Unit 2: Benefits of Microbes

contains many microhabitats for microorganisms, varies in moisture, temperature, molecules, and "food"

type of biofilm, bacteria eats sugars in the mouth and releases acid. resulting in this

common upper respiratroy tract resident, more than 90% of all pneumonia

normal microbiota gets into new space of body, grows and causes problems

common secondary infection after flu

has the most bacteria per gram of anywhere in the human body, potentially connected to obestiy and behavior

form of childbirth that results in the most microbes being transferred to the offspring

most commonly infected item in medical clinics

vitamins produced by normal human microbiota

organisms that exert scientifically proven health benefits, work by taking up space and resources, changing microenvironment, and changing immune response

non-digestible food additives that promote growth of "good" bacteria

old way of determing what microbes are present within a person, not typically used due to large amount of microbes present

profiling of microbiome-wide gene expression, directly informs of activity in microbial communities

determination of small-molecule metabolite profiles (metabolomes), performed using mass-spectronomy or NMR spectroscopy

amplification of 16s rRNA gene hypervariable regions, used to measure composition of gut microbiome by clustering amplicon reads into bins called Operational Taxonomic Units (OTUs) or determining Exact Sequence Variants (ESV)

allows identification of whole genomes including larger range of microorganisms

study of all protein samples recovered directly from environmental sources

disease that was discovered to be treatable in gnotobiotic mice with antibiotics

gut-brain connections, vitamins, immune training, food digesting/processing

causes ulcerative colitis, particularly in patients that have been given certain broad spectrum antibiotics, causes chronic cramping and dyssentery, antibiotics often cause it to sporulate (fecal transplants being used as treatment)

connects intestinal tract nerve network to brain

responsible for producing serotonin and dopamine

“feel-good” molecule, involved in preventing depression and regulating sleep, appetite and body temperature, 95% produced in the gut

signals between gut neurons

Change in the properties of a food that makes it undesirable for human consumption

non-perishable, semi-perishable, perishable

culture medium, water content, pH range, physical structure, oxygen availability, temperature

heat, cold, osmotic pressure, drying, chemical preservatives, radiation

1/3 of all food that goes uneaten through loss/waste

preserves food, makes commerical products, bacteria excrete enzymes, break down substances in environment to absorb as nutrients, excrete waste into environment

false idea that food is safe if picked up fast enough, bacteria highly adapted to attach to surfaces however

improper holding, poor personal hygiene, cross contamination, inadequate cooking, unsafe food sources

makes bacteria less likely to attach to food

Bacteria that live in digestive tract of many vertebrates, don't cause disease but indicate fecal contamination

animals, plants, microbes

chemical and physical environments

cyanobacteria and algae, etc., fix carbon from CO2 into glucose

primary consumers, depend upon microbes to release glucose from cellulose

release CO2 through respiration (and fuel consumption)

return CO2 to the atmosphere

percent of the atmosphere that is nitrogen gas

convert N2 into ammonia

bacteria convert ammonia into nitrate, form of nitrogen best used by plants (Nitrosomonas and Nitrobacter)

bacteria return nitrogen back to the atmosphere as nitrogen gas

approximately 670 lb/acre of surface soil

approximately 703 lb/acre of surface soil

production of antibiotics to kill competition

produced by actinomycetes, bacteria, and fungi

the soil immediately surrounding the root, significant carbon transfer from plants to soil occurs here

organic acids, amino acids, sugars, polysaccharides, etc

make minerals available to the plant, influence root growth, protect root from pathogenic microbes

bacterium which lives in the soil, invades legume roots, forms root nodules and fixes nitrogen, symbioitic relationship where atmospheric nitrogen is made available to the plant

provided to symbioitc bacteria by plant, allows binding of oxygen to keep nitrogen fixing bacteria and their nitrogenase enzyme functioning

symbiotic root fungus where fungi gets more food from the root and plant benefits from more efficient uptake of water and nutrients and becomes more tolerant to stressful environments

the use of microorganisms to remove or detoxify unwanted chemicals in the environment

transformation of parent compound to daughter compounds

complete biodegradation of organic containment to its inorganic constituents (CO2, H2O, etc)

transformation of a containment without the provision of carbon or energy to the microbe

addition of nutrients or other amendments to stimulate indigenous microbes in soil or water

inoculation of containment site with microorganisms to facilitate biodegradation

synthetic chemicals, not naturally occuring substances

heat-loving

moderate-loving

cold-loving

salt-loving

high pH-loving

low pH-loving

microbes on the leaves and stem

microbes directly within the plant

drough resistance, salt resistance, heavy metal resistance, temperature fluctuation resistance

mostly acid and some side products made (yogurt)

alcohol and carbon dioxide made

process used to fix "sick wine" in France in the 1860s, still used today

"molecular scissors," includes hundreds of different enzymes that recognize specific sequences, can leave sticky or blunt ends

origin of replication, antibioitc resistance gene (selectable marker), and LacZ gene

creates enzyme Bgalactosidase, causes colonies to turn blue when expressed (inserting gene of interest breaks this, colonies are white instead)

ice-minus bacterium, allows plants to survive at lower temperatures

used to convert waste (eg urine) into an electrical current

5' end of DNA

3' end of DNA

adenine and guaning, have 2 rings

cytosine, uracil, thymine; have 1 ring

type of bond between nitrogen base pairs

number of hydrogen bonds between adenine and thymine

number of hydrogen bonds between cytosine and guanine

description of DNA replication, each daughter molecules contains one strand from the parent

adds base pairs to separated DNA strand during replication to create new strand

describes the direction DNA replication occurs

caused by errors in DNA replication, change in the nucleotide sequence of DNA

chemical or physical agents that cause mutations

process of creating mRNA from DNA template

adds RNA nucleotides to DNA template to create mRNA strand

direction RNA polymerase moves along DNA strand (builds mRNA opposite of this)

region of DNA where RNA polymerase binds (TATA box), not actually transcribed, common location of gene expression

region of DNA where RNA polymerase leaves

the process of creating protein from mRNA

amino acid structure

bonds that link amino acids together to form proteins

responsible for carrying amino acids to the ribosome

3 letter group of nitrogen bases read by ribosome on mRNA

process regulated by DNA binding proteins binding to promoters

always expressed/turned on

gene that is expressed only when inducer is present

gene that is turned of when repressor is present

found in bacteria, group of functionally related genes that are controlled by the same regulatory sequences (promoter)

type of horizontal gene transfer, replication and passage of DNA through bridge by connected pilli

gene transfer with the assistance of bacterial viruses (phage)

phage encoded genes to be toxins

naked DNA can be picked up from environment and will be incorporated into the place of similar (homologous) sequences