Gut Microbiota - Microbiology Flashcards
What is a microbiome?
A complex community of trillions of bacteria, viruses and fungi that are present in the human body
Where are microbiomes usually found?
Gi tract, oral cavity, lower urogenital tract, upper respiratory system
Which kind of organs do not have microbiomes?
The sterile ones: brain, heart, lower respiratory tract etc.
Why do different parts of the body have different microbiomes?
Because of the differences in the environment, certain bacteria thrive in different environments compared to the rest
What are microbiota?
The types of organisms that are present in an environmental habitat, bacteria, viruses ir eukaryotes.
What are microbiomes mainly composed of?
Bacteria, viruses and fungi are much less
Why is the gut microbiome important to our health?
It performs numerous important biochemical and biological functions for the host.
What is the gut microbiome?
Vast collection of symbiotic microorganisms and metabolites
What is dysbiosis and what does it cause?
Alteration in microbiome and it is associated with disease
What makes gut microbiota important for our health?
Their richness and diversity in microorganisms
What are microbiota?
Beneficial microorganisms that live within us in symbiotic relation –> non-pathogenic
What are pathogens?
Harmful microorganisms that cause disease in human, less than 1% of bacteria are pathogenic
What are opportunistic pathogens?
Cause disease only when the individual is immunocompromised
Where are most gut microbiota present?
In the large intestine and mainly in the cecum, less bacteria are found in the small intestine
Why are there only few bacteria in the stomach?
Because of the acidity of then stomach only few can survive and thrive
How many bacteria does the colon contain compared to the small intestine?
More than 1000 fold more bacteria
Gut Microbiota Distribution:
Colon: > 10^11/ml
Stomach: 10^2 or 10^4 / ml
Small intestine: 10^7 to 10^8/ml
How many bacteria does the human body have compared to human cells?
10 times more bacteria than human cells
How many different species of bacteria have been identified?
10000 different bacterial species
How many genes does the gut microbiome have?
3.3 million genes
Are human microbiomes identical to one another? Why?
No, they are not identical, even if people are twins and live in the same home.
That is because of their different lifestyles, environments and habits.
What is the human microbiome like in healthy conditions?
Diverse, rich and complex
Thick mucus layer
Protects against penetrating pathogens
What are the roles of the gut microbiome?
- Protection against pathogens
- Synthesis of vitamins
- Immune system development
- Promotion of intestinal angiogenesis
- Promotion of fat storage
- Short Chain Fatty Acids Production
- Modulation of CNS
How does the gut microbiome help with immune system development?
Lamina propria knows which the microbiota are and can thus differentiate between them and pathogens
How are short chain fatty acids formed?
Through fermentation of dietary fibre
How is the production of SCFA important?
Promote the gut layers of epithelium and help with immunity.
What are the functions of gut microbiota?
Digestion
Defense
Detoxification
Gut Microbiota Function: Digestion
Synthesise secondary bile acids
Metabolizes indigestible carbohydrates
Gut Microbiota Function: Defence
Maintains gut homeostasis
Stimulates host production of antimicrobial peptides and secretory IgA
Maintains gut mucosal barrier
Gut Microbiota Function: Detoxification
Antibiotics alter the microbiome, certain inactivate orally ingested digoxin
Metabolises environmental chemicals
Which factors influence microbiome development?
Birth and Perinatal Colonisation (C-section or normal birth)
Familial Exposure (Household factors)
Antibiotics & Other Drugs (Impact Diversity & Quality)
Host Susceptibility (Genetic Factors)
Diet & Food Quality (High Fibre & Complex Carbs)
How does C-section affect microbiome?
The newborn does not pass through the vaginal tract so it does not collect the healthy microbiota from the mother.
Higher chance of becoming obese
Where do microbiomes come from?
They are obtained from mother during birth and breast feeding
When is the infant microbiome established?
During the first year of life
What is gut microbiota responsible for?
Energy production from food, production of SCFA which is energy for epithelial cells and important for immune system
What is an example of SCFA produced by the microbiota?
Butyrate
How does diet impact gut microbiota?
Their composition and metabolic function
Do gut microbiota dominant change with age ?
Yes, for instance, bacteroidetes decrease with age
What is bifidobacterium?
A genius of a gram-positive, saccharolytic, anaerobic bacteria.
Where are bifidobacteria found?
GIT, Vagina and Mouth
What is one of the functions of bifidobacterium?
Help colon regularity
Prevent GI infections by competitive exclusion of pathogens
Where is bifidobacterium found?
In yogurt and kefir
What family do bifidobacterium fall under?
Firmicutes
What are Firmicutes?
> 250 genera, mostly gram + bacteria
What re Bacteroides?
About 20 genera, gram - bacteria
What are Bifidobacteria?
Actinobacteria: gram +
What are Verrucomicrobia?
Akkermansia: gram -
What are proteobacteria?
Gram - bacteria, include a wide variety of pathogens like E. coli, salmonella, etc.
How does diet shape our microbiomes?
High fibre diets enrich and diversify the gut microbiome by increasing the number of good bacteria species
What is orthorexia?
Unsafe obsession with healthy food
What is the consequence of a fibre-deprived diet?
May degrade the colonic mucus barrier and promote enteric pathogen infection
What are the advantages of thick mucus layer?
Prevents mucosal pathogens and protects epithelial cells
More fiber-degrading bacteria
Less mucus-degrading bacteria that break down mucins
What can dysbiosis lead to?
A leaky gut: increase in permeability which leads to viruses and inflammatory factors (endotoxins) leaking through
What are poor diets associated with?
Obesity and decline in cognitive function
What are flavonoids?
Found in plants, vegetables and fruits: Compounds that have been associated with improved metabolic parameters in obesity
Given that microbial flavonoid conversion is important…
Flavonoid-derived neuroactive compounds may be functionally crucial in the gut microbiome - brain axis
What can reduced inflammation lead to?
Cardiovascular disease
What can immune tolerance lead to?
Autism
What can the lack of killing pathogens lead to?
Colorectal cancer
What are the causes of dysbiosis?
Unbalanced diet
Inflammatory process
Presence of intestinal helminths
Uncontrolled rectal cleaning with enemas
Use of chemotherapy, antiviral drugs
Antibiotics
DM, cancer, liver/pancreas diseases
Infections
What is obesity recognised as?
A multifactorial disorder which is a result of the interaction of host and environmental factors
When does one become obese?
When the energy intake exceeds energy expenditure
What have studies shown regarding microbiota in obese individuals?
They are more efficient in extracting energy from dietary components as a result they can store more energy as fat in the adipose tissue compared to a lean person’s ability to do so
How does altered gut microbiota promote obesity?
Increased calorie extraction
Enhanced fat storage
Metabolic signaling disruption
Inflammation and insulin resistance
What is energy intake?
Appetite and eating habits
What is energy harvest?
Microbiota help digest food, and generate SCFA
What is energy expenditure?
Regulation of metabolic rate
What is energy distribution?
Regulation of body adiposity
What are the consequences of an unbalanced diet?
Alter gut barrier functions (leaky gut), promote metabolic endotoxemia, ROS and inflammation
What is A. muciniphila?
Gram -, strictly anaerobic, non-motile, oval-shaped bacterium
What is the relation between obesity and A. muciniphila?
Obesity is associated with lower abundance of A. muciniphila in the gut
What is the function of A. muciniphila?
Can use mucin as its sole source of carbon and nitrogen, increased thickness of mucus layer.
Which drugs help promote A. muciniphila?
Metformin and vancomycin
Why were COVID patients affected in a GI level too?
ACE2, the entry receptor of COVID, is widely expressed in the membranes of GI epithelial cells
How can one increase gut microbiota?
Prebiotics
Probiotics
Diet
FMT
What is FMT?
Fecal Microbiota Transplant: introduction of gut microbiota from a donor, through transfer of an infusion via NG tube, ND tube, rectal enema or the biopsy channel of colonoscopy.
What is transient dysbiosis associated with?
C. difficile infections, C. difficile diarrhea
What are probiotics?
Live microorganisms that confer a health benefit on the host
What are prebiotics?
A selectie fermented ingredient that results in specific changes in the composition and activity of the GI microbiota
What are synbiotics?
Mixtures of probiotics and prebiotics that beneficially affect the host
How is microbiome investigated?
Total DNA sequencing and you look for 16S ribosomal RNA gene –> identification of bacteria (hyper variable regions)
Which bacteria families make up 90% of microbiota composition?
Fiirmicutes & Bacteroides
What are the different approaches of investigating microbiome?
DNA - based
RNA - based
Protein - based
Metabolite - based
Detection with DNA - based approaches of microbiome?
16s RNA, 18S , ITS gene sequencing
Detection with RNA - based approaches of microbiome?
Metatranscriptomics
Detection with protein - based approaches of microbiome?
Metaproteomics
Detection with metabolite - based approaches of microbiome?
Metabolomics
