micro unit 4

NOT FINISHED

ch 27

ch 27

ectosymbiont

one organism that lives on the surface of another organism

endosymbiont

one organism located within another

consortium

a host w/ more than one associated symbiont

microorganisms can be permanently associated w/ host or intermittently associated with host

example: humans

mutualism

A helps B, B helps A

some degree of obligation, if organisms separate, neither of them grows

ex: aphids (insect) and B. aphidicola (bacteria) have coevolved (they have gone through genome reduction as a result)

protozoan-termite relationship- termites eat wood & cant break it down. protist breaks down lignocellulose for termite in exchange for protection. protist relies on bacteria for nitrogen fixation

cooperation

positive symbiosis that benefits both organisms, but there is no obligation here

A helps B, B helps A, they can survive w/o the other

ex: bacteria and nematode relationship- bacteria helps nematode kill insect, and nematode helps transport bacteria to another insect

bacteria and human relationship- gut microbiome

commensalism

A benefits (commensal), and B is neither harmed nor helped

ex: syntrophic organisms- do cross feeding- one organism feeds off of the metabolic products of another species (one organism is unaffected)

nitrification- nitrosomonas makes nitrite waste, nitrobacter uses nitrite waste and benefits from it

microbial succession during spoilage of milk

formation of biofilms

skin or surface microbes on plants or animals

predation

A obtains biochemical precursors and energy after killing prey

ex: bdellovibrio penetrates cell wall and grows outside of plasma membrane

vampirococcus uses epibiotic mode of attacking prey

daptobacter penetrates the prey and directly consumes cytoplasmic contents

myxococcus “wolf pack” cells use gliding motility to creep, overtake prey, and release degradative enzymes (facultative predators)

parasitism

parasite harms host, but does not kill it

obtain biochemical precursors while prey is still alive

some co-existence, organisms go through genomic reduction

amensalism

negative impact of one organism on another based on release of a specific compound

antibiotic (amensalism example)

kills organism that does NOT look like itself

bacteriocin (amensalism example)

kills organism that does look like itself

competition

2 organisms compete to obtain the same resource

2 outcomes:

-one organism dominates and has environment all to itself

-2 organisms keep fighting and share the share the environment

microbiome

normal microbiota

superorganisms

gene encoded metabolic processes of the host becomes integrated with those of microbes

E. coli and streptococci make a reducing environment in the gut, which…

helps inhibit pathogens growing in the gut

enhances growth of bifidobacteria (found in breastfed babies)

milk helps select for non-pathogenic bacteria

bifidobacteria

found in breastfed babies

prototrophic- can synthesize all amino acids

can do fermentation

used as probiotics

gnotobiotic (germ free animals)

have zero microbes

used to study the effects of microbes→ compare germ free and normal animals, and introduce a single microbe

coupled w genomic studies for maximum benefit

skin

bacteria cannot get past skin unless its broken

inhospitable environment:

-slightly acidic pH

-high NaCl conc.

-many areas low in moisture

substances like lysozymes and cathelicidins (disrupt cell membranes of bacteria) are produced by macrophages and granulocytes to inhibit pathogens

oleic acid is produced by gram positive c. acnes to inhibit gram negatives

acne vulgaris

caused partly by cutibacterium acnes

opportunistic pathogen

sebum accumulation encourages growth

eye

no bacteria on inside of eye, but small number of commensal bacteria on conjunctiva

prominent bacteria: staphylococcus epidermidis

allergic rxn is redness of eye

viral infection is redness + lacrimation

bacterial infection is redness + pus

external ear

similar to skin flora

also has fungus- c. auris- not dangerous as long as it doesnt move

mouth

oral cavity colonized by microorganisms from the surrounding environment

after teething, obligate anaerobes become dominant (found between gums and teeth)

stomach

acidic environment

bacteria can survive if ingested w/ food particles

H. pylori causes ulcers, and it thrives when it changes pH of stomach

small intestine

duodenum: contains a few organisms

jejunum

ileum: flora similar to colon, pH more alkaline, anaerobic gram negative bacteria and enterobacteriaceae

(microbes collected as we move out of stomach)

large intestine

largest microbial population of body

replaced rapidly due to high reproductive rate

most microbes grown here are anaerobes

bacteria shed during bowel movement

nose

s. aureus and s. epidermidis are predominant bacteria

found in nostrils

nasopharynx

may contain low numbers of potentially dangerous pathogens

oropharynx

a-hemolytic streptococci

diphtheroids (gram positive)

gram negative cocci

anaerobes in tonsillar crypts

lower respiratory tract

no normal microbiota here

microbes moved by:

-continuous stream of mucus generated by ciliated epithelial cells

-phagocytic action of alveolar macrophages

-lysozymes in mucus

genitourinary tract

unfavorable environment for foreign microbes

urine and vagina have low pH

vagina has lactobacilli

toxic metabolic end products in urine

hypertonic nature of kidney medulla

urine and mucous flush bacteria away

distance barrier of male urethra prevents infection

normal flora of genitourinary tract

kidney ureters and bladder do not have microbes

distal portion of urethra has some microbes

female genital tract has complex microbiota in a state of flux due to menstrual cycle, and acid tolerant lactobacilli predominate

metabolome

waste products being made by microorganisms in gut microbiome

colonization resistance

based on competitive exclusion

normal flora of gut is competitive against colonization of pathogens

gut brain axis

gut microbiome may affect CNS and determine certain traits such as inquisitiveness, sociability, anxiety, and depression

ways microbiome can influence CNS:

-microbiome effect on immune system

-microbiome activating vagus nerve, leading to brain modifications

-soluble microbial products like short chain fatty acids (SCFAs)

metabolic syndrome

3 out of 4 signs:

-large waist circumference

-high blood triglycerides

-high blood pressure

-elevated LDLs and fasting blood glucose levels

IBD

inflammatory bowel disease

disproportionate number of proteobacteria in gut

produce long chain fatty acids instead of short chain, leading to release of inflammatory cytokines

cardiovascular disease diet issue

red meat and high fat

little fiber means microbes cannot make anti-inflammatory short chain fatty acids

cancer

human viruses and bacterial products can alter host cell cycle to favor proliferation and prevent host cells from repairing DNA damage

ex: h pylori dysregulates host cell cycling

bacteria can activate inflammation, and inflammation can promote metastasis of tumors to distant sites

probiotics

“live microorganisms, which, when administered in adequate amounts, confer a health benefit to the host” (FAO-WHO)

not FDA regulated (health benefits have not been rigorously tested)

prebiotics

food that probiotics (live microorganisms) require for survival

synbiotics

foods or supplements that include both a prebiotic and a probiotic

ch 31

ch 31

infection

pathogen is present and replicating (not causing harm yet)

disease

pathogen has reached a certain number/has released a toxin and causes damage

pathogens must overcome these to cause harm

surface barriers (skin)

resistance by host (immune system)

innate immunity

nonspecific resistance→ resistance to any microbe

born w/ it

does not get better w/ age

natural, first line of defense, lacks memory

physical barriers

ex: epithelial cells, leukocytes, phagocytic cells, dendritic cells, NK cells, proteins part of complements system

adaptive immunity

specific immune response→ resistance to a particular foreign agent

gets better as you encounter pathogens (acquired)

involves memory B and T cells (lymphocytes)

immune system role

identify self from non-self

recognizes foreign substances/microbes and destroys them

immunity

ability to resist a particular disease or infection

antigens

large complex molecules that elicit an immune response

skin (physical barrier)

pathogen cannot enter unless there is a break in the skin

mucous membranes (physical barrier)

binds to pathogen before it can get into epithelium

constantly shedding, takes pathogen w/ it

mucociliary escalator (physical barrier)

cilia that beats to move mucous out of the way

antimicrobial peptides and proteins (chemical barrier)

most ancient primary defense mechanism (most eukaryotes have it)

amphipathic; can bind to pathogen cell membrane and cause damage

ex: lysozyme (breaks b-1,4-glycosidic bonds)

lactoferrin (sequesters iron, bacteria cannot perform ETC)

granzyme (causes holes in cell membrane)

2 types of antimicrobial peptides

cationic antimicrobial peptides (CAMPs)

bacteriocins

CAMPs

cationic antimicrobial peptides → produced by host cells

3 diff classes

first class CAMPs

made as inactive proteins, activated when needed

broad spectrum

produced by a variety of cells

ex: cathelicidin

second class CAMPs

made as precursor protein

broad spectrum

produced by specific cells: neutrophils, intestinal paneth cells, intestinal cells, and respiratory epithelial cells

ex: a- and b-defensins

third class CAMPs

large peptides found in human saliva

selects for mitochondria of fungi, binds to mitochondria, makes ROS, increase in ROS leads to fungus death

ex: histatin

bacteriocins

produced by normal microbiota

kill organisms that look like itself (related species)

colicins

bacteriocins produced by gram negative cells

iantibiotics

bacteriocins produced by gram positive bacteria (streptococcus, bacillus, staphylococcus, and lactococcus spp.)

complement system

supports immune system

composed of more than 30 serum proteins (in inactive form until needed)

part of blood circulation

pathways of complement system

1) alternative pathway: protein splits into 2 pieces and process starts

first pathway that is activated

2) lectin pathway: activates based on lectin found on surface of bacteria

3) classical pathway: activates in presence of antibodies, which are produced in adaptive immunity

last pathway to be activated (adaptive immunity takes time)

outcomes of complement system

3 possible outcomes: (can result from any of the pathways)

1) complement proteins activate other cells for help (inflammation)

2) opsonization→ complement proteins coat pathogens, making them easy to identify by phagocytes

3) lysing→ hole created in cell membrane if pathogen, pathogen dies

leukocytes

WBCs

all cells in immune system are leukocytes

involved in innate and adaptive immunity

arise from pluripotent stem cells and differentiate according to the needs of the host

granulocytes (leukocytes)

darkest stain/least in circulation→ B E N → lightest stain/most in circulation

basophils

stain bluish black w/ basic dyes (hard to see nucleus)

found mostly within tissues (only a few in circulation)

release vasoactive mediators and play a role in development of allergies and hypersensitivities

eosinophils

stain red w/ acidic dyes (absorb eosin)

a few seen in circulation (3-100)

release cationic proteins and reactive oxygen metabolites into circulation

role in allergic rxns (type I hypersensitivity)

neutrophils

stain at neutral pH, lightest in color granules, highly phagocytic

lots of neutrophils in circulation, first line of defense

macrophages call for help when there is a problem, and neutrophils are the backup

neutrophils eat pathogen, destroy it, and die (constantly remade)

pus= accumulation of neutrophils

monocytes

very large, circular nucleus

spends time in circulation, then exits into tissue

in the tissue, they differentiate into macrophages

macrophages

larger than monocytes

phagocytic

out of circulation

what monocytes are called AFTER they differentiate

present in every tissue, first to identify infection and call for backup

dendritic cells (DC)

phagocytic

show up if neutrophils are unable to kill pathogen

samples the microbe (do not destroy) and take info to secondary lymphoid tissue (LT), where it is presented to B and T cells

activates adaptive immunity

lymphocytes

all lymphocytes are leukocytes

T cells, B cells, innate lymphoid cells (ILC) like NK cells

NK cells

part of innate immunity (most lymphocytes are involved in adaptive immunity)

survey cells for signals asking for help

NK cells kill infected/mutated cells

number of NK cells stays consistent (do not increase in sick individuals, research trying to figure out how to increase number of NK cells)

primary organs and tissues

where lymphocytes mature and differentiate

B cells differentiate in bone marrow; they are constantly being made

T cells differentiate in thymus, which atrophies w/ age (no longer functions when you reach early 20s)→ limited number of T cells

secondary organs and tissues

lymphocytes encounter and bind antigen here

ex: spleen, lymph nodes, MALT (mucosa associated lymphoid tissue) and SALT (skin associated lymphoid tissue)

M cells

found in mucosa associated lymphoid tissue (MALT)

in between epithelial cells

act as gateway: under M cells, lots of leukocytes are found- they recognize if something in gut lumen is foreign

M cells allow pathogen in, so that leukocytes can respond

inflammation does not occur here