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MGG Exam 4 – Complete Q’s and A’s
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MGG Exam 4 – Complete Q’s and A’sWhat percentage of the human gut microbiota is Bacteria, as opposed to
Archaea or fungi? - - 98%
- Primers used to amplify segments of 16srRNA for metagenomic analysis
bind to sequence - - Flanking a variable region
- Which of the following bacterial phyla are Gram (+) - - Firmicutes
- What characterizes Gram (-) bacteria? - - Double membranes; less
peptidoglycan than Gram (+)
- Salmonella, Shigella, and Escherichia belong to which class of
Proteobacteria? - - Gamma
- Which of the following pathogens is in the phylum Actinobacteria? - -
Mycobacterium tuberculosis
- Which of the following is in the phylum Firmicutes - - Staphylococcus
- What percentage of the human microbiota is in the colon, as opposed to
the stomach, nose, throat, skin, etc? - - 90%
- What two types of data do you use form the GreenGenes database in
metagenomics? - - A pre-made phylogenetic tree and the sequence found at
each leaf
- Why do we use the MAFFT alignment program in Taxonomic Classification
in QIIME? - - To assign our 16S rRNA sequence to the 16S rRNA sequences
from the GreenGenes
- In Taxonomic Classification in QIIME, what are the three feature tables of
data we use? - - A "Tree of Life" (GreenGenes), 16S rRNA sequences
(GreenGenes), 16S rRNA sequence (our data)
- What spurious sequences does the Taxonomic Classification help you
eliminate form your metagenomics dataset? - - Non bacterial sequences
- What gaps are formed in the aligning of two sequences, the computer
assigns two types of penalties for these gaps - what are they? - - Gap
formation versus extension
- In a distance matrix, why are the values down the diagonal always 0.0 by
definition? - - Your re comparing each sequence with itself
, - What do you do with sequences that dont match exactly to a sequence in
the reference table? - - Use a fragment insertion program to shoerun the
sequence into the standard tree
- Beta diversity among two samples is measured as: - - The sum of (that
sample's species - shared species) for each sample
- Faith's Alpha Diversity Index uncles everything that Shannon's index
includes plus what extra component - - The evenness of the species
distribution across the phylogenetic tree
- What question does a rarefaction curve answer? - - Have I captured the
bulk of the diversity of my sample x number of reads?
- Which is not one of the aces of a rarefaction curve? - - Diversity index
- Weighted UniFrac, in addition to species evenness across the phylogenetic
tree,a low condiers - - Abundance data
- Where does FeatureData(taxonomy) come from? - - GreenGenes
- What is the most commonly used dataset for bacterial micro biome
metagenomcs? - - "GreenGenes" databases for 16sRNA
- In GreenGenes Each leaf is... - - Species-specific variant of 16s rRNA
- MAFFT - - Multiple Alignment using Fast Fourier Transform
Multiple sequence alignment algorithm
- Machine learning is better than MAFFT. Why? - - Train the machine on
sequence of known taxonomy
The algorithm is now ready to classify unknown sequences
Pre-trained machine learning algorithms are available for free for 16S rRNA
assignment
Machine learning > MAFFT
- 3 things you can do with your taxonomic data... - - 1) Filter out spurious
taxa
2) collapse your feature table
3) create beautiful graphics
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