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immunology and microbiology > The human microbiota and its microbiome L7 > Flashcards

The human microbiota and its microbiome L7 Flashcards

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Biology 101 flashcards
1
Q

how many bacteria are in the microbiota

A

number of bacteria in our bodies is actually of the same number as the number of human cells
each defecation event may flip the ratio to favour human cells over bacteria.

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2
Q

what are the two methods of identifying bacteria in our microbiota

A
  1. culturing
    - Grow ‘live’ microbes on agar that can be tested in lab-based mechanistic studies
    - Required for development of therapies
  2. DNA/RNA sequencing
    - DNA is easier to extract but RNA tells us more about what genes are being transcribed at the time sample was taken
    - Determine microbial community ‘fingerprint’
    - Rapid and high-throughput
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3
Q

what are the two methods of NGS microbiome profiling

A
  1. genus level profiling
  2. shot gun approaches
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4
Q

describe genus level profiling

A
  1. take 16s rRNA from bacteria
  2. amplify and cluster it
  3. data base mapping/ compare data to identify bacteria
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5
Q

what are the two shot gun approaches

A
  1. metagenomics (DNA)
  2. metatranscriptomics (RNA)
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6
Q

What type of profiling is metagenomics and metatranscriptomics

A

metagenomics: species/strain level and functional potential profiling
metatranscriptomics: species/strain level and function and activity profiling

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7
Q

describe metagenomics

A
  1. sequence DNA
  2. map sequence to genomes/ gene or do de novo assembly of genomes then map it to new genomes
  3. can work out putative (generally considered or reputed to be) functional pathways
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8
Q

describe metatranscriptomics

A
  1. sequence RNA
  2. map sequence to pathways/gene or do de novo assembly of transcriptomes and organise it into pathways
  3. work out active pathways/ microorganisms
    - tells us function and how bacteria reacts to environment
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9
Q

give 2 other ways to identify bacteria in microbiota

A
  1. Metabolomics- what is being consumed by microbiota
  2. Proteomics- know which proteins are being made to inform you on pathways being used,
    May not know what they are being used for
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10
Q

how does the type (taxa) of bacteria and metabolic pathways relate

A

the type of bacteria in different compartments very but the metabolic pathways remain stable

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11
Q

what is culturomics

A

technique developed to culture and identify ‘unknown’ microbes
important for:
- improving reference databases for further NGS approaches
- phenotypic/mechanistic studies
- culture collections
- therapy development
expensive and labour intensive

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12
Q

which human organ is most densely colonised by bacteria

A

intestine
2500+ bacterial species capable of colonising colon
Broad range of physiological conditions
- creates distinct niches for colonisation

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13
Q

what are the main bacteria phyla

A
  1. proteobacteria
  2. actinobacteria
  3. firmicutes
  4. Bacteroidetes
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14
Q

what is the major functions of the microbiota

A
  1. bacteria degrade complex carbohydrates that we can’t break down
  2. educate immune system
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15
Q

why are bacteria better at degrading complex carbs

A

B. thetaiotaomicron has close to 300 genes encoded for carbohydrate digestion
- they use sugar as their main nutrient
- What you eat determines composition of microbiome- may start eating mucus that lines intestine if no food so makes you more suspectable to disease

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16
Q

what does fermentation of complex carbs result in

A

fermenting sugars makes short chain fatty acids (SCFA)
- good for health
Some bacteria can target the indigestible carbs, they can release them in more soluble components which then makes it easier for other bacteria can degrade

17
Q

what are short chain fatty acids used for

A

liver: sugar metabolism and storage
adipose tissue: fat uptake and storage
brain: appitite regulation
Strengthen tight junctions

18
Q

what are HMOs
- where are they found

A

human milk oligosaccharides
found in breast milk
encourages growth of bifidobacterium

19
Q

which bacteria digest HMOs

A

B. infantis
use them to form short chain fatty acids

20
Q

how does our microbiome develop

A

unborn: sterile
baby: Pioneer microbes, Low diversity, High instability
child: New species, out compete early ones, Rapid increase in diversity (via diet), High instability
adult: Highly distinct, diverse microbiota, Microbial community may continue to change, but at slower rate
elderly: Substantially different microbiota than younger adults, Lower diversity

21
Q

what early life factors can influence a babies microbiome

A

during pregnancy: Maternal exposures: stress, weight gain, antibiotics, smoking
Length of gestation: term vs. preterm
Weight at birth: < 1500g
at birth: Mode of delivery: vaginal vs. C-section
Contact with mother or healthcare professionals
Environment straight after birth: intensive care
after birth: Feeding modality: breast vs. formula
Antibiotics
Weaning or food supplementation
Home or family setting: rural vs. urban
Home structure: siblings/pets

22
Q

how did microbiome of C section baby and vaginal baby differ

A

V had bacteroides and bifidobacteria but C section did not
if C section baby was given stool sample from mother, microbiome became more like the vaginal baby

23
Q

what is colonisation resistance
why is it difficult for bacteria to colonies

A

Resistance to colonisation by ingested bacteria or inhibition of overgrowth of resident bacteria normally present at low levels within the intestinal tract

  • bacteria have to compete for niches- only one bacteria can occupy a niche
  • have to compete for nutrients
  • get killed by immune system
24
Q

how does the microbiota create immune development

A

microbiota inhibit colonisation and overgrowth of invading microbes due to colonisation resistance
this creates microbe-microbe interactions and microbe host interaction

25
Q

how does host-microbe interactions inform immune system

A
  • strengthening of the intestinal barrier
  • maturation/differentiation of the immune system
  • Maturation of secondary lymphoid follicles
  • induction of secretory IgA
  • Increasing numbers of innate immune cells
  • shaping of T cell subsets, including regulatory mucosal T cells and TH17 cells
  • Inducing anti-microbial peptides
26
Q

how does microbe-microbe interactions inform immune system

A

direct inhibition by release of inhibitory metabolites (i.e. lactic acid, acetate)
Bacteriocins
competition for niches and nutrients
manipulating nutrients in such a way as to suppress the growth of enteric pathogens
competition for specific adhesion sites (competitive exclusion)
biofilm formation

27
Q

how do pathogenic bacteria inform immune system

A

virulence factors that induce inflammation which is damaging to microbiota and also releases nutrients
Mucus layer is thicker if exposed more to bacteria
Affects maturation of T cells

28
Q

what happens if microbiota is disturbed

A

may cause disease
1. intestinal disease
2. metabolic disease
3. autoimmune disease
4. brain linked condition
5. immune disease
caused by Diet, Antibiotics, Birth mode, Infections, Genetics
High saturated fat, fructose, antibiotics = lower short chain fatty acids
If feed mice no-complex carb diet for generations then give offspring normal diet, wont develop bacteria that was lost

29
Q

how may underdeveloped microbiota cause certain growth phenotypes

A

Undernourished Malawian children with stunted growth had immature microbiota
even when given more food, their microbiota did not recover
Microbiota from healthy and undernourished Malawian children transplanted to germ free mice.

Mice transplanted with healthy microbiota gained more weight and lean mass

30
Q

can underdeveloped microbiomes recover

A

Specific strains identified that are different in mature microbiota to immature.
Stunted mice transplanted with those strains.
Treated mice increase in weight and lean mass compared to untreated control

31
Q

how does HMO link to malnutrition

A

microbiota from undernorished child put in, gnotobiotic mice and gnotobiotic piglets
germ free mice used as a control
they were then given a normal diet with HMO
germ free mice did not gain weight but gnotobiotic mice and piglets did

32
Q

is autism linked with defected microbiome

A

early studies suggested it did
more advanced studies found it was more linked with dietary preferences
dietary preferences mediate autism-gut microbiome association

immunology and microbiology (12 decks)

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