26. Metagenomics** Flashcards
1
Q
microbial metagenomics
A
- mixed microbial sample
- microbial isolation
- DNA extraction and purification
- DNA sequencing
2
Q
what is 16S rRNA amplicon sequencing?
A
- gene is ubiquitous across bacteria
- highly conserved region allow fo PCR amplification
- highly variable regions provide taxonomic infor
- microorganisms identified againts 16S rRNA gene databases
- no metabolic or functional info
3
Q
what is genom-resolved metagenomics?
A
- identification
- relative abundance
- matabolic potential
4
Q
what is the metagenomics workflow?
A
- total DNA extraction
– from mixed microbial community - whole-genome shotgun sequence
– shear all genomic DNA - amplicon sequencing
– PCR amplify gene of interest (16S rRNA)
5
Q
what is gene annotation?
A
- 5’ –> 3’
– open reading frams determined
– genes predicted - identified genes annotated by comparing sequences against gene databases
- contigs are assigned to genomes based on shared characteristics
– GC content
– abundance level
6
Q
what is binnning?
A
- contigs assigned to genomes based on shared characteristics
- GC content
– % of genome made of GC vs AT - abundance level
– coverage of organisms in sample - phylogeny
– genes present on contigs
– compared to known gene databases and phylogenetically profiled
7
Q
how are genomes recovered from metagenomes?
A
- DNA extracted
- shotgun metagenomic sequencing
– forms reads - assemply
– forms contigs - generate infor about contigs
– coverage
– sequence characteristics - binning contigs
8
Q
what are the applications of metagenomics?
A
- monitoring impact of pollutants on ecosystem
- discover new genes, enzymes, natural products
- human microbiome
– determien core microbiome
– understand changes linked to health
9
Q
what is anaerobic digestion?
A
- hydrolysis
- fermentation
- acetogenesis
- methanogenesis
10
Q
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A
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