10 - Techniques in Microbiome Studies Flashcards
define microbiome
The microorganisms in a particular environment (including the body or a part of the body) or the combined genetic material of the microorganisms in a particular environment
define microbiota
The ecological community of commensal, symbiotic and pathogenic microorganisms found in and on all multicellular organisms studies to date from plants to animals (not walls, desks, and rocks).
what is 16S rRNA targeted Amplicon Sequencing?
The 16S rRNA genes from a particular sample are amplified from a sample and sequenced. This provides a look at which bacteria are inhabiting an environment
what is metagenomics?
All of the genetic material from an environment is sequenced. This provides a look at the functional potential of a microbial community with little or no information on individual organisms
what is single-cell genomics/read cloud sequencing?
: Sequences the genetic material from a microbial community either one cell at a time or after individual chromosomes have been labelled. This provides detailed genomic information about the most abundant individual organisms in a particular community.
what’s a 16S rRNA gene?
basically a bacterial barcode. present in all prokaryotes. not present in any eukaryotes.
how many base pairs does the 16S rRNA gene have?
~1542
to what kind of applications does 16S rRNA gene sequencing contribute?
- phylogenetic studies
- serves as a molecular clock
how many regions of the 16S rRNA gene are useful for phylogenetic identification?
9 hypervariable regions
why is the 16S rRNA sequenced?
- evolves very slowly, making more accurate links to taxonomy
- there’s already a large database with it sequenced along with reliable taxonomic info
limitations of 16S rRNA Targeted Amplicon Sequencing
- there are multiple 16S rRNA genes but this aspect is often ignored, so some bacteria are counted more than the ones with fewer 16S genes
- short reads are not suitable for accurate phyla richness estimates
what’s a rarefaction curve?
y axis = amount of phyla that exist
x axis is the amount we know
when 16S sequencing is great:
- comparing populations between 2 or more things (e.g. diseased/healthy state)
- determine how bacterial population changes over time or in response to an event
how does metagenomics work?
cut all of the DNA from an entire community into small pieces and sequence it. then try to put it back together
what does metagenomics tell you?
about the functional potential of a microbial community. won’t tell you about which bacteria do what
