The human and oral microbes Flashcards
What is the taxonomic order?
Domain, kingdom, phylum, class, order, family, genus, species
Definitions:
- Microbial community
- Microbiota
- Microbiome
- Metagenome
- Biofilm
- The micro-organisms that are present within a given habitat
- The micro-organisms within a microbial community
- The microbiota and all of its associated genes
- The total genomic DNA and all the organisms within a community
- A physically structured aggregate of micro-organisms, adhered to each other and a defined substrate.
Why are humans super-organisms?
We consist of many microbial communities.
So many more microbial genes in us than our actual human genes.
What are 3 important factors of the human microbiome?
- Health - some are protective against disease
- Disease - may cause disease
- Microbial genes - modulate fundamental physiological processes
What were the main aims of the human microbiome proejct?
- generate resources to help study human microbiome
- characterise the microbiome associated with human health and disease
- determines if humans share a core microbiome
- understand whether changes in the human microbiome result in changes to human health
What 2 ways do we study the microbiome?
- Traditional culture method - grow microbes directly from sample
- requites phenotypic identification of isolates
- cheap
- labour intensive
- only gross species discrimination possible - New molecular approach
- identifies organisms by gene sequence homology
- extract microbial DNA from samples
- sequence analysis of DNA
- can tell you what genes and species are present
- high discriminatory power
- expensive
- time consuming
16S rRNA gene approach
what is thus?
Uses 16S rRNA gene which all bacteria have. Has to have it to have ribosomes to survive.
Amplify the DNA using primers for the constant region. Then we can look at the variable regions bounded by the primers and compare to a database to work out what species it is.
- Extract the DNA from sample
- Add primers for the conserved regions for the 16S rRNA gene and amplify across the variable regions
- This means that we have a load of sequences which are bounded on either end by the conserved sequence with a variable sequence in the middle which can be used for identification
- Sequence and analyse (shows which species and their abundance)
How does shotgun metagenomics work?
Extract DNA and sequence for EVERYTHING rather than particular genes and assemble after to see what we have. relies on high-throughput sequencing.
This is good as it covers all the kingdoms.
Because we get all the genes, we can look beyond taxonomy to see function aspects (e.g what genes affect metabolism)
Compare the 16rRNA approach with shotgun metagenomics
Both we get a phylogenetic view of community composition (work out taxonomy)
We can work our frequencies and abundant with the 16S
More information can be found out with shotgun I.e. different variants and polymorphisms
How do we make sense of our sequences and what are the limitiations?
Compare the A, T, C and G with databases for identification.
- can only identify sequences in database
- need to perform whole genome sequencing of more organisms so the genetic information can be added to the database
- need to annotate all your data
What is the importance of annotation?
makes sense of the A, T, C and G
identifies open reading frames
predicts functions for genes
What are the problems with annotation?
- only a prediction
- takes 100 hours per genome
- mistakes made
- genes shared and vary between species
Definitions:
- Virulence genes
- Resistance genes
- Diagnostic markers
- Genes for biotechnology applications
- Genes that contribute to the pathogenicity of the organism
- Genes that induce antibiotic resistance
- Genes that aid in the rapid diagnosis of disease
- Novel production processes
What do we know about the microbiome so far?
- colonisation begins at brith
- microbiome changes over time
- influenced by diet, lifestyle and environment
- microbiomes are characteristic of each body site
- an individual is the largest determinant in the microbiome composition
- plays a role in disease e..g obesity
Give details of these microbiomes
- Stomach
- Small intestine
- Large intestine
- Skin
- Oral cavity
- Thought to be sterile orignally byt tgere is colisation by food. Helicobacter pylori is the main coloniser
- Numebr increases as we get towars the distal end, microbes are acid resistant as they come from stomach
- Heavily populated with anaerobic bacteria, anaerobic greatly outnumber the aerobic ones
- Varied microbiota, low numbers on exposed surfaces, large number in protected areas, most are associated with acne
- High numbers in mouth loads of different habits eg. hard surfaces and then tongue, gums, tonsils. Associated with oral disease meaning the microbiota is not in harmony with the host.
