ALLEN VERCOE SET 1

3 questions that microbial ecology asks

whats microbes are present? what do they do? how do they respond to different conditions?

3 ways to figure out "whos there"

culture, RNA seq, DNA seq

________ occurs naturally in about 50% of insect species, but not in ________ mosquitos 

wolbachia, anophleles (malarial)

amensialism example in class: streptomyces coelicolour, why?

streptomyces coelicolour acts similar to a fungi though it is a bacteria, it produces natural antibiotics and releases them into the soil to kill and consume other bacterias (non specific). amensialism requirements 

amensialism requirements 

- one species benefits, other species harmed (non specifically)

anopheles mosquitos carry malaria, describe how wolbachia can be used to help fight malarial mosquitos.

if males are infected with wolbachia, uninfected females that mate with these males have eggs that cannot hatch (cytoplasmic incompatability) which helps to lower population.

wolbachia also competes with plasodium (malaria) and dengue. 

Bary Marshall discovered 

H. pylori was found to cause gastric ulcers (rather than diet, lifestyle...), by injesting the H. pylori himself and then treating it with an antibiotic. 

define labile

not stable

endosymbiosis requirements

- must live within host
- can be mutualistic or parasitic- hard to tell 

example of commensalism in class: beggitoa sulfur spring microbes, why?

Beggitoa consume H2S and oxidize sulfur to the less toxic elemental sulphur. The beggitoa simply is doing its metabolic process and other organisms benefit due to reduced environmental toxicity. 

example of parasitism in class: legionella phemophila, why?

freshwater ameoba that infects air vents, water fountains, and causes legionella disease when enters and infects specifically the lung cells macrophages.

example of synegism in class: rumanent cows, why?

cows stomachs have microbes that ferment complex polysaccharides to H2 +CO2, then this is taken up by methanogens and converted to methane. the cow recieves energetic byproducts and microbes cross feed. however these organisms can survive seperately.

Hess determined to use agar intead of gelatin why?

gelatin would melt in summer

High throughput is great why?

reduces labour, use AI and robots to simulate hundreds of conditions, isolate, identify, compare many thingsa t once and sequence DNA (gDNA)-genomic

how is integrating the host (ex. animal or human) data beneficial to studing the microbes?
how can this data be used?

-how host and microbe interact
-how host epigenetics, metabolite, proteins, etc... effect the microbes

used in personal medicine research (ex. zoey project match perfect foods for individual microbiomes)

in adults H. Pylori is considered a ______, however in children H.Pylori can protect against athsma and train the immune system making this reltionship _______

parasitism, synergism 

is human gut even or uneven in species?

very uneven

it used to cost _____ to sequence a genome now it is as little as ______

millions, $70

lipidome
secreteome
resistome
phenome

lipidome- lipids in sample
secreteome-secretions by cell (dont open cell)
resistome- AMR in sample
phenome- phenotypic data (ex. spatial assortments)

many ____ species are infected by intracellular bacteria (endosymbiosis)

insects 

meta transcriptomics

RNA seq the mRNA content- see active transcription and see what cells are doing in response to the environment in this moment. 

metabolomics

extract metabolites, subject to NMR or MS, use computer to see whats being made. con being that you dont know who made it (what microbe)

microbes in cow stomach can live in protozoa (T/F)

T

mitcochondria 16S rRNA is a taxonomic prokaryote marker that shows ________ is one of the closest relatives to the mitochondria

ricketsia (small microbe that causes typhis and can communicate ith mitochondri in cells) 

mitcochondria and cloroplasts do  ______ endosymbiosis. 

mutualistic 

mutualism example in class: litchen, what is it made of, why is it mutualistic?

lithcen= fungi + alga (or + cyanobacteria, or both)
fungus- UV protetcion, provides minerals
cyanobacterium/algae- provide photosynthetic products 

Mutualism requirements

-cannot survive independantly 
-genomes advanced degradation
-products produced by one bused by other

omics revolution involved new tech with _____ capabilites and high power computing

high throughput

parasitism can become mutualism when?

if orgnanisms figure out how to live together

parasitism requirements

- one species benefits, other killed or harmed
- specific, obligitory interaction for the parastie

Photorahbodos Luminescens lives in neamatod (heterohabditis bacteriophora) making them glow. the glow attracts worm predators and it is consumed. in the insect the bacteria from the nematod kill the insect. the worm and bacteria use the nutrients of the insect and then reassociate. what symbiosis is this?

synergism 

proteomics

extract proteins, sequence with MS, match peptide to protien, match protein to gene (from metagenome) and you can see what is occuring in the specific time you took the sample. (can have inaccuracies as some protiens break down fast)

seawater was once thought to be sterile why?

microbes did not grow on culture plates, need ecosystem, often oligotrophic or have specific nutient requirements

staphylococcus epidemidis uses dead skin cells as nutrients and is not problematic to host this is ________. 
new evidence shows staphlococcus epidemidis is antagonistic and competes against the human pathogen staphlococcus aureus (which is bad for ppl)(mursa) this relationship between staphlococcus epidemidis and humans is now ________.

commensialism (rare type of interaction), synergism

symbiosis is always good (T/F)

F

Synergism requirements

-removal of one= decreased growth of other
-each benefit from eachother
-partners can grow independantly

the issue with omics methods is often that you only get a snapshot in time but microbe communities are dynamic, how can this issue be solved to take better measures?

longitudinal sampling- takes samples over time to get dynamics of microbial community 

types of insect endosymboiants mentioned in class (3)

wolbachia, wigglesworthia, sodalis 

VBNC

viable but not culturable

what in prokaryotes is the main taxinomic marker? it has shown the realtion of mitochondria and _____, a small bacteria responsible for causing typhis (parasite) 

16S rRNA, ricketestia

what is amplicon sequencing and how does it compare to metagenomic (aka shotgun) sequencing?
pros and cons of each?

amplicon:
- target specific gene amplified, barcoded and sequenced (commonly the 16S rRNA)
-con being that 16S is prokaryote specific, doesnt show eukaryotes

metagenomic:
- gDNA broken up and directly barcoded and sequenced (sequences all genes not only a specific one), computer sorts and pulls out genes to see whats in sample
-con being it requires a lot of computer power

both types show species richness, alpha diversity (diversity within sample), eveness and dominance 

what is it called when a cows stomach is made accesible to remove food/bacteria by hand?

fistulation

what is metadata? how is it used?

information about other factors such as environment, sex, age, weight, etc...) provides a context to see bigger picture

what required for commentialism 

- one species benefits
- other species neither harmed nor benefits 

why use RNA sequencing over DNA sequencing to see whats there even though RNA is unstable and needs converted to cDNA anyways?

RNA generally only seen in active alive cells that are transcribing, DNA is present in both dead and alive cells

cornelius van neil

every molecule in nature can be used by a microorganism somewhere- an idea by

2/3, bacteria and algae

what fraction of earth is ocean? what are the oceans primary producers?

a submarine that sank and stayed 1500 m deep in ocean, when recovered, a sandwich in a lunch box had not been eaten after about a year on the ocean floor- tells us how slow metablolisms are down there

what is ALVIN? what key insight did it provide?

Neusten- 10microm on surface of ocean, high tension and most bacterial life

Euphhotic zone- gets sunlight, near coast there is less due to muddied waters

Aphotic zone- dark no light

Bethos- deepest part of ocean

name and describe the 4 main layers of ocean:

4 degrees C

the ocean temp is relatively uniform past aphotic zone and stays around ____

Holger Jamash found ocean microbes under microscope that were not seen as culture on plate previously (many oligotrophic and reliant on eachother with specific nutrient requirments- often want little nutrients due to slow metabolisms)

the ocean was once thought to be sterile, who proved this wrong?

reduced sewage dumping because microbes in ocean cannot metabolise it fast, it just ends up as a pollutant (metabolisms more than 100x slower than on land)

Holger Jamash advocated for _______ (ALVIN helped to prove)

Estimated 25 000 different microbial species per litre of seawater, 70% of these were previously unknown to science

(In a single drop (one millilitre) of seawater, there are 10 million
viruses, one million bacteria and about 1,000 small protists)

Sorcerer II Global Ocean Sampling expedition found what?

Tara Oceans and Tara Pacific, major finding that temp is major player in what microbes grow where (climate change will greatly effect)

what projects have created a database of all ocean micobiomics? what was major finding?

symbiosis with altermonas that removes toxic hydrogen peroxide produced by prochlorococcus photosynthesis

(CO2 rising is harmimg symbiosis and reducing O2 production in ocean)

prochlorococcus lives in the neusten and does photosynthesis, it is very hard to culture why?

barophiles, psycrophiles, oligotrophs (like nutrient poor), slow metabolic rate and often have heavy metal resistant genes

bethic microrganisms are commonly:

hydrothermal vents with nutrient rich geezers and black Ca2+ chimneys (black smokers), sulfate chimneys that are oasises for life that can live without sunlight

ocassional areas of extreme heat and nutrients on the ocean floor are formed by:

fallen whales, shipwrecks, wherever there is carbon there can be life

cold nutrient oasies formed by:

smell when die, need sulfur and extreme pressure (also note deep sea eyeless shrimp and tube worms)

pompeii worms

decaying organic matter and minerals

soil:

O- organic horizon decomposing matter (fungi, slimemold, actinomycetes)

A- aerated horizon decomposed and minerals (aerobic roots, microbes)

E-eluviated horizon of insoluble particles that is bad at supporting microbes

B- horizon of clay and minerals (last before water table)

4 aerobic layers of soil

water saturated horizon

broken down rock and mineral

bedrock

(here endolith methanogins, chemolithotrophs where mineral e- source)

what anaerobic layers of soil after the watertable?

plants, lithotrophs such as amonia oxidizers

fungi and bacteria (feed nematods and protists that are then eaten by invert&verts)

major producers

major decomposers

distrupts equalibrium and harvested plants dont return carbon to soil

why are fertilizers harmful to soil microbiomes?

decay product of organic matter great source of carbon

humus?

• diverse antibiotics

• produces geosmin (rain smell)

streptomyces soil bacteria

protect from pathogens, fix nitrogen (diazotrophs), feed on plant root nutrients that offer special microhabitat

microbes in rhizosphere relation to plants:

endomycorhizzae- grow inside plant cells, colonize host, no sex cycles, dependant on host, few but important species form arbusculars in root cells

ectomicrohizzae- thick protective mantle around root extending to help plant reach nutrients

wood wide web of mycorrhizae help trees communicate

endomycorhizzae

ectomicrohizzae

part of legume root with nitrogen fixing bacteria nodules that contain leghemoglobin (gives pink colour due to iron), keeps O2 away from nitrogenase enzyme

what are rhizzoids

commensialists

most bacteria in /on us in our non-sterile body areas are ________

in abnormal location of body (ex. sterile sites like bloodstream and urinary tract)

even probiotics can cause disease when ______

microflora (not plants in our gut)

which term is no longer used: microbiota, microflora, microbiome

microbes that live in protists of the termite gut

termites eat lignin, how is lignin digested?

mites that live on human face follicles and digest sebum, have a very efficient microbiome, so efficient that they were once thought to have no anus. due to little waste production, they do not irritate us.

what are demodex mites? what is special about their metabolism?

1:1.3

what is the ratio of human:bacteria in our bodies?

200

species term is hard to define with bacteria because they dont sexually reproduce so its more of a gradient between bacterial types

how many bacterial species per person? why is it hard to tell how many species?

in last 4 years there was a great renaming

why did many microbe phyla change names?

200 students in the USA metagenomic sequencing of various body regions

found many pathogenic bacteria in samples but subjects were still healthy (pathogens can live in us and not cause harm)

who was sampled in human microbiome project? what did this study reveal?

parkinsons, autism, juvinile diabetes, colorectal cancer, chronic depression

some diseases mentioned that can be maybe caused partially because of microbiome:

get lag and time change as well as diabetiies show loss of chonicity in microbiome (the cycles microbes are timed with hormones, meal times, sleep, etc…)

what does time change and diabetes have in common with effect to microbiome?

dry, salty, oily, acidic

mostly gram positive are able to resist these harsh conditions, most found deep in folicules

(staph epidermitis, cutibacterium acnes- doesnt necessarily cause acne)

skin is difficult for microbes to colonize, why?

what type of microbes are found on skin?

gram pos and neg cocci from milk, more bacteria colonize once teeth begin to grow

which bacteria types colonize the infant mouth first? when do more bacteria grow?

F, most mouth bacteria are actually anaerobic and hide in the gums from oxygen

most mouth bacteria are aerobic (T/F)

they are our only non sheading surface

why do teeth harbour so many bacteria?

bacteria ferment sugar making acids that break down the enamal (strep mutans)

why does sugar harm teeth?

oral/respiratory

where is most common infection site in humans?

how many microbes in most areas of body?

how many on skin?

10^12

10^4 or 10^6 (way less)

nose and oropharynx is normally colonized by gram ______ bacteria and species normally (even or not even?)

positive, usually not even- one species dominates (note: different species in diff people and some do better than others at protecting and dominating)

dominance in the nasal/oropharynx could be used for what biotech/medical application?

new probiotics to protect against pathogen by using dominant bacteria

________ lives in about 10% of adults without being pathogenic

menengitis

what is surface area of lungs?

75m²

the lungs were once thought to be a sterile site but actually are colonized by many ______ microbes

anaerobic bacteria (contrary to what u would think for oxygenic environment)

what constantly sweeps particles out of lungs into throat?

mucocillatory escalator

the kidney and bladder are sterile sites (T/F)

T, bacteria can cause UTI

(only some exist around urethra)

vagina microbiome changes with menstural cycle and is healthy when:

less species diversity, best when lactobacillus dominates and not other species

lactobacillus protects from STI, increase reproductive sucess, etc…

condition where you are disposed to vaginal infections and hav reduced reproductive sucess is called

bacterial vaginosis

very few bacteria survive in stomach due to acidic pH, H.Pylori seems to be an exception as it is able to ___

use urease enzyme to make urea into ammonia and create a protective barrier around itself and bury into stomach lining causing ulcers

what is hypochloridia? what are causes? why is it bad?

a lack of acidity in the stomach caused by malnourishment, ppi meds (proton pump inhibitors for acid reflux), now use is questionable due to potential intestinal damages and if you lack acidity more pathogens can survive in stomach.

facultative anerobes always prefer _______ environments (aerobic or anaerobic)

aerobic as respiration is much better at producing energy than fermentation