The human microbiota and its microbiome L7 Flashcards
how many bacteria are in the microbiota
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.
what are the two methods of identifying bacteria in our microbiota
- culturing
- Grow ‘live’ microbes on agar that can be tested in lab-based mechanistic studies
- Required for development of therapies - 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
what are the two methods of NGS microbiome profiling
- genus level profiling
- shot gun approaches
describe genus level profiling
- take 16s rRNA from bacteria
- amplify and cluster it
- data base mapping/ compare data to identify bacteria
what are the two shot gun approaches
- metagenomics (DNA)
- metatranscriptomics (RNA)
What type of profiling is metagenomics and metatranscriptomics
metagenomics: species/strain level and functional potential profiling
metatranscriptomics: species/strain level and function and activity profiling
describe metagenomics
- sequence DNA
- map sequence to genomes/ gene or do de novo assembly of genomes then map it to new genomes
- can work out putative (generally considered or reputed to be) functional pathways
describe metatranscriptomics
- sequence RNA
- map sequence to pathways/gene or do de novo assembly of transcriptomes and organise it into pathways
- work out active pathways/ microorganisms
- tells us function and how bacteria reacts to environment
give 2 other ways to identify bacteria in microbiota
- Metabolomics- what is being consumed by microbiota
- Proteomics- know which proteins are being made to inform you on pathways being used,
May not know what they are being used for
how does the type (taxa) of bacteria and metabolic pathways relate
the type of bacteria in different compartments very but the metabolic pathways remain stable
what is culturomics
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
which human organ is most densely colonised by bacteria
intestine
2500+ bacterial species capable of colonising colon
Broad range of physiological conditions
- creates distinct niches for colonisation
what are the main bacteria phyla
- proteobacteria
- actinobacteria
- firmicutes
- Bacteroidetes
what is the major functions of the microbiota
- bacteria degrade complex carbohydrates that we can’t break down
- educate immune system
why are bacteria better at degrading complex carbs
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
what does fermentation of complex carbs result in
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
what are short chain fatty acids used for
liver: sugar metabolism and storage
adipose tissue: fat uptake and storage
brain: appitite regulation
Strengthen tight junctions
what are HMOs
- where are they found
human milk oligosaccharides
found in breast milk
encourages growth of bifidobacterium
which bacteria digest HMOs
B. infantis
use them to form short chain fatty acids
how does our microbiome develop
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
what early life factors can influence a babies microbiome
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
how did microbiome of C section baby and vaginal baby differ
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
what is colonisation resistance
why is it difficult for bacteria to colonies
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
how does the microbiota create immune development
microbiota inhibit colonisation and overgrowth of invading microbes due to colonisation resistance
this creates microbe-microbe interactions and microbe host interaction
how does host-microbe interactions inform immune system
- 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
how does microbe-microbe interactions inform immune system
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
how do pathogenic bacteria inform immune system
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
what happens if microbiota is disturbed
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
how may underdeveloped microbiota cause certain growth phenotypes
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
can underdeveloped microbiomes recover
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
how does HMO link to malnutrition
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
is autism linked with defected microbiome
early studies suggested it did
more advanced studies found it was more linked with dietary preferences
dietary preferences mediate autism-gut microbiome association
