Genomes-L8-The Microbial Genome: Human Microbiome

where are there different microbiomes in the human?

gut, skin, vaginal, lung, blood

difference between microbiota and microbiome

microbiota- microorganisms themselves

microbiome- genome content within the environment- the whole ecosystem

what dictates what type of predominant species in human microbiome?

in the gut- anerobic and moist and warm- dictate it

depends on conditions etc

how were microbiomes discovered?

• in 1600’s-microscopes were invented

• mid 1800s- golden age of microbiology: development of isolation and culturing microorganisms- germ theory was created

• 1990s- seminal studies of DNA/RNA- that coudln’t be cultured in the lab

• 2000s onwards- cultural independent techniques allowed identification of microbial communities

what are humans also colonised with?

viromes- not just bacteria in microbiome

• viruses can cause infection but also protect the host from viral infections

factors that influence the human virome un infants and adults

1. diet

2. breast milk or formula feedings

3. medications

4. host egentics

5. geography

6. presence of disease

7. ageing

how does breast milk or formula feeding affect viromes in human body? and an example

• plays role in viral colonisation as breastmilk has viral components such as lactopherin

• lactopherin protects against other bacteria and viruses such as SARS-COV

what is in the gut mycobiome? what is a mycobiome? what are the predominant species and what do they do?

the part of a microbiome that has fungi

• small and critical part of the gut microbiome

• candida and aspergillus

• candida- plays a role in assembly and function of the gut BACTERIAL microbiome

what can IBD and type 2 be linked to and why?

pre-term birth, onset of IBD and type 2 diabetes- as didn’t see mothers microbiome for enough

discuss gut microbiome- what type of origin and what does it influence?

• microbial orogin

• metabolic activities have a role in gut immunity/mood/behaviour- gut and brain are constantly communicating

• have a role in educating the immune system

discuss the skin microbiome- and what does it influence? an example

• human skin is categorised by wet/dry areas- different composition

• have a role in educating the immune system

• bacteria such as staphylococcus in moist areas

• fungi are low in numbers- even if diversity is high

discuss the vaginal microbiome

• predominately lactobacillus- established in 1829

• still don’t have a deep understanding

discuss the respiratory tract/lungs? what used to be believed- what occupies them

• upper respiratory tract- don’t have a large number

• lower respiratory tract used to be considered sterile

• consist of transient microorganisms

tools and concepts to understand microbiota- pros and cons

1. culture based methods- selects for microorganisms that can grow in artificial growth

2. 16S sequences- low cost- resolution is low though, in fungal species it is ITS1

3. shotgun metagenomics- but DNA sequencing cant distinguish active colonised/damaged/dead

4. shotgun metatranscriptonomics- allows for real time functional profiling

shotgun- dont need a target region though!!

urban microbiome example in NYC and their findings

• pathomap.org project- sampled subway stations

• important to study our own microbiome and the environment we live in

• station rich in most bacteria have been flooded during Hurricane sandy and 10 unique species

why do we need to study urban microbiomes?

understand microbial life in dense human populations and the way they impact human health

how does the soil microbiome impact anyone?

• human and animals microbiomes are affected by soil microbiome

• in soils we can see antimicrobial resistance and hosts act as reservoir

• also- when we treat animals with antibiotics it may affect humans

difference between natural birth and C section birth on the microbiome

vagina- lactobaccilus

c section- staphylococcus usually found on skin

ways which microbes interact with eukaryotic hosts- 6 types

1. mutualism- both benefit ie such as the gut bacteria

2. commensalism- one benefits and one is unaffected- such as microbes on our skin

3. predation- one destroys or eats another

4. interference competition- microbes compete by harming eachother

5. exploitation compeititon- using shared up nutrients and leaving less foe others

6. specialisation- microbes evolve genetically to use different resources- reducing competition

ethical issues of human microbiome research

• studying gut microbiomes they can sequence DNA from fecal samples

• from feral samples- they could predict sex and re identify individuals from their DNA

can reveal private genetic information