Micro Exam 3

The Human Microbiome Information

your microbiome is crucial to your wellbeing. What does it do? (8)

• digest our food to release unavailable nutrients

• produce vitamins and minerals

  • may not get these without microbes

• break down toxins and hazardous chemicals

• protect us from disease

  • they can outcompete pathogens

• affect the way we smell

  • ex: sweat

• promote development of organs and the nervous system

• train our immune response

• affect our behavior

what are germ free mice?

• live shorter lives

• grow more slowly

• develop abnormal guts and immune systems

• susceptible to stress and infections

• “a miserable creature”

you are what you eat. certain bacteria release …

• dopamine when you eat foods they need to survive

rabies virus. what system does it infect? what happens?

• infects the nervous system → hosts become aggressive and bite and scratch allowing the virus to transmit to the next host

toxoplasma gondii. what is it and how does it reproduce? what does it do to the infected?

• parasite that can only sexually reproduce in cats

• infects rodents → reverses affect of cat odors from fear to attract and rodents run toward cats

  • rat won’t hide from smells like cat urine

  • rat may run towards cat smells

Wolbachia pipientis. Wasps!

• maternally inherited bacterial endosymbiont that manipulates host reproductive capabilities

• antibiotic administration to a colony of asexual, all female wasps causes males to reappear and both sexes start mating again

  • antibiotic kills the bacteria so males can reemerge

• bacteria that transmits to next host through egg

• females get infected, is spread to next generation via eggs

  • females reproduce asexually (cloning self), only females are born

Plasmodium falciparum. what does this do to humans?

• humans become magnets for mosquitos that transmit Malaria or aphids attract the marmalade hoverfly

• this makes you smell better to mosquitoes so disease can continue transmission

what type of microbe is found in the nose, mouth, stomach, sexual organs, skin

• nose

  • staphylococcus

• mouth

  • streptococcus mitis

  • species above and below gum line differ

• stomach

  • bifidobacterium give way to bacteroides

• sexual organs

  • lactobacillus

  • proteus

• skin

  • staphylococcus

  • corynebacterium

  • propionibacterium

  • micrococcus

every individual has a unique microbiome. what impacts it? (6)

• genetics

• environment

• diet

• lifestyle

• hormones

• industry

function of microbes in nose, mouth, lungs, stomach, colon, sexual organs, skin

• nose

  • mucus production

  • antimicrobial chemicals

• mouth

  • assist digestion

  • ward off pathogens

• lungs

  • lubricate pulmonary tissues

• stomach

  • prevents gastric complications

• colon

  • digestion of complex carbohydrates

• sexual organs

  • maintain pH and H₂O₂ production to kill microbes

• skin

  • fortify immune system

  • scent production

your microbiome begins developing before you are born. how does the mother and birth impact

• early on, changes in the maternal microbiome support fetal development that shift the diversity towards a microbiota with reduced diversity

  • reduced diversity of mother’s microbiome to pass to child to highlight specific microbes that are essential

  • modulate the maternal immune system to prevent against infections (avoid complications such as preterm birth)

  • supports the hormonal environment for placental function (enables nutrient supply to the fetus)

  • aids in digestion and effective use of nutrients and regulate insulin sensitivity

• proposed placenta, amniotic fluid and umbilical cord blood may contain microbes that influence fetal immune system development and postnatal colonization

how does vaginal microbiome change when pregnant

• ~20% sharing with other body sites compared with over 50% sharing with other body sites

• at birth, vaginal microbiota shifts such that in more than half of the bacteria in the vaginal canal can also be found at a second body site

• the vaginal microbiota is a pluripotent organ ready to colonize every body site of the infant

differences arise from exposures. how does vaginal birth vs cesarean section impact microbiome of fetus? what bacteria?

• vaginal delivery promotes contact with the vaginal and fecal microbiota

  • lactobacillus species

  • bifidobacterium species

  • normal intestinal microbial colonization

  • proper immune system development

• cesarean delivery leads to acquisition from skin and hospital surroundings

  • staphylococcus species

  • abnormal intestinal microbial colonization

  • disrupted immune system development

  • increased risk of atopic disease, asthma, celiac disease, allergic reaction

how many births in the US are cesarean now compared to 1997

• ~30% births in US are delivered by CD compared to 20% in 1997

compared to babies born vaginally, babies born via Cesarean have differences in

• microbial diversity

• brain development/protein exp

• immune system development

• metabolism

perinatal exposures have long term health consequence. what are the exposures? (5)

• exposures

  • maternal high fat food diet

  • maternal and infant antibiotics use

  • placental microbiome dysbiosis

  • formula feeding

  • cesarian delivery

• **early and excessive bathing can leave baby vulnerable by washing away beneficial microbes

he gastrointestinal tract has the …

• largest mucosal surface with the greatest bacterial diversity

  • 500 different species

  • firmicutes and bacteroidetes phyla are dominant in gut

• assist with digestion, nutrient synthesis, immune system development and regulation, inflammation, neurological processes

birth mode dependent association between pre pregnancy maternal weight status and the neonatal intestinal microbiome ????

significant postnatal factors that influence differences at the genus level and functional metabolic capacity

• several factors influence genus and species level community profiles between 3 and 18 months

• bacterial metabolic potential (functionality of the microbes) was associated exclusively with the consumption of breast milk (3-14 months)

breastmilk carries bioactive molecules that have critical functions

• CD4+ (regulates a lot of stuff in immune response)

• beneficial bacteria

  • lactobacillus species

  • bifidobacterium species

  • firmicutes species

• nutrients

  • human milk oligosaccharides (HMOs) → immune response

    • give ruse to SCFA

Bifidobacterium longus infantis (3)

• breaks down oligosaccharides into SCFA (short chain fatty acids) → seals gut (need seal or stuff can get through)

• sialic acid → brain growth

  • signaling molecule

• human milk oligosaccharides (HMOs) → glycan mimic (pathogens bind)

short chain fatty acids regulate host cell metabolism which is closely related to disease process.

• can modify microbiome through what you eat

  • dietary fiber

  • supplementation with exogenous SCFAs

  • gut microbiota

• which provides SCFAs to gut

• lack of SCFA can cause

  • cardiovascular diseases

  • appetite suppression

  • oxidative stimulation

  • neuroinflammation

  • mitochondrial impairment

  • hepatocellular carcinoma

  • non-alcoholic fatty liver disease

  • hepatic cancer

  • acute pancreatitis

  • pancreatic cancer

  • end stage renal disease

  • chronic kidney disease

  • diabetes

  • diabetic complications

  • gastric cancer

  • ulcerative colitis

  • colorectal cancer

populations of microbes in the gut are related to the following diseases

• acne

• Alzheimer’s disease

• asthma/allergies

• autism

• autoimmune diseases

• cancer

• dental cavities

• depression and anxiety

• diabetes

• eczema

• gastric ulcers

• hardening of the arteries

• inflammatory bowel diseases

• malnutrition

• obesity

• Parkinson’s disease

• bacterial infection (clostridium difficile)

the gut brain axis

• greatest number and diversity of microbes

• after the brain, the gut contains the most neurons

• immunity, metabolism, activation of the vagus nerve, neurotransmission

what is depression

• transfer of the microbiome depressed into a healthy rodent = depression

SCFAs and the brain

• SCFAs

  • metabolites produced via anaerobic fermentation

  • reinforce BBB, modulate neurotransmission, neurotrophic factors and memory

the rise in immune/metabolic diseases is linked to microbes. what are the 2 hypotheses

• vanishing microbes (human adapted)

  • microbes that used to be present in environment are not anymore so we don’t get exposure

• limited exposure (hygiene hypothesis)

  • washing away microbes limiting our exposure to the microbes

manipulation of the microbiome with diet (3)

• fermented foods → increase bacterial diversity

• dietary fiber → fruits, veggies, and grains

• increasing fiber uptake is not sufficient, need to replace vanished organisms that utilize that fiber

  • giving fiber doesn’t help unless we have the organisms capable of using it

• microbes + diet = impact

how does the indoor microbiome influence our microbiome

• exposure to plants and soil

• exposure to pets (especially if they go outside)

• cleanliness (cleaning too much

• green cleaner

• temperature control, air exchange, light

where we live influences our microbiome

• pollution is increasing which decreases presence of good microbes in cities

• more species in rural environment

  • more access to soil microbiome

how can you create heath promoting indoor spaces?

• living green wall

• household pets increase microbial exposure

• increased ventilation

• natural lighting

• increased indoor microbial diversity exposure

• microorganism enriched sprays and mists

• microorganism enriched materials

• diverse animal communities increase internal biodiversity

• diverse plant and soil microbial communities increase internal biodiversity

manipulation of the microbiome: what is a probiotic? what are common probiotic organisms? which disorders?

• probiotic → pill containing live microorganisms that benefit health if consistently consumed in large enough quantities

• common probiotic organisms include

  • bifidobacterium and lactobacillus

• used as therapies for some disorders

  • diabetes

  • Crohn’s

  • cystic fibrosis

  • reduction of c reactive protein

  • cholesterol

  • depression

• remodel microbial communities

manipulation of the microbiome: what is a prebiotic?

• prebiotic → a nondigestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon and this improves health - Gibson and Roberfroid 1995

• include complex sugars used by commensal bacteria

• compounds must be resistant to host digestion and absorption

• enhance the activity, or promote the growth of resident bacteria

manipulation of the microbiome: what is an antibiotic? what do they do?

• antibiotic → any substance or compound that inhibits bacterial growth/survival

• administer to suppress or eliminate certain populations of microbial pathogens

• results in profound changes in the population

  • diversity

  • total bacterial density

Immune Response Information

infection does not equal disease (3)

• you are constantly being infected

• an effective immune response

• transmission

Innate immune response

• innate immunity

  • present at birth (defenses that exist immediately)

  • barriers to infection

  • nonspecific responses to destroy invading cells

physical and chemical barriers (3)

• the integumentary system

  • skin, hair, nails

    • prevent pathogen from gaining entry

    • hair like eyebrows/eyelashes filter to prevent bacteria from gaining entry and slows down entry of pathogen

  • mucous/mucous membranes

    • traps pathogens and holds onto them so body can get rid

• physiological barriers

  • pH

  • temperature

• chemical defenses

  • enzymes

  • nitric oxide

  • complement

what is included in the mucociliary escalator? what type of barrier is this considered?

• coughing and sneezing

• mucous and intact mucus membranes in airway and lungs

• cilia in respiratory tract trap foreign material

part of integumentary system barrier

skin

• strong mechanical barrier to microbial invasion

  • keratin is produced by keratinocytes in outer layer

    • makes it harder for pathogens to penetrate

• inhospitable environment for microbes

  • indigenous microbiota compete with pathogens

  • attached organisms removed by shedding of outer skin cells (mechanically removing pathogens, especially when skin is dry)

• pH is slightly acidic (ex: sweat)

• high NaCl concentration (ex: sweat)

• subject to periodic drying

  • bacteria don’t like dry environments

what is included in physiological barriers (3)

• acid in sweat

• acid in stomach

• competition from commensal bacteria in gut and genital tract

fevers. what is a fever? why does it occur? what does it do? what substances cause a fever? what do they stimulate the production of?

• elevated body temperature

• natural reaction to infection

• the hypothalamus acts as the body’s thermostat

• pyrogens are substances that cause fever

• stimulate the production of prostaglandins

what do prostaglandins do

• cross the BBB (why you feel a bit off when sick)

• change the responsiveness of the thermosensitive neurons that makeup the thermoregulatory center

chemical defenses in depth

• enzymes present in mucus membranes

• nitric oxide inhibits DNA synthesis so bacteria can’t reproduce

  • byproduct of L-arginine

  • signaling molecule (gas)

  • can work in cell bc gas can cross membrane

• complement

  • series of proteins

  • proteins/enzymes that aid defense efforts

enzymes in mucous membranes and secretions. what do mucous membranes and their secretions do? what are the 3 secretions we discussed?

• protective covering that resists penetration and traps many microbes

• secretions often contain a variety of antimicrobial substances

• secretions

  • lysozyme

  • lactoferrin

  • lactoperoxidase

what does lysozyme do

• hydrolyzes bond connecting sugars in peptidoglycan

what does lactoferrin do? what are they secreted by?

• secreted by activated macrophages and leukocytes

• sequesters iron from plasma

  • taking iron away from pathogens so they can’t function as well

what does lactoperoxidae do

• produces superoxide radicals

your skin acts as a natural barrier from microbial infection. what are 4 reasons why the skin is an excellent barrier?

• the sloughing off of dead skin cells

• sweat

• acidity

• resistant to penetration

complement’s role in innate immunity. what is a complement protein? where are complement proteins it made?

• complement was first discovered as a heat-labile component of blood that enhances (or complements) the killing effect of antibodies on bacteria

  • stable in heat and blood

• complement consists of about 20 proteins naturally present in serum

  • several are proteases (proteins that can cleave proteins) that sequentially form and cleave other complement factors

• the liver is the main source of complement proteins.

complement rids the body of pathogens via 3 main mechanisms. what are the mechanisms?

• opsonization

  • enhancement of phagocytosis by coating with C3b

• cytolysis

  • bursting of microbe due to inflow of extracellular fluid through transmembrane channel formed by membrane attack complex C5b and C6-C9

• inflammation

  • increase of blood vessel permeability and chemotactic attraction of phagocytes

complement cascade

• activated C3 splits into C3a and C3b

• C3b binds to microbe, resulting in opsonization

  • enhancement of phagocytosis by coating with C3b

• C3b splits C5 into C5a and C5b

• C5b binds to C6-C9 to form membrane attack complex, forming channels in the invading cell’s membrane and resulting in cell cytolysis

• C3a and C5a cause mast cells to release histamine, resulting in inflammation

  • C5a attracts phagocytes

cells involved in opsonization

• link to innate immunity

• antigen presenting cells

  • neutrophil

  • macrophage

  • dendritic cells

detecting and killing microbes. what are the 3 types of phagocytes we discussed

• neutrophils

• macrophages

• dendritic cells

• also called antigen presenting cells

what do neutrophils do

• invade tissue from blood in response to injury and infection

what do macrophages do

• reside in various tissues

  • LN, spleen, lung, brain, liver, etc

what do dendritic cells do

• while phagocytic, key role is in bridging the innate and adaptive immune responses

opsonization in depth

• extracellular bacteria approach macrophage (or any antigen presenting cell)

• opsonization: antibodies bind to C3b on bacteria and to C3b receptor on the macrophage’s surface

• ingestion by macrophage: antibodies link bacteria and macrophage, aiding in phagocytosis

• enhances phagocytosis by using C3b receptor and C3b

  • C3b is stocky so bacterium won’t slip away from phagocyte

what 3 WBC’s produce histamines

• mast cell

• eosinophil

• basophil

what are MAMPS

• despite their extreme heterogeneity, pathogens share highly conserved molecules called microbe-associated molecular patterns

  • microbial signatures that our cells lack which allows our cells to recognize them

• host cells do not share MAMPs with pathogens

how are MAMPs recognized?

• MAMPs are recognized by innate immune recognition receptors called pattern-recognition molecules/receptors (PRMs, PRRs, TLRs)

• TLRs = toll like receptors

  • inside endosome (3, 7, 9)

    • important for viruses

what are the 6 typical MAMPs we discussed

• lipopolysaccharides

• peptidoglycan

• capsular polysaccharides

• certain nucleotide sequences unique to bacteria

• other bacterial components (pili)

  • anything on bacterial surface that our cells do not have

antigen

• anything that elicits an immune response

toll like receptors

• microbes possess unique structures that immediately tag them as foreign

• microbe-associated molecular patterns (MAMPs) are recognized by Toll like receptors (TLRs) on cells

• binding to TLRs triggers an intracellular signaling cascade

  • causes cell to release proteins called cytokines

• class of proteins that are expressed on sentinel cells that recognize MAMPs from various pathogens

  • upon recognition, TLRs activate cellular signaling pathways leading to the appropriate immune response

communicating a response. how do immune cells communicate?

• cells of the immune system must be able to communicate with each other

• they use cytokines

• cytokines bind to receptors on nearby cells

• influence growth, differentiation, movement, or cell death

what are the 4 types of cytokines we discussed

• chemokines

• interferons

• interleukins

• tumor necrosis factors

chemokines

• important in chemotaxis of immune cells

• movement!

interferons

• glycoproteins important in the control of viral infections

• also help regulate cells involved in immune response

• **interferes with viral infections

• **interferes with viruses being able to infect other cells

interleukins

• important in innate immunity, inflammation, and adaptive immunity

tumor necrosis factors

• help kill tumor cells, initiate programmed cell death (apoptosis)

• engagement with tumor necrosis factors triggers apoptosis

detection of what initiates the adaptive immune response

• MAMP detection

• antigen presenting cells recognize MAMPs

  • APCs process pathogens into antigens and present them via MHC to T-cells

• activate cell communication

  • different pathogens = different cytokines

T cells respond only when presented with what 2 signals

• antigen presentation (and recognition)

  • happens first

• cytokine communication

  • happens second

what 4 things act as the first line defense against microbial invaders

• antimicrobial proteins

• intact skin and mucous membranes

• complement

• inflammation

• *all of these are innate immunity

adaptive immunity

• reaction to specific antigens

  • parts of foreign proteins, sugars, chemicals

• develops specific immune response as invaders are encountered

  • vaccines, exposure

• specific targeted reaction developed

• retains “memory” of those antigens

  • remembers what it has already seen before

• faster response if exposed a second time

• matures throughout life

innate immunity, adaptive immunity, cytokines

• innate immunity → first nonspecific defense

  • directs adaptive immune response

• adaptive immunity → adapts to and clears invading pathogens

  • long lived, has memory, removes specific antigens

• cytokines → chemical messengers that facilitate innate and adaptive immunities

  • allow innate and adaptive immunity cells to communicate

adaptive immunity has 2 parts, what are they

• humoral immunity

• cellular immunity

humoral immunity and cellular immunity

• humoral immunity → works to eliminate antigens that are extracellular

  • B lymphocytes (B cells) are involved in producing antibodies against epitopes

• cellular immunity/cell mediated → works to eliminate antigens that are intracellular

  • T lymphocytes (T cells) provide resistance through lysis of infected or abnormal cells

B cells and T cells have memory, what does that mean

• immunological memory is the ability to “remember” past pathogen exposures

• allows the body to fight off any subsequent infections

• **will remember past infections so it can fight them off if you are infected again

what are the 3 phases of adaptive immunity

• recognition phase (self vs non-self; antigen)

  • recognize there is a foreign antigen

• activation phase (mobilization)

  • T cell (or B cell) is activated when antigen on APC is presented

  • driven by cytokine support

• effector phase (attempt to eliminate invader)

  • full potential of T/B cell is reached, tries to rid antigen

what are antigens

• antigens are microbe parts that provoke an immune response

• the immune response recognizes unique antigenic determinants (epitopes)

  • epitope = small part of antigen

antigen presenting cells (4)

• include macrophages, dendritic cells, B cells

• recognize / identify

• present / activate

• regulate / release cytokines

movement of APCs

• APCs engulf pathogens at sites of infection

• APCs present antigens on their surface and move into reginal lymph nodes

• in the lymph node, free antigens interact with B cells

  • APCs engage T cells

  • activated B cells differentiate into plasma cells and memory cells

  • CTL cells are activated

• plasma cells, memory cells, and CTLs leave the lymph node and enter circulation

• plasma cells and memory cells enter bone marrow

  • CTLs migrate to infection site

T cells belong to what arm of the immune response

• cell mediated immunity

overview of cellular immunity. what is it mediated by? what must happen? 2 types of cells

• mediated by T lymphocytes (T cells)

• antigen must be presented to it by another cell

• 2 types

  • T-cytotoxic cells (CD8)

  • T-helper cells (CD4)

T-cytotoxic cells (CD8) and T-helper cells (CD4)

• T-cytotoxic cells (CD8) → destroy infected cells

  • toxic to cells, kills cells when they have intracellular infection

  • kill your cell that is allowing pathogen to grow

  • make cell go through apoptosis

• T-helper cells (CD4) → support B cells (all immune cells)

interacting with APC. what are MHC’s and what are the 2 classes

• T-cell receptors and co-receptors allow T cells to recognize and bind to the major histocompatibility complex (MHC)

• MHC proteins are unique for nearly all individuals

  • they mark the body’s cells as “self”

• 2 classes

  • Class I MHC proteins

  • Class II MHC proteins

Class I and II MHC proteins

• Class I MHC proteins → found on the surface of nearly all the body’s cells

  • presents intracellular antigens

  • microbial proteins found inside the cell are degraded

  • peptides are imported into the ER and loaded onto MHC class I molecules

  • found on all nucleated cells

  • take immature T-cell and make it into T-cytotoxic cell

• Class II MHC proteins → proteins on the surface of APCs

  • present antigen fragments to Helper T cells

  • presents extracellular antigens

  • microbial proteins found outside cell are endocytosed in an endosome

  • they are then degraded and placed on MHC class II molecules

  • found only on antigen presenting cells

  • take immature T-cell and make it into T-helper

cytotoxic T cells (CD8 T cell, Tc)

• host cells infected by viruses

  • degrade viral antigens and present fragments on MHC-1 on the cell surface

• activated cytotoxic T cells

  • recognize and bind to the MHC-1/peptide complex on infected cells

  • release perforin and granzyme to cause cell death

  • T cells can also recognize and kill tumor cells

• Need T helper cells to release cytokines to do function

what does perforin and granzyme do

• perforin → make holes in membrane of infected cell

• granzyme → go through pores made by perforin and cause apoptosis

T helper cells (CD4 T cell)

• antigen presenting cells, present antigen to T-helper cells on MHC class II

• if T helper cells recognize the presented antigen as foreign

  • activate macrophages

  • release cytokines that recruit and activate other cells of immune system

  • stimulate Natural killer and cytotoxic T cells

antigen presentation of external antigen

• an APC encounters and ingests a microorganism

  • the antigen is enzymatically processed into short peptides, which combine with MHC class II molecules and are displayed on the surface of the APC

• a receptor on the surface of the CD4 T cell binds to the MHC antigen complex

  • if this includes a toll-like receptor, the APC is stimulated to secrete a costimulatory molecule

  • these 2 signals activate the CD4 cell which produces cytokines

• the cytokines cause the CD4 cell to proliferate and to develop its effector functions

• a T cell that recognizes a dendritic cell that is producing costimulatory molecule becomes activated

humoral immune response. what is it mediated by? what does it do? what are antibodies?

• mediated by B lymphocytes (B cells)

• encounter antigen → differentiate and proliferate into plasma cells and memory B cells

• plasma cells make Y-shaped molecules called antibodies

  • antibodies bind to antigens, providing protection to host

antibodies. what does epitope recognition require. what is the structure of an antibody

• antibodies are proteins called immunoglobulins

• epitope recognition requires antibodies to have a special structure of

  • 2 identical heavy (H) chains

  • 2 identical light (L) chains

• each light and heavy chain have

  • a constant region (Fc), which determines the location and functional class of the antibody

  • a variable region (Fab), which contains different amino acids for the many antibodies produced

the variability allows formation of the specific antigen binding site. what does Fab and Fc do

• the Fab fragment of an antibody combines with the epitope

• the Fc fragment performs functions in

  • opsonization

  • activation of the complement system

  • allergic reactions

there are 5 immunoglobulin (Ig, antibodies)

• IgG (gamma globulin)

• IgM

• IgA

• IgE

• IgD

IgG

• the major circulating antibody

  • provides immunity to the fetus and newborn

  • longest lived, biggest we have

  • found in breast milk, can cross placenta

IgM

• the first (but short lived) Ig to appear in circulation after B cell stimulation

  • binds a lot of pathogens at once

IgA

• provides resistance in the respiratory and gastrointestinal tracts (mucosal immunity)

  • is found in colostrum (produced after birth before milk)

  • passed in breast milk

  • important to mucosal surfaces

IgE

• plays a role in allergic reactions