GDB 103 Midterm Flashcards
What is a disease?
any condition that impairs the normal functioning of the body
What is the Disease Triangle and how do all three components contribute to disease?
host, pathogen, environment. Interaction of susceptible plant host. A virulent plant pathogen. Favorable environment
pyramid or tetrahedron disease triangle
effects of microbes and symbiosis interactions
examples of plant disease and symptoms in plants
fire blight of apple, apple scab, late blight potato
examples of human disease
athlete’s foot, strep throat, measles
mutualism
both species benefit
commensalism
one organism benefits from the other without affecting it
parasitism
one species benefits at the expense of another
binary symbiotic interaction
fungus and cyanobacteria. fungus receives nutrients, cyanobacteria enjoys moist environment and surface attachment
three way symbiotic interaction
late blight of potato. phytopathora infestans and greater than average rainfall, low temps.
Carl Woese and advent of ribosomal SSU sequences
three domain system. universal phylogenetic tree based in SSU rRNA sequences
Aspects of 16S SSU RNA that make it well suited for microbiome analysis
good to place into evolutionary context.
Molecular markers for microbiome analysis in fungi
18S, 5.8S, 28S
importance of PCR
extract DNA, run primers, represent diversity in sample. oligonucleotide primers used to start DNA replication in PCR
Typical work flow
sample collection, extract DNA, SSU rRNA gene amp, DNA sequencing, data analysis
How do we know unculturable organisms exist?
most microbes can’t be cultured in the lab. great plate count anomaly and culture independent approaches
abundance table
quantify and interpret the microbial diversity within samples and/ or between samples
rarefaction curve
plots number of species as a function of the number of sampled organisms
species richness
measure of diversity (unweighted)
Simpson’s index of diversity
number of times each species is observed (weighted)
jaccard dissimilarity
% of species common between 2 sites (unweighted)
bray-curtis dissimilarity
% of individuals within a species that are common between 2 sites (weighted)
UniFrac
“species” similarity. accounts for evolutionary distance
importance of replication
reduce biases, build confidence, more reliable conclusions
life without microbes
increased susceptibility to infectious disease agents, poor immune systems, vitamin K must be supplied and swelling of cecum. more susceptible to LD50 salmonella
germ free animal
entirely free of all “contaminating” organisms
gnotobiotic
controlled environment containing one or a few kinds of organisms
ability to transplant microbiome from one individual to another
properties in our microbiome can have effects on our physiology. trait emerges from genetics of mice and microbiomes
implications of touch for transfer and acquisition of microbiomes
skin: largest human organ, mobile phones, athletic equipment, kitchen surfaces, indoor bacterial communities, importance of environment
effects of feeding behavior and source impacting microbial composition. sources of microbes
microbes in fecal bacteria or other parts of deer, now part of vulture. plant: surfaces, roots
animal: skin, hair, feathers, GI tracts
pasteurization
heat to destroy pathogens in food
irradiation
expose foods to ionizing radiation to prevent spoilage
probiotic
live microorganisms, health benefit to host
prebiotic
diet based influences, not living,
probiotic and prebiotic supplements
not suitable for clinical use, is it FDA approved?
everyday situations that could lead to acquisition of your microbiome
mobile phones, behavior, social interactions
environment contribute to microbe acquisition
types of bacteria correspond to use of those surfaces
horizontal transmission: iguanas
consume soil or parent feces to establish microbial fermentation system
horizontal transmission: bees
feed bee bread, mouth to mouth
horizontal transmission: kissing
8x10^7 bacteria/ intimate kiss of 10s
birthing
c-section vs vaginal birth
feeding
breastfed vs formula fed
antibiotics
lower bacterial diversity
community assemby
composition/ diversity of microbial species within given environment
metacommunity
interconnected microbial communities that exist
succession
composition of microbial community change overtime
Why is the cow rumen an example of a complex symbiosis?
~ 1000 distinct microbial species present. diversity creates symbiotic relationship degredation of cell well requires diversity
dysbiosis and examples
microbial imbalance on inside the body.
psoriasis or obesity
biofilm
collection of microorganisms that stick together and to a surface. common in nature
obligate symbiosis
necessary interactions, close relationship where one cannot survive without the other
“we are at least from the standpoint of DNA, more microbial than human”
the human body contains significantly more DNA than human DNA
emergent properties
function that can emerge uniquely from interactions, or from complexity of interaction
hologenomic speciation
evolution of species influenced by a host and its microbiome. gut bacteria causing hybrid lethality in Nasonia. natural selection acting on a trait that emerges from the interaction
origin of nucleus
cell membrane infoldings. endomembrane system encloses nucleoid to make the membrance bound nucleus
origin of mitochondria
proteobacterium becomes symbiont, gets engulfed. eventually absorbed and becomes a mitochondrion
origin of chloroplast
eukaryotes acquire additional endosymbionts (cyanobacteria). eventually become chloroplasts
how is eukaryotic life an example of ancient, obligate symbiosis
one cell engulfs another, such that the engulfed cell survives and both cells benefit
What are Asgard?
proposed superphylum of archaea
What is Asgard significance in the origin of eukaryotes?
contained many key components that govern eukaryotic complexity
how are rickettsia and cyanobacteria related to mitochondria and chloroplasts?
genome attrition, metabolic coordination, obligate lifestyle
Who is craig venter?
environmental shotgun sequencing of the Sargasso sea
What did he discover?
> 1800 species including 148 previously unknown organisms. however his findings were patchy
What is a pangenome?
collection of all the genes in a species or population. for bacterial species, associated with genetic diversity. for humans, associated with adaptations and capacity to live in new environment
populations
set of organisms from a single species
communities
group of populations of 2 or more species
types of measures to describe populations and communities?
alpha, beta and gamma diversity
ancestry, nucleotide distance, gene content
horizontal gene transfer in bacteria, asexual fungi and viruses
how new gene forms can move between lineages, shape structure and function of microbial communities
horizontal gene transfer play a role in evolution like formation of gametes
exchange of DNA between lineages. meiosis, fertilizations and mutations
nitrogen cycle
nitrogen gas to ammonia to nitrate
haber bosch process
nitrogen and hydrogen into ammonia, driven by oil and fossil fuels at 600 degrees celsius
nodule
part microbe/ part plant
how did nitrogenase enzyme become widely distributed among bacteria and archaea?
through horizontal gene transfer. sharing of information
is the nodule microbiome more complex than just nitrogen fixing rhizobium species?
microbes inside nodule more complex. has a characteristic and distinct microbial community
microbiome component functions
digestion, cellulolytic, lipolytic, amylolytic
does diet have an effect on the rumen microbiome?
highly variable. forage poor: high levels of fungi. high cellulose: high level cellulolytic
researchers interest in biofuels
the cow’s rumen microbiome is a source of enzymes that might contribute to more cost effective biofuels
oligochaete worms and obligate microbes
benefits to worm: energy production and handling waste. derive carbon and energy by consuming bacteria as food.
benefits to microbes: housing, environment
