The human and oral microbiome 2 Flashcards
Give the taxonomic order
Domain Kingdom Phylum Class Order Family Genus Species
Give the definition of:
- Microbial Community
- Microbiota
- Microbiome
- Metagenome
- Biofilm
- The micro-organisms that are present in a given habitat
- The total collection of micro-organsims within a microbial community
- The microbiota and all of its associated genes
- The total genomic DNA of all the organisms within. a community
- A physically structured aggregate of organisms, adhered to each other and a defined substrate
Why are humans considered super organisms?
So many more microbial genes in us than our actual human genes. Genetic potential is higher in the microbial community than the human one.
Can use the bacterial genes to beneficially help us.
Can think of the microbiome as another organ inside the body.
Why is a microbiome important in the body?
Heath : specific microorgansims are protective against disease, and pathogenic bacterial species
Disease: changes in microbiome composition is associated with disease
Microbial genes: can modulate fundamental human processes e.g. metabolism
What was the aim of the Human Microbiome Project?
- Generate resources to help study the human microbiome
- Characterise the microbiome associated with human health and disease
- Determine if humans share a core human microbiome
- To understand changes in the human microbiome and how that changes human health
What are the two methods we use to study the microbiome and give details on both
- Traditional Culture Approach:
- grow microbes directly from sample
- requires phenotypic identification of isolates
- + cheap
- labour intensive, only gross species discrimination possible, not many species can grow, need to know what species to expect to test for them - The New Molecular Approach:
- Identifies organisms by gene sequence homology
- extracts microbial DNA from samples and sequence analyses them
- tells you what species is present, can see what genes are present, can determine strains
- expensive, time consuming and primer specificity leads to bias
How does the bacterial 16S rRNA gene sequencing work?
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 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. Uses 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)
How do we make sense of sequencing data?
- We get a list of a,t,c and g
- Compare these to databases for identification
- can only identify sequences present in the databases
- have to perform whole genome sequencing of more organisms so this genetic function can be added to database
- then need to annotate the DNA you have to see what it codes for
What is the importance of annotation?
Makes sense of the a,t,c and g.
Identifies the open reading frame of genes and predicts functions for those genes.
Problems with Annotation:
- Only a prediction
- Takes 100 hours per genome
- Mistakes can be made
- Genes shared and vary between species
Give the definitions of these:
- Virulence genes
- Resistance genes
- Diagnostic genes
- 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 are some of the microbiome findings we have so far?
- Colonisation begins at birth
- Microbiome changes over time
- Influenced by diet, lifestyle and environment
- Microbiomes are characteristic of each body site
- The individual is the primary determinant of the composition of the microbiome
- Microbiome plays a role in disease
Give details on the stomach microbiome
Traditionally though to be sterile but there is colonisation from food.
Helicobacter pylori is the main coloniser (causes ulcers).
Give details on the small intestine microbiome
- Lower number of organisms (more microbes are you move closer to large intestine)
- Microbes found are acid resistant from passing through stomach
Give details on the large intestine microbiome
- Heavily populated with highly varied bacteria
- Anaerobic microbes outnumber aerobic ones greatly
- Heavily studied for health and disease associations
