Interphase förel 1-6 Flashcards
NCD
Non-communicable disease, medical condition/disease not caused by infectious agents. Can refer to chronic diseases.
Main types are cardiovascular diseases, cancer, chronic respiratory diseases and diabetes. Also allergic disorders such as food allergy and allergic rhinitis among others.
The probability of dying of a NCD is the highest in developing regions.
We’re expecting an increased cost of NCDs in upcoming years.
NCD triggers
Stress
vit D deficiency
global mobility
air pollution
alcohol & smoking
consumption of antibiotics and other pharma-products
increased sanitation and hygiene
C-section as birth mode
formula feeding
Direct health effects of human microbial residents (local)
- Further digestion; provides 10-15% of host energy
- Nutrients for the gut epithelium
- Colonization resistance against pathogens
- Formation of health-promoting metabolites
- Formation of (geno-)toxic compounds
Indirect health effects of human microbial residents (systemic)
- Interaction with gut-associated lymphoid tissue (GALT) = 60-70% of our immune system
- Gut microbiome is largest endocrine organ, producing >30 hormone-like compounds
- Interaction with brain through gut-brain axis.
Humoral response of gut-brain axis
Gut-brain:
- Gastrointestinal hormones
- Inflammatory mediators
Brain-gut:
- HPA axis
Neural response of gut-brain axis
- Autonomic nervous system
Enteric nervous system
Issues related to microbiota-gut-brain-axis
- Stress
- Metabolic disorder
- Obesity
- Diabetes
- Functional Gastrointestinal Disorders
- IBS
- Neurodegenerative Disorders
- Alzheimer’s
- Parkinson’s
- Neurodevelopmental disorders
- Autism
- Schizophrenia
- Addiction
- Alcohol dependence
Microbiology
monocultures in test tubes
Microbiome
totality of microbes, their genes and their interactions with the environment. An ecosystem inside the human, highly organized, interactive and dynamic ecological union.
Resident microbiome
symbiotic interactions with the host
Transient microbiome
passing through stimulating resident microbiome; supply metabolites for cross-feeding and growth factors etc., reducing/inhibiting pathogens, indirect impact through interaction with host epithelium
Two types of selective pressure
- Bottom up : due to competition between microbes, stimulating the developement fo new and specialized niches
- Top down: by the host resulting in functional redundancy to maintain itself
Multiple species that represent a variety of taxonomic groups can share similar, or even identical roles in the ecosystem
Functional niche
Not a physical location in the ecosystem. Has functional role of the microbe in the ecosystem.
Positive interactions between microbes create new niches. Occupation of all niches; all nutrients in the ecosystem are used.
Negative interaction: negative feedback to community. Balance of + and - results in a ‘climax community’. Dynamic stability.
Colonization resistance
Pre-emptive colonization. Fewer chances for pathogens. Comes from interaction processes between and with all microbial groups; not from a single organism. Every organism in the climax community has a specific role.
Quorum sensing
Regulating bacterial gene expression in function of the population density by production of signaling molecules, ‘auto-inducers’
Bacteria sense the population density. There is a critical cell population. Two/three types of auto-inducers. They are important for biofilms and microcolonies among others
Types of Quorum sensing
Type-1 or AI-1: Species-specific, intraspecies communication = AHL ring with carbon chain specific for the species (G-)
Type-2 or AI-2: Not specific, international language for interspecies communication and communication with other microorganisms (fungi, protozoa) = Furanosyl borate diester
Type-3 or AI-3: Found in EHEC, bacterium-human host communication (cross talk AI-3 and hormone epinephrine)
Quorum sensing gene regulation for:
Biofilm formation
Virulence and toxin production
Conjugation; exchange genetic material, e.g antibiotic resistance
Enzyme production and uptake of micronutrients
Bacteriocin production
Therapeutic potential of Quorum sensing (3)
Development of pharmaceuticals specifically inhibiting the QS system → avoiding virulence/toxicity
Quorum quenching = induce QS system at low cell density to stimulate a host response long before the pathogen population is large enough to sustain infection
Signals as a biosensor marker; e.g recognizing cancer microenvironments
Abilities of top-down host microbiome
Outgrow chemical and physical stresses such as pH, bile acids and peristalsis etc..
Fend off immune response from host
Tissue tropism
Tissue tropism
Choice of a specific species to adhere to a specific place
Different types of host cells; extracellular matrix, other microbes, excretion molecules
Mechanistic explanation: receptor on host tissue recognizes complementary adhesin from microbe.
Microbiome homeostasis
property of a microbial community to maintain their stability while adjusting to conditions optimal for survival. Stability attained is actually in a dynamic equilibrium, in which continuous change of the conditions occurs between pre-set limits (homeostatic range).
Dysbiosis
Term for microbial imbalance, when microbiome homeostasis on or inside the host is not successful. Tipping points; depending on resilience.
Rivet hypothesis
Removal of either type of species does not affect the structure of the community much and it is likely that the function of the community will be preserved. Only removing many species will give a functional change
Walker’s “drivers and passengers hypothesis”
Removal of a low-abundance species does not alter the structure significantly, but removal of a keystone species gives a major structural change, which is likely associated with loss of community function and major reorganization for the community.
Alpha diversity
mean species diversity in sites or habitats at local scale
Beta diversity
differentiation among habitats/sites, absolute species turnover
Gamma diversity
total species diversity in a landscape. Gamma = alpha * beta
Nutritional and physicochemical laws concerning bacterial colonization
Liebig’s law: law of the minimum.
Bacteria dependent on many parameters. One specific parameter determines growth of the bacterial cell. Growth of bacterium follows rate limiting component in the ecosystem.
Shelford’s law: law of the tolerance.
Has to do with non-nutritional factors such as pH and temperature. Every factor has boundaries within which the organism is able to grow. Organism will only grow if environmental parameter values are within proper range (homeostatic range)
3 general steps of metabolism of carbon sources in the large intestine
1st step: Hydrolysis to oligomers and monomers
2nd step: Fermentation of monomers to fatty acids
3rd step: Is situation dependent. Further conversion to methane (colon)
Sequential steps by different microbial groups
Physicochemical aspects affecting bacterial colonization
- Temp
- pH
- Oxygen
- Redox potential
- Atmospheric composition
- Water activity
- Salinity
- Light
- Shear forces and microgravity
Nutritional aspects affecting bacterial colonization
- Building blocks of biomass
- Co-factors of enzymes
- Other micronutrients
- Vitamins
Sources; host, other bacteria, nutrition (only for GI tract)
Carbon source: Skin - lipids, respiratory tract - Mucins and proteins, large intestine - non-digested food
Which chemicals does epithelial skin membrane produce that destroy MO?
- Skin acidity (pH 3-5) - inhibit bacterial growth
- Sebum - toxic to bacteria
- Stomach mucosae secrete conc HCl and protein-digesting enzymes
- Saliva and lacrimal fluid contain lysozyme
- Mucus - trap MO entering respiratory and digestive system
Mucus
Components made by Goblet and epithelial cells
Host defense system vs nutrient source
- Has receptors for some bacterial adhesins (lectins): bacteria are ‘trapped’
- Effector molecules from innate and adaptive immune system: antimicrobial components
- Continuous secretion
- Protection against physical and chemical processes, e.g. enzymes and acid
- Humidifies and lubricates: transport of components, passage of digested food through GIT
Difference mucus and mucin
Mucus contains >90% H2O, inorganic ions, organic compounds. 2-10% mucin. Mucin is 70-80% carbohydrates.
Mucin
Can be gel forming or non gel forming
Serves as a nutrient substrate
Complex structure to give bacterial collaboration for breaksdown
keratinisation
Occurs on epithelium skin layer. Making it dry, chemcially and physically reistant surface inhospitable to microbes.
Desquamination
Process that removes any microbes that have succeeded in colonizing the epithelial surface.
Apical and basolateral side of epithelium
Apical - Contact with “the other world”
Basolateral - contact with basal lamina and underlying tissue
MAMP
Microbe associated molecular patterns
- LPS
- Peptidoglycan
- Lipoprotein
- Protein
Are recognized by PRR; pattern recognition receptors
TLR
Toll like receptor
10 different types
Specific for different modulins
Interaction of TLR with ligand activated signalling pathway
Immune control by endogenous microbiota
- Pathogens induce pro-inflammatory response
- Immune suppressive effects from microbiota
- Induction of pro-inflammatory cytokines
- Induction of TGF-beta by Lactobacillus sp
- Antimicrobial peptides
Biofilm
A way of spatial organization of a microbial community. Adhesion, growth and reproduction when nutritional needs are fulfilled. Hydrodynamic and mechanic forces counteract the adhesion process. Daughter cells can adhere somewhere else when mobile. Shedding of epithelial cells; desquamation.
Biofilms are the most natural form for microbes to occur in nature
Microcolonies
adherent microbial aggregates in extracellular polymeric substances (EPS)
How microcolonies form biofilm (5 steps)
- Reversible adhesion
- Irreversible adhesion
- Maturation I
- Maturation II
- Dispersion
The biofilm is formed on body tissue when it has proper anatomical conditions and on particles in colon. Has a high hydration. Only 10-50% of the biofilm is bacterial.
Colon mucosal biofilm
Atypical biofilm. Growth within a dynamic mucus layer; bacterial and host compounds, host inflammatory responses, continuous mucus renewal. Low densities of around 10^5-10^6 CFU/mL mucus. Always “immature”
Bioavailibility
- Gastrointestinal digestibility and solubility
- Endothelial absorption
- Distribution
- Utilisation
Can be studied in vivo with animal studies and human studies
Bioaccessibility
- Degree of digestive enzymatic hydrolysis
- Release of components from food
Can be studied in vitro with solubility assays, dialysability assays, simualted gastrointenstinal model
Bioactivity
- Endothelial absorption
- Transportation
- Transformation
- Tissue uptake
- Physiological response
Can be studied in vitro using Caco2 cell line or HT-29 cell line or in vivo using animal studies or human studies
Redox tower of microbial metabolism
MO can use a wide range of e- donors (edibles) and e- acceptors (breathables) to generate energy for metabolism. Can couple any oxi reaction to nearly any red reaction as longer as the e- donor is higher on the tower than the e- acceptor.
Host microbe metabolic interactions at 3 levels, which?
- Macronutrients
a) Carbohydrates e.g starch, poly/oligosaccharides, lactose…
b)Proteins eg peptides, albumin, hemoglobin, insulin…
c) Lipids eg triglycerides, fatty acids, cholesterol, phospholipids…
d) Combinations of the above
- Glycoprotein (=protein + oligosacc. side chain) e.g mucin
- Lipoprotein (=protein + lipid) e.g HDL and LDL - Micronutrient level
- Special focus on bioactive “extranutritrional” compounds like antioxidants, antiinflammatory, anticarcinogenic etc.
- Phytoestrogens - plant hormones that resemble natural human hormones. Can be used to prevent hormone-related diaseases as well as to fix distrubed hormone balance during menopause. - Xenobiotics
- Pollutants, “foreign to biota”
- Carcinogens, drugs, environmental pollutants, food additives, hydrocarbons, pesticides.
- Host metabolism - focus on excretion
The pan-genome/supra-genome
= the full complement of genes in a clade (species for Bacteria and Archaea)
a) Core pan-genome
b) Shell pan-genome
c) Cloud pan-genome
a) Core pan-genome: genes present in all individuals
b) Shell pan-genome: shell genes present in two or more strains
c) Cloud pan-genome: unique cloud genes specific to single strains Also referred to as accessory or dispensable genome
a) Closed pan genome
b) Open pan genome
a) Closed: very few genes added per sequenced genome after sequencing many strains, size can be predicted
b) Open: so many genes added per additional sequenced genome that predicting the size of the full pan-genome is not possible
Pan genome size affected by..
…population size and niche versatility.
What is meant with “Old friends” concerning hygiene and microbes?
Drastic decrease to MO because of use of antibiotics, antimicrobials and disinfectants. Giving lack of immune training, causing immune system to be overly sensitive → exaggerated responses. There are diseases in the industrialized western world that do not occur in rural areas.
Due to lack of exposure of MO in western world today we may actually need specific microbial compounds to train our immune system, so called “old-friends” such as B fragilis and H pylori or Helicobacter hepaticus. H. hepaticus uses a type 6 secretion system common to 25% of all bacteria which is a defense mechanism of MO against other MO. This can calm the immune system in the body. We rely on the system to upregulate Treg. However, at certain conditions it becomes a renegade and behaves as a pathogen which stresses the relationship. This means that certain alleged pathogens can have an important symbiotic relationship with the host.
Factors affecting microbiome developement (6)
- Pregnancy: uterine microbiome, third trimester, placental microbiome. In the third trimester the intestinal barrier is still very thin, giving a higher risk of obtaining pathogens.
- Time of birth: preterm versus term. Premature babies are more sensitive, less immune development.
- Mode of birth: vaginal delivery versus C-section
- Diet: breastfeeding versus formula
- Exposure to antibiotics
- Others: place of birth (hospitalization versus at home), presence of siblings, daycare attendance…
Birthmode contribution microbiome development
Study performed ten years ago saw that babies born vaginally had a microbiome resembling the mother’s vagianl microbiome whereas those delivered with C-section developed a microbiome similar to the mother’s skin.
It was also shown that birth mode had no big effect on microbiome development and that possible initial differences fade away one a feeding pattern is established.
However, higher levels of pro-inflammatory cytokines of vaginally born babies suggests that children born with C-section might have a higher risk of developing asthma and allergies since their immune system is less alert.
Rubbing of swabs from vagina and anal to the skin and mouth of the child could be performed to partially restore the vaginal microbe to children born with C-section. Studies performed in this currently.
Aging, factors affecting the microbiome (3)
- Elderly people experience dietary changes - less supportive of microbiome fitness.
- Medication and drug use typically increases, so does degree in hygiene.
These contributions give a higher vulnerability to and frequency of developing diseases.
Onset of physiological changes depend on the individual and is affected by lifestyle.
- From studies it has been seen that depending on residence location, different microbiota. Long stay residential care gives higher vulnerability.
Exposome
Assembly of exposures over a lifetime; Ab, drugs, environmental pollutants. Combination and accumulated effects over time may give changes in immune and microbiome status that can negatively affect our health status.
Other antimicrobial agents that are not antibodies
- Organic acids: Carboxylic acids able to alter physiology of bacteria, causing metabolic disorders preventing proliferation and causing death. Can increase bodyweight, improve feed conversion ratio, reduce colonization of pathogen in the intestine
- Antimicrobial peptides: Novel therapeutic agents, small molecules, broad antimicrobial spectrum
- Phytogenics: Essential oils etc
Antibody perturbation of human gut microbiome, timeline + risks
At day 4 of Ab treatment you’re able to see a significant drop in species richness. After 180 days, the value has gone up but is still low. Might also be new composition of microbiome. The difference depends on the individual.
If the microbiome does not recover, blooming can occur.
Every single use of antibiotics will increase the prevalence of resistance
Recovery associated bacteria (RABs)
20 bacterial species associated with post antibiotic recovery. Primary colonizing species. Able to use both host and diet-derived energy sources. Break down complex carbohydrates to support growth of other bacteria.
Primary colonizers - take the first steps in colonization
Secondary and tertiary and further making the range broader.
Restoration of metabolic interaction can be evaluated by seeing cross-feeding.
Positive feedback loop.
Blooming
Overgrowth of ab-resistant MO that benefit from empty space both physically and functionally. Certain of these species are harmless. May become life-threatening, such as Cl. difficile infection with diarrhea. Colonization becomes possible because it has an “open” field to play on
Developement of Antimicrobial resistance, mechanisms (3)
- Selective pressure; resistant mutant will have large fitness advantage → rapid spread.
- Horizontal gene transfer: resistance transferred from non-pathogen to pathogen. Exchange between individuals but also species.
- Resistome: Collection of AMR genes and their precursors in both pathogenic and nonpathogenic bacteria. Consists of four types of genes.
Resistome gene types (4)
Resistance genes found on pathogenic bacteria
Resistance genes found on AB producers
Cryptic resistance genes: Embedded in chromosome, can confer AMR but have not been selected in response to recent exposure of AB
Precursor genes: Do not confer AMR, encode proteins with other metabolic functions but with a basal level activity against the antibiotic molecule or affinity to the molecule. May evolve to a full resistance gene under appropriate selective pressure.
Antimicrobial strategies that spare the microbiome (3)
Use of compounds more benign to the microbiome flora.
Bacteriophage therapy
Disarming pathogens instead of killing them. Block virulence factors and regulate virulence to control the pathogens.
Plant based diet vs animal based diet
Plant based diets give increased fiber and nutrient intake and reduced fat and protein intake whereas an animal diet had the opposite effect. This also has a large effect on the microbiome.
- With animal based diets the lipid consumption is higher, giving a higher amount of bile salts to digest the lipids. Bile salts acts as a natural detergent but also AM causing stress to the microbiome.
- Bacteria specialized in fiber degradation also decreases with animal based diet, which is negative since these also produce butyrate. Butyrate gives energy to the cells in our intestines and also acts anti-inflammatory and anti-carcinogenic.
- AA fermentation products increase which is related to production of compounds that are toxic and able to damage the gut epithelium giving a reduced gut barrier integrity. AB diet may also give a higher tolerance to certain MO.
Importance of human milk given to babies, constituents in milk
Human milk contains IgA, lysozymes which cow milk lack.
Human milk also contains other things than nutrients. Human milk oligosaccharides (HMO) stimulate bifidobacterium infantis which is an efficient HMO degrade and acts as a prebiotic for the child.
> 150 HMOs have been identified. Composition differs between mothers and throughout the breastfeeding period. Four distinct milk groups. Have been found also in amniotic fluid → continuous exposure to them from conception onwards.
HMOs cannot be digested, but is meant for the MO. Normally pathogens are able to bind mucin structures in the gut, but with HMOs the pathogen will bind to those instead of the epithelium. HMOs also have an effect in brain development. HMOs have many different important aspects.
HMOs are lacking in formula milk. Even Though the other differences are small, the impact can be huge.
Human milk offers the neonate a vital protection against infections and harmful substances. Breastfeeding is the most important contributing factor to the gut microbiome development in the first years of life.
Prebiotics
“A prebiotic is a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon host wellbeing and health”
