L3: Human Microbiome I Flashcards
(68 cards)
1
Q
explain the ratio between microbial vs human CELLS in the human body
A
- ~100 trillion microbial cells vs ~30 trillion human cells
- microbial cells outnumber human cells by: 10:1/3:1/1:1
2
Q
explain the ratio between microbial vs human GENES in the human body
A
- microbial genes: ~2,000,000
- human genes: ~23,000
- microbial genetic repertoire (microbiome) is ~100x greater than humans
3
Q
what do the numbers of microbial vs human ratio depend on
A
- the location of the sample
- ex: blood vs gut
4
Q
where is the majority of the microbes in the human body
A
in the gut
5
Q
how so you get a good representation of microbes in the digestive system
A
- feces
- take it and dry it, then weight it
- will find: 75% water and the remaining 25% is 1/3 fiber, 1/3 dead bacteria, and 1/3 is live bacteria
6
Q
what is the human genome project
A
researchers took people from all over the world, sequenced their genomes, and put the results in a tree
7
Q
human genome project - what was the trend seen
A
every sample had bacterial DNA
8
Q
what is the human microbiome project
A
- researchers took healthy people to see what the baseline of a healthy microbiome is
- had two main phases
9
Q
human microbiome project - main phase 1
A
- HMP1: 2007-2014
- used 300 healthy individuals and still generated so much data
- observed their microbiomes to see variation during a particular time frame
10
Q
human microbiome project - main phase 2
A
- HMP2: 2014-2016
- chose 5 major parts of the body and observed thousands of people’s microbiomes
- did longitudinal studies and used other omics
- found some context for diseases
11
Q
human microbiome project: main phase 2 - what were the major parts chosen
A
- nasal
- oral cavity
- gastro-intestinal
- urogenital
12
Q
human microbiome project: main phase 2 - what are the disease context
A
- pregnancy and preterm birth
- inflammatory bowel disease
- type 2 diabetes
- but remember positive correlation =/= biological meaning
13
Q
human microbiome project - what did it achieve
A
- over 650 peer-reviewed publications
- cited over 70,000 times
- development of databases and catalogs
- development of tools and methods
- establishment of research centers
- include microbiome research as one of the NIH Roadmap of Medical Research
14
Q
human microbiome project - what questions did they solve
A
- what is the identity of the microbes that populate their host?
- what are these microbes doing?
- how is the host responding to them?
- what are the forces that maintain equilibrium among the populations?
- what are the unique characteristics of each individuals
15
Q
the microbiome project - what is the core human microbiome
A
- none
- no universal or core species of microbes were found
- every individual had a different set of microbes
16
Q
the microbiome project - what are the variable human microbiome
A
- host lifestyle
- host genotype
- host pathology
- host environment
- transient community members
- host immune system
- host physiology
17
Q
explain the diversity of the human microbiome across habitats
A
- oral cavity and gut microbes are more similar to each other and are more stable
- hair, skin, and nostril are more variable and less stable
18
Q
diversity of human microbiome - interpersonal vs intrapersonal differences
A
- interpersonal: between two or more people
- intrapersonal: between you and yourself
- intrapersonal differences (over time) were smaller than interpersonal differences (on each day) within all habitats examined
19
Q
diversity of human microbiome - habitat vs temporal differences and people variation
A
body habitat had more influence on microbial community composition than temporal differences and variation among people
20
Q
carriage of microbial taxa vs function
A
- carriage of microbial taxa varies
- function remains stable
- example of functional redundancy
21
Q
carriage of microbial taxa vs function - define functional redundancy
A
even if you have very different species of microbes, they often play similar roles
22
Q
carriage of microbial taxa vs function: functional redundancy - why is this important
A
- if you don’t have functional redundancy and take antibiotics, you may lose a specific function
- if you do have functional redundancy, it does not matter what species is targeted as long as there’s another one from the same functional group
23
Q
explain the carriage of specific microbes
A
- there are different species within a microbiome but there is variation between species
- when comparing bacteria and functional role, certain strains do not have certain enzymes or proteins
24
Q
define the gut microbiome
A
microbial communities that reside in the digestive tracts of animals
25
gut microbiome - explain the compartments
- stomach
- traverse colon
- distal colon
- proximal colon
- small intestine
26
gut microbiome - what is the differentiation of the compartments shaped by
- pH
- as pH increases, number of cells/g increases
27
gut microbiome - what are the dominant bacterial groups
- Firmicutes
- Bacteroidetes
- Actinobacteria
- Proteobacteria
- Tenericutes
- Fusobacteria
28
gut microbiome: dominant bacterial groups - which are most prominent
Firmicutes and Bacteroidetes
29
gut microbiome - explain the overall diversity
- defined and unique
- Firmicutes and Bacteroidetes are always competing for the top spot and needs to be in balance (Firmicutes/Bacteroidetes ratio)
30
gut microbiome: overall diversity - explain
the Firmicutes/Bacteroidetes ratio
- a measure of the balance of the 2 largest phyla in the human gut microbiome
- the ratio is often used as a biomarker for a number of conditions
31
gut microbiome diversity: the Firmicutes/Bacteroidetes ratio - what happens when its high
- Firmicutes levels are high and Bacteroidetes levels are low
- indicator for obesity
32
gut microbiome diversity: the Firmicutes/Bacteroidetes ratio - what happens when its low
- Firmicutes levels are low and Bacteroidetes levels are high
- indicator for IBD
33
gut microbiome diversity: the Firmicutes/Bacteroidetes ratio - is it a good indicator for gut health
- no
- bc some studies showed opposite results
34
gut microbiome diversity: explain alpha diversity and its relation to the Firmicutes/Bacteroidetes ratio
- alpha diversity is associated with the Firmicutes/Bacteroidetes ratio
- more Firmicutes = more diversity
- more diversity = healthier individuals
35
what are the factors shaping the gut microbiome
- diet
- pharmaceuticals
- geography (connected to diet)
- lifecycle stages (connected with diet)
- birthing process
- infant feeding method
- stress (exercise, metabolic, psychological)
36
factors shaping gut microbiome - diet
- you can predict what type of diet based on an organisms microbial composition
- and place them within a food web
37
factors shaping gut microbiome: diet - dietary groups
- research shows a 1:1 relationship between dietary groups and bacterial species
- food diversity increases microbial diversity
- microbiome responses to similar foods are personalized between individuals
38
factors shaping gut microbiome: diet - fiber-rich diet
mature mucus layer and intact barrier function
39
factors shaping gut microbiome: diet - why are there mucus eating microbes even when fiber is present
- it is beneficial since too much mucus is bad for the cells
- but these microbes must be kept in low density
40
factors shaping gut microbiome: diet - fiber-free diet
- microbiota eroded mucus layer and barrier is dysfunctional
- bacteria goes into bloodstream
41
factors shaping gut microbiome: diet - why do the microbes eat the mucus layer when there is no fiber
- the mucus layer is full of sugars and microbes will eat it
- in a fiber rich diet, the microbes will eat the fiber instead since its their preferred substance
42
factors shaping gut microbiome: diet - what happens when there is no fiber intake
after a few days, microbiome composition will change and the bad microbes will proliferate
43
factors shaping gut microbiome - lifestyle stages
each stage has a different microbial composition and diversity based on the food's they eat
44
factors shaping gut microbiome: lifestyle stages - neonatal
- reduced diversity
- high state of microbial flux
- species of microbes are efficient at braking down milk (breast or formula)
45
factors shaping gut microbiome: lifestyle stages - 2-3 years
- introduction of food solids and exploration of new foods
- formulation of adult-like microbial signature
46
factors shaping gut microbiome: lifestyle stages - 6-12 years
- greatest diversity in dietary intake
- greatest microbial diversity
47
factors shaping gut microbiome: lifestyle stages - adult
- habitual diet based on lifestyle, availability, and palate
- stable microbial composition
48
factors shaping gut microbiome - stress
- when cortisol levels are high, it is associated with certain types of enzymes
- bacteria can directly or indirectly (via producing other molecules) interact with cortisol
49
factors shaping gut microbiome - pharmaceuticals
some microbes that are beneficial may die and disappear completely when taking antibiotics
50
gut microbiome and how it prevents disease
- improves the integrity of the intestinal barrier function
- supports a healthy immune response
- builds healthy keystone gut bacteria
51
list the integral functions of the gut microbiome
1. interact with immune cells: cytokines
2. trigger production of neuroactive molecules (ex: serotonin)
3. production of neurotransmitters (ex: butyrate)
4. gut bacteria can travel to the brain (via vagus nerve)
5. affects the structure and function of the epithelial barrier
52
integral functions of the gut microbiome - production of neurotransmitters (ex: butyrate)
- butyrate is produced after metabolism of fiber
- more fiber = more butyrate = less inflammation
53
integral functions of the gut microbiome - affects the structure and function of the epithelial barrier
- leaky gut syndrome happens if this function fails
- no more mucus layer and molecules come into bloodstream, inflammation responses are then activated
54
specific responses to diet - LPS and TMAO
- LPS: Lipopolysaccharides
- TMAO: Trimethylamine N-oxide.
- both are molecules produced by bacteria that can produce impacts within the intestines
55
specific responses to diet: LPS and TMAO - how can these impact the intestines
- LPS: immunity
- TMAO: Associated with adverse cardiovascular outcomes due to atherosclerosis and thrombosis
56
how can the metabolism of fiber affect the hosts body?
it can impact:
1. Immune system
2. Brain health
3. Insulin resistance
57
metabolism of fiber - what molecules are produced by bacteria after the metabolism of fiber
all are SCFAs (Short-Chain Fatty Acids):
- acetate
- propionate
- butyrate
58
how can the gut microbiome response to fiber and polyphenols
- western diet (animal based protein and fats) introduces bacteria that will produce LPS and TMAO
- Mediterranean diet (plant based fats and protein) introduces bacteria that produce SCFAs
59
how can the gut microbiome response to fiber and polyphenols - consequences of western diet to overall health
- inflammation
- endoxemia
- dyslepidemia
- hypertension
- obesity
60
how can the gut microbiome response to fiber and polyphenols - consequences of Mediterranean diet to overall health
- anti-oxidant effect
- anti-inflammatory effect
- metabolic regulation
- vasculoprotection
61
gut microbiome - industrial vs nonindustrial diet
- industrial: Opportunist bacteria are more common
- nonindustrial: Commensal bacteria are more common
62
gut microbiome - effect of migration
- Higher risk of diseases: higher when migration happened in infancy/early childhood
- Bc it is time where kid is forming microbiome
63
gut microbiome - what is *Lactobacillus*
- negatively correlated with disease (more *Lactobacillus* = less diseases)
- Alleviates lactose intolerance
64
gut microbiome - what is *Bifidobacterium*
- Efficient fiber degraders
- produce vitamin B
65
gut microbiome - what is *Akkermansia mucinophilia*
- A type of bacteria that restores mucus production in the gut
- Accounts for 1–4% of the total fecal microbiota
66
gut microbiome - what is *Helicobacter pylori*
- Highly prevalent.
- Causes ulcer disease and gastric cancer
67
gut microbiome - what is *Clostridium difficile*
- Most common in people who have recently taken antibiotics over a long period of time or high doses
- Causes colitis
68
gut microbiome - what is *Prevotella spp.*
Positively associated with several diseases
