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METAGENOMICS - Coggle Diagram

- - - - bacteria, viruses, fungi, protozoa etc.
  - - - most studies correlate between diseased and healthy control individuals, not intra-individual
    - - is it cause or effect?
  - - - endotoxaemia
    - - used microbiota from twins, discordant for obesity
        
        removes many factors contributing to variation
      - four pairs of twins
        
        acquired microbiota from stools
        
        no culture, intact
      - inoculated into germ-free mice
  - - - within an individual, between individuals, breeds, races within age, sex etc
      - with disease
    - - Illumina-based metagenomic sequencing, assembly and characterisation of 3.3 million non redundant microbial genes, derived from 576.7 gig abases of sequence, from faecal samples of 124 European individuals
      - the gene set, ~150 times larger than the human gene complement
      - the genes are largely shared among individuals of the cohort. over99% of the genes are bacterial, indicating that the entire cohort harbours between 1000 and 1150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared
- - - - 16S ribosomal RNA (or 16S rRNA) is the component of the 30S small subunit of a prokaryotic ribosome that binds to the SHine-Dalgarno sequence. The genes coding for it are referred to as 16S rRNA gene (DNA) and are used in reconstructing phylogenies, due to the slow rates of evolution and ubiquity of this region of the gene
      - unbiased survey of 16S rDNA in samples has demonstrated a more realistic picture of diversity
      - extract DNA from sample
      - amplify 16S rDNA - broad specificity primers
      - sequence
      - sequence, look at variation in gene
- - - - map them onto one another
        
        can tell us if certain bacteria are present
        
        amount of reads usually proportional to abundance of species
  - - - gc content
      - the presence of known genes eg. copy genes should only be there once
      - coverage, contains found in roughly the same proportion likely come from the same speceis
      - other logical assumptions about the data
- - - - de novo assembly of a draft genome of the outbreak strain
      - depth of coverage of the outbreak strain genome was determined in each sample
      - sample sequences compared with known bacteria to identify pathogens other than the outbreak strain