Lc4: commensal microbes Flashcards
cellular microbes of the human body
fungi
protists
bacteria
archaea
fungi
yeasts (unicellular - division by budding)
molds (multicellular - (a)sexual repdroduction
protists
- Phylogenetically diverse, mostly unicellular, lack tissue organization
- Important components of many terrestrial, aquatic, and marine ecosystems, contribute to nutrient cycling
- Many are parasitic in humans and animals
- Include:
o Algae (photosynthetic, possess cell wall produce main part of planet’s oxygen)
o Protozoa (many motile by presence of e.g., flagella, cilia, pseudopodia)
o Slime molds
archaea vs bacteria
Nucleus –> A:no B:no
membrane bound organelles –> A:no B:no
chromosome –> single circular DNA
cell wall –> A: no peptidoglycan
DNA machinery –> A:eukaryote like
environment –> A:extreme B:everywhere
taxonomy - Dear King Phillip Calls Out For Good Soup
domain
phylum
class
order
family
genus
species
host-microbe interactions
- Commensals –> organisms that are normally found on those parts of the body exposed to the external environment
- Symbionts –> organisms that are normally found on those parts of the body exposed to the external environment and have a mutually beneficial relationship with their host
- Opportunistic pathogens –> An organism that can cause an infection in individuals with abnormal host defences.
o Commensals can be opportunistic pathogens - Pathogens –> organisms that cause infections in an individual with normal host defences
microbiota niches
sterile: blood and organs
colonized: skin, RT, GI and UT
skin
- Different niches depending on environmental conditions
o Oily less diverse than dry skin - Cutibacterium acnes digests lipids from hair follicles (subaceous glands) to create a low pH which is prevents infections of pathogens
- other strains produce inflammatory agents that may cause acne - S. epidermidis
o Secrete antimicrobial peptides
o Increase tight junction tightness
RT
- Environmental conditions (pH, humidity, oxygen level) determine microbiota composition
- Nasal microbiota resembles skin microbiota
- Many viruses also present in upper RT
- Oropharynx most densely populated
- Lower RT long thought to be sterile
GI
- Bacteria:
o 500-1000 different bacterial species
o 30-40 species make up 99% of total population - Archea: only three archeal species discovered so far
- Viruses: 10-100 species, many to infect bacteria (bacteriophages)
- Fungi/yeast: 10-100 species (many of which we eat, e,.g. Baker’s yeast)
- Parasite egg’s: better not!
- Unique composition in each individual!
- Increasing numbers from stomach to colon
- Complexity also increases towards colon (slow transit time)
- Anaerobes outnumber aerobes in distal GI tract
- 100 billion (1013-1014) microbes ~1,5 kg
- Low pH in stomach limits bacterial growth
- Bile acids and pancreatic juice in proximal intestine limit bacterial growth
small intestine mucus
- 1 loose and permeable layer
- consists of mainly MUC2 (highly glycosylated mucin)
- glycocalyx: membrane bound mucins
- in crypts the mucus is very dense to protect stem cells
colon mucus
- 2 layers –> resembles crypts of small intestine
- deep layer is impermeable to microbes
metabolic effect of GI microbiota
bacteria ferment:
- starch, NSP and oligosaccharides into organic acids (SCFA) and alcohols and gases
- proteins/AA into nitrogenous metabolites and gases
archaea can produce methane
metabolism of indigestible carbs
amylases can break alfa(1-4) glycosidic bonds
bacteria can use CAZs to break beta bonds
products can be used by other bacteria or us
bile metabolism
- cholesterol –> primary bile acids conjugated with AA - glycine or taurine (liver)
- gall bladder
- into duodenum
- bacteria transform primary into secondary (active)
bacteria also assist in recycling of bile acids
prudent diet
- omega-3, phytochemicals, fiber lead to formation of SCFAs
- increased mucus secreation
- increased AMP secretion
- increased barrier function
western diet
- high sugar, high fat, low fiber
- enhanced mucus degradation
- reduced AMPs
- reduced barrier function
- inflammation
colonization at birth
- First microbes originate from:
o Maternal vagina and gut in vaginally born infants
o Environment and skin from hospital staff and parents in C-section born infants - Early facultative aerobic bacteria (E. coli, streptococci) reduce the environment (consume O2)
- This sets the stage for colonization by strict anaerobic bacteria
human milk
- Maternal milk contains >100 different human milk oligosaccharides (HMOs):
- Cannot be digested by our own digestive enzymes
- Bifidobacteria are specialized to ferment HMOs into acetate and lactate
- Acetate and lactate are an energy source for the baby and lower intestinal pH –> Lower pH prevents colonization by (opportunistic) pathogens
- Maternal milk also contains bacteria (incl. bifidobacteria) that can seed the infant gut
- Formula-fed infants have more diverse collection of gut microbes, including opportunistic pathogens
immune maturation
- cryptopatches become mature lymphoid follicles
- mesnetric and peyer’s also mature
- large role for microbiota in this proces –> sterile conditions lead to lack of maturation
SCFAs as antiinflammatories
- bind to GPR43 on Tregs
- release of IL10
- inhibit effector T cells
