Microbiome Flashcards
Definition of the microbiome
“The totality of microorganisms and their collective genetic material present in
or on the human body or in another environment “
- Human microbiome outnumbers human cells by 1.3 fold, microbial genetic
content is 100-1000 fold greater than human genome
Describe the organization of the microbiome
it has regional and spatial organization (vaginal microbiome is different from skin microbiome)
How do we characterize and analyze the microbiome
- many species resist colonization so specific requirements for isolation and growth are unknown
- Molecular approaches (Metagenomic analysis) involving 16srDNA sequences are used to identify bacterial species in absence of colonization (if colonization isnt possible)
- Dna from a biological sample is used to analyze 16S sequences of all bacteria in the microbiome to determine community structure and diversity
- -the total DNA is sequnced and mapped to microbial genome databases to determine community structure and for genetic and metabolic profiling
- RNA is also sequenced and mapped for profiling
So how do we characterize and analyze the microbiome in Allie’s words
- colonization would be nice but isn’t always possible
- so genetic sequencing can be done looking specifically at the 16S rDNA sequences for determination/identification-there are databases so you can look at the total DNA sequences and RNA sequences for metabolic and genetic profiling of the microbiome
Regional Differences in the microbiome
- different regions have a distinct microbiome
- a majority of the microbiome is in the human gut
What region of the body has a majority of the microbiome? Tell me abut the microbiome in that region
-the human gut contains most of the microbiome
-the gut has about 400-500 bacterial species
-
How does the microbiome change throughout a persons life
-besides from extreme ages, as long as a person is not ill or taking an antibiotic their microbiome should stay relatively stabel throughout their life
How does my microbiome compare to Katherine’s
- everyone microbiome is a little bit different! it differes in community structure and composition
- but we still have similar composite function
Regional differences in microbial composition in the GI tract
- depending on where you are in the gut, the microbiome is a little different
- the differences are driven by the specific microenvironment of each area of the GI system
- cmplexity and number vary throughout the gut, but increase greatly in the distal colon
- as you move from proximal to distal there is a move from aerobic to anaerobic
Why does it make sense that as you move from proximal to distal throughout the Gi tract, that there would be a shift from aerobic to anaerobic bacteria in the microbiome
Because the mouth is the start of the GI tract, and obviously being exposed to the air there will be a lot of aerobic bacteria growing in the mouth. however as you travel deeper and deeper there isn’t really oxygen in the intestines. therefore you will have mostly anaerobic bacteria
Where within the gut is there the larget microbiome
in the colon!!
how do we develop our microbiome
a combination of host immune, nutritional and environmental factors shape microbial composition
What are some nutritional factors that shape the microbiome
mucus and surface carbohydrates
What are some immune effectors that shape the microbiome development
-AMPs/defensin
(bacteria in the microbiome release AMPs! helps kill others to make room for more of themselves.
-IgA from mom
-undetermined immunolgical factors
What are some non-immune factors that shape microbial composition
- bile salts
- digestive enzymes
What are some luminal/microenvironment factors that shape microbiome composition
oxygen
pH
-ionic composition
List 6 factors that are host-derived regulation of the microbiome composition
- Species-species select for specific microbial composition
- Host genetics-
- Immune factors, including IgA and antimicrobial peptides. Also innate immune factors modulate intestinal colonization
- Oxygen
- Host nutrition
- Bacterial-derived antimicrobials
List three ways that environmental exposure can shape the microbiome
- Diet
- Antibiotics
- Exposure to environmental microbes
For the first 1-2 years of life describe a persons microbiome
it is unstable. t is developing into what a normal microbiome would look like. It is changing a lot and at first the Gi microbiome is actually relatively similar to an adult humans vaginal microbiome
how can oxygen tension regulate micobiota composition
- changes in oxygen tension can modulate whether a majority of the microbiome are more aerobic or anaerobic.
- these changes occur in mucosal associate bacteria
- in an experiemtnwith mice where oxygen tension was raised, there was a shift in the mucosal associated bacteria to have an increased abundance of facultative anaerobic bacteria
Bacteriocins
- plasmid-encoded antimicrobial peptides
- can be circular or linear
- the bacterial strain that has a bacteriocin plasmid produces an immunity peptide to protect itself against the bacteriocin, but all other bacteria do not have an immmunity to the bacteriocin and they can die from it, allowing more room for the bacteria that has the bacteriocin to grow!
- also bacteria can use the conjugation apparatus encoded by tha bacteriocin plasmid to transfer the plasmid to other bacteria that lack it
what are bacteriocins encoded on
pheromone responsive, conjuagte plasmids
what do bacteriocins do
they allow bacteria to target and kill bacteria of the same species
they also encode for immunity to the bacteriocin in the bacteria that has the bacteriocin plasmid
can bacteriocins plasmid be tranferred
absolutely! via the conjugation apparatus that is encoded in the bacteriocin plasmid
Name four factors that distinguish commensals from pathogens
- Genome size (commensals have larger genomes than pathogens)
- Ability to bind to mucin (carbohydrate-binding modules) commensas can do this
- Ability to digest mucus (glycoside hydrolases, polysaccharide lyases,
carbohydrate esterases) commensals can do this - Ability to bind and use luminal nutrients enhance commensal colonization and
competition with pathogens
What are the three main functions of the microbiota
- Protection
- Structural/Developmental
- Metabolic/Nutritional
how does the microbiota serve a protective function
- Compete for available binding sites (to block pathogens)
- Compete for nutrition (from pathogens)
- Produce toxins and antimicrobials (that can kill pathogens)
how does the microbiota serve a Structural/Developmental function
- Maturation of epithelial architecture
- Enhance barrier function (apical tightening of tight junctions)
- Immune development (and induction of IgA)
How does the microbiota serve a metabolic function
- Vitamin synthesis (eg biotin and folate)
- Production of Short Chain Fatty Acids (SCFAs) providing energy to epithelium
- Fermentation of non-digestible dietary components such as fiber
- Metabolize dietary carcinogens
- Energy salvage
- Ion absorption
Describe the relationship of the microbiome between host protection and host physiology in one word
symbiotic
Briefly describe the duality of the commensal microbiome
- mucosal surfaces are in constant contact with microbes
- the primary role of mucosal surfaces are to allow normal physiological function while protecting the host from infection
- the mucosal immune system protects the host from the microbiota
- the microbiota has a symbiotic role in host protection and host physiology
Approaches to study microbiota function
- Axenic/germ-free mice
- Gnotobiotic systems (gnoto=known)
study mice where they have absolutely to microbiome and we add back one microbe at a time and see what it does
How does the Microbiome-host interactions drive immune system development.
- Microbiota induces expression of epithelial antimicrobial peptides
- . Microbiota induces IgA
- Microbiota induces specific T cell subsets
- Microbiota metabolism and production of SCFA’s has local and systemic impact
-in general the microbiome helps develop the immune system and in mice with no microbiome there are a lot of immunological defects
The role of the microbiota in the host metabolism: How do commensal bacteria regulate digestion
- they mediate bile acid synthesis
- lipid absorption
- amino acid metabolism
- vitamin synthesis
- SCFA production
- byproducts of commensal fermentation (metabolites) regulate the immune system
What is the function of microbiota-associated metabolites
they shape mucosal immunity
Explain the idea that numerous diseases are associated with intestinal dysbiosis
- Many diseases are associated with abnormal colonization, but cause-effect relationships are unclear
- is it an abnormal microbiome that leads to disease
- or is it that the disease leads to an abnormal microbioem
What is dysbiosis
abnormal colonization of the microbiome
unsure whether the environment causes it or if disease causes it or if it causes disease!
Explain how the adult diet continues shaping the microbiota
- consumption of a westernized diet (low in fiber and veggies and good things) is associated with a decreased gut microbiome “richness”
- individuals with marked obesity, insulin resisitance, dyslipidemis and inflammatory phenotype have low bacterial richness
- increased consumption of an agrarian diet-rich in fruits and vegetables with higher fiber is associated with increased bacterial gene richness
- energy-restricted diets increase bacterial gene richness
How does the diet impact pathogen suseptibility
- having a diet rich in fiber leads to a rich microbiome
- having a rich microbiome leads to decreased pathogen suseptibilty
- therefore a healthy dieat and decreased ability of pathogens to infect
- having a nutrient poor diet leads to a not very strong microbiome.
- a weak microbiome leads to increased pathogen suseptibility
- so .an unhealthy diet can increase risk of illness
List the ways by which commensal microbiota prevent pathogen colonization
Bacteriocin production • SCFA production • Consumption (with pathogens) of oxygen • Competition (with pathogens) for nutrients • Competition (with pathogens) for attachment sites • Induction of epithelial antimicrobials (AMPs which are basically the microbiome releasing natural antibiotic) • Induction of mucus production and secretion this acts as a nice physical barrier as well!)
How does a clostridium difficile infection occur
- a person takes antibiotics and they kill lot of the commensal bacteria in the gut/colon
- the commensal bacteria are no longer there to protect against pathogens
- clostridium difficile bacteria (a pathogen) gains a foothold and produces toxins that cause mucosal injury
- neutrophils and RBCs leak into the gut between injured epithelial cells
- Also then Clostridium Difficile just takes over and it is the main bacteria preventing proper repopulation of the microbiome :(
List four ways by which you can manipulate the microbiome
- Antibiotics-not specific, collateral damage, potentially harmful (bc you knock out the microbiome which protects against pathogens. eg is clostridium difficile infection after taking widespread antibiotics)
- Probiotics (yay!?)
- Fecal microbiota transplant (yay!)
- Bacterial therapy with constructed consortia (yay!)
What are probiotics
A probiotic is “a viable microbial food supplement which beneficially influences the health of the host”……probably but this isn’t totally proven.
Criteria for probiotic selection
- origin of the microbe
- stability in the GI tract (acid and bile resistant)
- viability
- adherence to human intestinal mucus/mucosa
- Antimicrobial activity against pathogens
List 7 functions of probiotics
- improve intestinal barrier
- stimulation of mucin secretion
- stimulation of antimicrobial peptide expression (AMPs)
- inhibition of adherence and invasion of pathogens
- enhance IgA production
- in epithelial cell culture, some probiotics have anti-inflammatory activity (attenuate IL-8, and TNF-a secretion, inhibit NF-kB pathway, prevent apoptosis)
- Metabolic and neurologic effects are currently being examined
What is the best treatment right now for patients with Clostridium Difficile
Fecal microbiota transplant!
basically you are taking someone else’s microbiome and inserting it into the person who has no microbiome left. you are hoping to repoopulate their microbiome
Mucosal surfaces are colonized by
complex microbial ecosystems
the composition of the microbiome is regulated by
interactions between the host, bacteria and the environment
The indigenous microbiota is integrally involved in….
the development of the mucosal immune system and the establishment of mucosal homeostasis
the role of the mucosal immune system is to
protect the host from pathogens while maintaining homeostasis with colonizing bacteria and environmental antigens
breakdown of homeostasis at mucosal surfaces is often associated with dysbiosis and leads to
disease, including infection, inflammation, autoimmunity, and metabolic dysfunction
Fecal microbiota transplant and other approaches may be helpful for
re-establishing healthy microbial colonization and show promise for the treatment of autoimmune, allergic and infectious disease
