midterm 1 Flashcards
4 conditions for life
- essential elements
- energy source
- temperature
- atmosphere
biosignatures
-isotope ratios
-banded iron formations
prebiotic soup model
-reduced chemicals + lighting made organics and macromolecules
RNA world
RNA was first storage molecule instead of DNA
molecular clock
temporal information in macromolecular sequence based on random mutations
molecular clock requirements (3)
- gene has same function across organisms
- same generation time
- constant average mutation rate
maximum vs. minimum parsimony phylogenetic tree
max: fewest mutations to fit the data (simplest)
min: probability tree would produce observed DNA sequence
rooted vs unrooted phylogenetic tree
rooted: position of common ancestor
unrooted: doesn’t indicate common ancestor
phylogenetic tree building main points
- align sequences
- most probable phylogenetic tree
- visualize and customize with R
commonly targeted molecular clocks
-sugar utilization/metabolism
-virulence factors
-rRNA components
phylogenetic tree clade
group of related organisms
branch/lineage
lineage sharing common ancestor - length = # mutations
monophyletic
node and anything arising from it
paraphyletic
some members of a clade are excluded
polyphyletic
mix of taxa distinctly related
whole genome analysis
insight to relatedness of species other than single taxonomic marker
genomic changes (4)
- random mutation
- natural selection/adaptation
- reductive evolution
- horizontal gene transfer
horizontal gene transfer marker
changes in GC content (%GC)
long-term evolution experiment
12 populations of e. coli from 1 clone, transferred every 24 hours and evolved to grow on citrate
3 requirements for acquiring new trait
- potentiation (useful mutations)
- actualization
- refinement
selective pressure
present at low concentration antibiotic
identifying isolate mutations steps
- whole genome sequencing
- align to reference genome
- max parsimony phylogenetic tree
linear mutation evolution
every mutation increases fitness
logarithmic mutation evolution
each mutation increases mutation until it reaches a cap
parabolic mutation evolution
few mutations increase fitness, too many decrease fitness
mutation evolution model based on: (3)
- rate of ancestral decline
- rate of expansion
- time to fixation
hierarchy of taxa
domain, phylum, class, order, family, genus, species
candidate species
been cultured with physiological characterization, not officially named
defining bacterial species requirements: (3)
- SSU rRNA >95% -> same genus
- ANI orthologues > 95%
- ecosystem/metabolism shared
<97% 16S rRNA gene identity:
species may be novel
<95%-94% 16S rRNA gene identity:
genus may be novel
<91% 16S rRNA gene identity:
family may be novel
prioritizing isolates using isolateR main points:
- chromatogram / sanger sequence
- trim start/end of sequence (QC)
- isoQC - flag suspect, identiy 16S rNRA
- isoTAX - cluster basis of identity
- isoLIB - genetic diversity isolates
core genome
genes shared by group of related strains
accessory genes
present in one or more strains
pangenome
all genes in all members of a species
lachnospiraceae paper main goal
identify core and accessory genomes for therapeutic intervention use
short read next gen sequencing
find sequence, produce millions of 150-300bp long contigs
long term sequencing
span across repeat regions to stich contigs together
genome annotation main steps
- annotate open reading frame functions (rRNA, tRNA) and core genes
- search protein encoding genes
- compare to database to look for protein functions
- BLAST hypothetical proteins leftover to identify
dimension reduction (UMAP)
represent dataset with lower number of features while still capturing main points of data
lachnospiraceae final conclusion points
-60% core genome
-shows inter and intra species diversity
mag’s
2 contigs showing together often, most likely from the same genome and binned together
cyanobacteria examples
-synechococcus
-prochlorococcus
-microcystis aeruiginosa
carbon fixation occurs?
in carboxysomes, rubisco catalyze first step
nitrogen fixation uses?
nitrogenase, requiring anaerobic environment
nitrogen fixation techniques (3)
- heterocysts
- temporal segregation
- cell aggregates
a/b chlorophylls vs. bacteriochlorophylls?
bacteriochlorophylls don’t absorb photons to break down water
microcystis aeruginosa main points
-bloom formers, brackish water
-produce microcystin
-bottom layer hypoxia
-sucrose genes through HGT
gram positive phyla (3) and cell walls
-Firmicutes (low GC)
-Actinobacteria (high GC)
-Mycoplasmatota (no cell wall)
firmicutes -> baccilitota
-monoderm
-thick PG
-spore formers
-g+
lactic acid bacteria human microbiome experiment
666 metagenome assembled genomes from food samples grouped to species bins, most didn’t overlap with human MAGs -> food specific LAB
actinomycetota
-high GC, gram +
-branched & filamentous
streptomyces
-actinomycetota
-obligate aerobes
-geosmin -> soil odour
-large genome, linear chromosomes
antiSMASH main steps
- annotate genome -> antimicrobial gene clusters
- find secondary metabolite/antimicrobial regions
bifidobacteriales
early gut colonizers due to horizontal gene transfer from human milk oligosaccharide
pseudomonadota (proteobacteria)
alpha, beta, gamma, sigma, epilson
-diverse/modular metabolism
purple sulfur bacteria
-photolyse reduced sulfur
purple nonsulfur bacteria
-photolyse H2 and PSII for cyclic photophosphorylation
colonization resistance
healthy microbiota preventing pathogen expansion through SCFA/bile salt production
direct antagonization
type 6 secretion system delivering compounds and bacteriocidin
salmonella & e coli paper main point
-salmonella / e. coli replicate better when gut is inflamed
nos2/NADPH oxidase effects
increase with inflammation, releasing ROS and increasing oxidative environment, reducing strict anaerobes
sulfate reduction in microbiota
H2S -> sulfate (host)
thiosulfate -> tetrathionate (salmonella uses tetrathionate for respiration)
ttr operon in salmonella
tetrathionene as terminal electron acceptor during anaerobic respiration
molybdenum cofactor
allow e. coli to utilize nitrate as terminal electron acceptor
aminoguanidine hypochloride (ag)
inhibit iNOS&ROS production
-competitive advantage for e. coli to respire with nitrite
metabolic flexibility of proteobacteria solutions:
- target conserved pathway components (molybdenum w/ tungsten)
- introduce non-dangerous pathogen to compete (klebsiella)
