The Microbiota/Microbiome Flashcards
Whats the microbiota
the complex microbial community that inhabits a particular environmental niche (bacteria, viruses and microeukaryotes)
Whats the microbiome
the combined genetic material/potential of the microbiota
How many cells is the body comprised of but how many bacteria colonise us
An adult human body is comprised of about 4x1013 cells but is colonised by 1013-1014 bacteria, up to 2 kg!
Human genome = 3 x 109 bp, 20,000 genes, The Microbiome = approx. 3 x 106 genes - at least 150x more. Enormous metabolic potential
Studying the composition of the Microbiota
> Sequencing – typically Illumina (short-reads) but long read tech starting to be adopted (Nanopore and PacBio)
16S – will give you composition at the genus and occasionally species level- focuses on one bit of DNA- gene varies very slightly from one genus to the next - good because its cheap
Metagenomics (more common) use a mixed population – sequence everything. With good data you can even start to piece individual genomes back together.
MetaHit – 2010
identified 3.3 million unique genes from 124 Europeans- massive numbers of unique bacterial genes
1150 dominant bacterial species – at least 160 in each individual colonizing each of these people
75 species common to >50%, 57 species common to >90%
The Human Microbiota
The human body is a collection of unique ecosystems
eyes have anti microbial peptides etc- not a hospitable bacteria- found 10-1000 bacteria- still a large bacterial biomass present
colon - where the largest biomass resides
The kitome
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Kitome is a high density study. Finding DNA in molecular biology kits everyday in the lab - everything on the planet is contaminated with bacterial DNA
The more you dilute a sample, the more contaminated it gets
Has the kitome affected previous papers
2014: the placenta harbours a unique microbiome
2019: Human placenta has no microbiome but can contain potential pathogens
The Gut Microbiota
Largest and most diverse – up to 1011 bacteria per ml and 100/1000s of species in each person
But metabolic potential is conserved – many ways to achieve the same equilibrium - > health of microbiome and host
There is an optimal biochemical potential of the microbiome
Factors which affect composition
Age has a big impact- some of its down to diet- other age related issues- complex things- different microbiome to 80 year old grandma
people with some diseases have signatures showing up in population
some bacteria respond to different hormones so gender is a big impact
Geography and ethnicity may have differences
Invasive species can disturb microbiome
All links back to socio-ecomonic cultural aspects such as diet- diet flags up differences in geography and ethnicity
Use of antibiotics- biggest impact- generally kill whole classes of bacteria - wipe out entire groups of bacteria - largest factor
What has the Microbiota ever done for us
Training the immune system – immune tolerance and modulation
Colonisation protection
Metabolic functions – amino acid and vitamin synthesis, digestion of some complex carbohydrates…
Vitamin B12- bacteria in our gut help us digest plants
Consequences of disruption
Links to obesity and diabetes, chronic inflammation and asthma
Bifidobacterium species in infants
Gut sterile in utero – colonisation begins at birth so route of delivery has huge impact
Increase is C sections correlates with increase in cases of asthma, allergies, eczema, childhood obesity, etc. - > is there a connection? Looking more likely
Infants delivered by C section have a different microbiome, with a particular reduction in Bifidobacterium species
Vaginal swabbing seems to be able to correct this but also potentially risky and needs more data…
Preterm infants have a particularly weird microbiome and far more likely to develop asthma later on
Also highly susceptible to infection with Clostridium perfringens
C. difficile a paradigm for colonisation resistance
Dysbiosis a prerequisite for CDI
Microbiota recovers as infection is cleared
Can be exploited to treat infection
