted vs unrooted
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rooted: has an out group, shows you evolutionary progression
unrooted: does not show an evolutionary pathway,but it does show evolutionary distance |
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outgroup
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more distantly related
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UPGMA
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unweighted paired group method using arithmetic averages
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why doesn't UPGMA work?
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assumes evolution is at a steady state
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Neighbor joining
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another way to build a tree where you start from the inside and work your way out
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What is bootstrapping?
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to assess accuracy
columns are randomized, realigned and reassembled if tree constructed is in more that 70% of bootstrapped trees, it is consider valid |
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LUCA
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Last universal common ancestor
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How does microbial evolution occur?
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mutation and horizontal gene transfer
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what is horizontal gene transfer?
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process in which genes are transferred from one mature, independent organism to another
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how does HGT affect the phyolgenetic tree?
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ask tang
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How to researchers deal with this problem?
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ask tang
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What are two microbial evolutionary processes?
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metapopulation model and ecotype model
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what is metapopulation model?
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microbes live in individual patches/niches
start to colonize which then drifts becoming heterogenous diverge to a point where they are no longer in the same taxa |
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what is ecotype model?
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a genetic event occurs which allows one group of organism to thrive on others which lead to extinction
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what is core genome?
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a set of genes that are homologous and found in all genomes of a phylogenetically cohesive group
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what is pan-genome?
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core-genome and all other genes
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Speciation is driven by _________ while rapid adaptation is driven by ________
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mutation;HGT
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What is Bergey's manual?
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a book where it has all the official names of all bacterial organisms
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