Metagenome Flashcards
(32 cards)
What is genomics?
→ The whole cell content
What is transcriptomics?
→ whole cell gene expression
What is proteomics?
→ Whole cell protein content
What is metabolomics?
→ cell metabolite content
How do you purify DNA?
→ Culture the organism in isolation
Why in practise is DNA not able to be purified?
→ organisms do not live in isolation
→ they are a complex mixture of species
What is a microbiota and what does this include?
→ Ecological community of commensal and pathogenic microorganisms
→ bacteria, archae, prostists, fungi and viruses
What is a microbiome?
→ Collective genomes of the microorganisms in these communities
What diseases have changes in the microbiome been associated with?
→ Cancer
→ Depression
→IBS
What can gut microbiome classify?
→ individuals as being obese or lean
What are early life gut microbiomes linked with?
→ Development of allergic conditions such as asthma
What are the 4 human microbiomes?
→ Gut microbiome
→ Skin microbiome
→ Oral microbiome
→ Vaginal microbiome
What can cure a clostridium difficile infection and why?
→ Stool transplant
→ the microbiome in CDI is different to a healthy microbiome
Why is 16S targeted PCR used?
→ 16S is a ribosomal component of the 30S subunit in prokaryotes
→ all bacteria have the 16S subunit
Describe how 16S targeted PCR amplification works?
→ Sample (urine, blood, etc)
→ DNA is extracted from a mixed population of bacteria in the sample
→ 16S PCR amplification - the 16S gene amplifies
→ sequence the PCR
Why are there biases in 16S PCR?
→ Some bacteria purify better than others
→ some sequences amplify better than others
What is done with the sequences after 16S PCR?
→compared to a database of known 16S sequences
What bacteria changes during the first year of life and how?
→ Actinobacteria drops after the first years of life
What bacteria is present in babies when breastfeeding?
→ Bifidobacteria
What 2 things do you need to consider when doing PCR on a bacterial variable region?
→ If it contains enough information to separate the genus
→ amplicon length
Why is sequencing a smaller region better?
→ The sequencer can read it twice and any errors will cancel out because the two sequences are combined into one region
What are disadvantages to the 16S method?
→ It is sensitive to contamination
What is the 16S method used for?
→ Low biomass sample
How do you mitigate contamination?
→ Randomise the samples
→ Note batch numbers of reagents
→ Sequence negative controls
