GDB 103 Final Review Flashcards
quorum sensing
genetic switch that allows traits within a bacterium to be activated based on the density of bacteria in the environment
low cell densities
low concentration of cells
high cell densities
high concentration of cells
cells reach threshold
receptors in or on cells are activated, resulting in new gene expression and a switch in bacterial behavior
diffusible signal factor (DSF)
lipid based
DSF- high cell density
high DSF
- virulence off, biofilm on
DSF- low cell density
low DSF
- virulence on, biofilm off
DSF- high cell density explanation
suppression of virulence and motility. activation of attachment and biofilm formation
DSF- low cell density explanation
expression of virulence and motility gene. no expression of attachment and biofilm formation genes
low cell densities of Homoserine lactone (HSL)
HSL regulated genes off
high cell densities of Homoserine lactone (HSL)
HSL regulated genes on
DSF and HSL
both activate new gene expression and traits in a density dependent manner
xyllela fastidiosa and pierce’s grapes
induces water stress by plugging the water conducting xylem vessels
vibrio fastidiosa and bobtail squid
symbiotic relationship
- bioluminescent properties, heterotrophic, moves in means of flagella, survive on decaying matter
What makes xyllela fastidiosa worse?
environmental drought and water limitation to improve berry quality
benefit to bobtail squid
bioluminescence to find mates. avoid predators, attract prey, communicate with other organisms
benefit to bacterium
nutrient rich environment, active release of progeny to increase fitness
pseudomonas fluorescens and mycoparasitism
builds up in soils and colonizes plant root. parasitic to G. gramminis
production of broad spectrum antibiotic to kill fungal pathogen
agrobacterium tumefaciens
sharing of metabolic capacities. plants make opines, rich sources of C and N.
How does opines work
individual strains utilize specific opines, but not others.
- share necessary gene with other members of the community through horizontal gene transfer
therefore, optimize metabolic capacity of larger agrobacterium community
rhizobium nodulation genes
rhizobium bacteria exhibit high degree of host specificity
how does rhizobium nodulation work?
all bacteria that fix nitrogen with legumes share a common set of genes “nod genes”
- acquired by horizontal gene transfer
how does rhizobium nodulation work cont
encode bacterial signal that triggers development of nodule organ on the plant root
Nod factor
signal molecule made by the bacterium and perceived by the plant
endophytes
within a plant (inside)
low alpha diversity, high selectivity
epiphytes
on the plant surface
peripheral communities
nearby in the soil
what do plant breeders do
routinely manipulate host genes to create resistant crops
plant immune system
controlled by host and pathogen genetics. plant pathogen behavior often host dependent
Number of taxa changes
decreases significantly from soil, to root surface to plant interior
changes in microbial communities
reproducible among plants and between locations, indicating a high degree of selectivity
What does selectivity suggest
co-evolution between plants and microbes. functional relevance to such associations
Koch causality 1
organism must always be present
koch causality 2
organism isolated from host and grown in pure culture
koch causality 3
sample of the organism taken from pure culture must cause same disease when inoculated into healthy, susceptible animal in the lab
koch causality 4
organism must be isolated from the inoculated animal and must be identified as same organism first isolated from the originally diseased host
16S DNA sequencing
for prokaryotes. amplicon based and not very deep. specific region (PCR and amplify)
18S DNA sequencing
for fungi and other eukaryotes
microbiome experiment
each sequence is a separate observation of a particular microbe. data can be used in statistical tests for enrichment of microbial taxa in diseased plants
pseudomonas fluorescens
builds up in the soils and colonizes plant roots and is parasitic to G. gramminis
parasitism and G. gramminis
involves production of a broad spectrum antibiotic to kill the fungal pathogen
p. fluorescens and quorum sensing
P. fluorescens antibiotic production is regulated by quorum sensing
trichoderma virens
produces enzymes that degrade fungal cell walls and anti fungal compounds
biological control of trichoderma virens
activate immune systems in plants to better defend themselves
bacillus subtilis
targets a wide range of fungal and bacterial pathogens
reductionist science
frequently hypothesis driven
features of reductionist science
manipulate only one aspect
- gnotobiotic systems
- modify host status or genetics
- antibiotic treatment
discovery science
not hypothesis driven, usually discovery
features of discovery science
focuses on features, patterns and statistical correlations
- 16S sequencing
- metagenomics
- whole genome sequencing
16S sequencing
targeted portion of a genome
metagenomics
bulk sequencing of environmental DNA
- sacrifices sequencing depth and therefore sensitivity
whole genome sequencing
sequencing of pure strain isolates
proper experimental design
system appropriate to the question
- choosing subjects
- selecting landscape
- designing experiment
design lend power and suitable for statistical analysis
- replication
- nature of manipulation
- types of analyses
Surfer example
discovery science. characterizing/ describing and not manipulating
NY subway
microbiome of inanimate geographical space. lots of human DNA (skin and bodily fluids) match back to ethnicity and origins
measuring data from NY subway
ability compare sequences back to taxa and what we know. single nucleotide difference can identify human ancestry. human ancestry predictions mirror census data
Yersinia pestis and humans
looking at short read data for evidence of a pathogenicity gene from the black plague pathogen
yersinia pests effect on humans
responsible for deep tissue invasion
sampling arctic microbiome
largely inaccessible area of the planet, spacial issues- among fastest changing ecosystems on the planet and strongly impacted by climate change
microorganisms in arctic microbiome
microorganisms found within and below the sea ice form the foundation of the marine food web
where to collect data via levels
biological, geological, atmospheric, chemical
replication
sampling multiple times in same environment and same area
seasonality/ frequency
multiple times during year and times a day
mice and arabidopsis for model systems
extremely well characterized biology. extensive genetic resources in public domain
- traditional genetic stocks
- mutant collections
- full genome
- mutant tools
plant immune signaling pathways
in plants:
- jasmonic acid
- salicylic acid
- ethylene
controls in mouse vs human studies
multiple inoculations with fecal bacteria. use of twins to control genetic factors. replication with 4 pairs of twins
significance of co-housing mice
converts obese to lean mice.
conversion of Bacteroidales from lean to obese mice
observation of phylogeny with families of gut bacteria
phylogeny of two major families of gut bacteria has the same topology at the homind host
How would this arise
isolation (genetic drift) or selection and co-evolution
What does this relationship indicate
very long standing (stable) interactions
gyrB gene
better for closer relationships
encodes an enzyme involved in regulating DNA structure
chloroplast phylogenies in plants
the phylogeny of established endosymbionts mirror the phylogeny of their host genome
resiliency
rate of recovery after disturbance
resistance
intensity to disturbance
stability
a function of resilience and resistance
ecological resistance
many stable states in which a community may reside
Human gut microbiome and ciproflaxin treatment
huge drop in alpha diversity. drug has huge effect on microbiome. patient specific differences
control and amoixicilin
similar shift, immediate shift in frequency
tylosin
delay in maturation in the microbiome
children with sever malnutrition
microbiome does not mature with children with severe malnutrition
antibiotic use: spontaneous recovery
slower, typically complete recovery of microbiome
probiotics
recovery of microbiome delayed and incomplete
FMT
fast and complete recovery of microbiome
alpha diversity for antibiotics
control: steady amount
sp: took a little longer but still complete
pro: incomplete and declined
FMT: bounded back quickest
beta diversity (unifrac, distance to baseline)
control: closest
sp: mid
pro: far from baseline
FMT: joined
role of appendix
acts as a “house” for healthy gut commensals. possible reservoir of healthy gut microbiome
removal of appendix
correlated with gut dysbiosis
effect of gut dysbiosis
correlated with increased risk of colorectal cancer. immediately after appendectomy, there is a shift in the gut microbiome
clearing gut of dominant microbes
can lead to dominance of C. Dif as gut is recolonized. C Dif can cause ineffective diarrhea
phosphatidyl choline
promotes cardiovascular disease
trimethylamine-n-oxide
gut microbiota linked to CVD risk and other human outcomes
maternal immune activation
epidemiological studies suggest that activation of the material immune system during pregnancy increases risk of ASD
bacteroides fragilis
normal component of the human gut microbiome. can suppress 4EPS levels
treatment of MIA ASD mice with human Bacteroides fragilis corrects
ASD related behaviors
restores gut permability
alters the microbiome to a new state
4EPS
can induce ASD like behaviors in normal mice
What does the data suggest
a gut microbiome brain connection and may lead to pharmacological therapies for ASD
Belgian and Dutch subjects
two genera of bacteria, Coprococcus and Dialister were missing from the microbiome of the depressed subjects
lactobacillus rhamnosus
decreases production of stress hormone. regulates emotional behavior and central GABA receptor expression
GABA
naturally occurring amino acid, works as a neurotransmitter in your brain, can boost mood, having calming/ relaxing effect on the nervous system,
GABA acronym
gamma aminobutyric acid
Vagus nerve
main proposed gut-brain connection. food satiation and reward
zombie ants and Ophiocordyceps
fungus produce different chemicals that grow on brains of different ant species. fungus erupts from ant’s head to produce spores that fall to forest floor
Toxoplasma gondii
aggregate neuorticism (anxiety, fear, moodiness). cat odor activates sexual arousal pathways in brains of toxoplasma gondii infected rodents
toxoplasma and humans
tend to show long terms personality changes
- women: more intelligent, affectionate, social
- mean: less intelligent, more loyal, frugal and mild tempered
both genders
higher level of neuroticism: more prone to guilt, self doubt and insecurity
The Force analogy
microscopic organisms that exist symbiotically in all living cells. enhance natural, physical and mental abilities
mealworms and styrofoam
antibiotic treatment resulted in reduction in bacterial numbers in the gut and less depolymerization and mineralization of styrofoam
sheep developing “staggers”
many cool season grasses are infected by “endophyte” fungi that produce toxic alkaloids
alkaloid examples
LSD: halucinogenic
morphine: pain control
opium: psychoactive
nicotine: stimulant
vinblastine: anti tumor
mosquitos and humans
A. gambiae: highly attracted to humans based on olfactory cues derived from human skin
individuals attraction to A. gambiae
higher abundance but lower diversity of bacteria on their skin
Japanese population and seaweed
transfer of enzymes from marine bacteria to Japanese gut microbiota
microbes alter scents of hosts
scents correlated with sex, species and reproductive status. can attract pollinators and repel pests. removal of floral microbiota reduces floral terpene emissions
dr Domingues bello
urbanization, new diseases, processed foods, medicine influences the microbiome structure
health issues
obesity, asthma, celiac disease
less hunter gatherer and gardening
yanomami
in direct content with western civilization. competition against soil bacteria
informed consent
full knowledge of procedure and risk. free will without any coercion. understand what they’re consenting to
