5 Written Questions

1. 40%
2. 1 Gb = 1000 Mb = 1,000,000,000 bp
3. 10^23- 10^24
4. metagenomics
5. MetaGenomics

5 Matching Questions

1. 99% of genes in our body are in fact encoded in our
2. **Compare top-down selection on microbial community vs. bottom up
3. Prevalent genes
4. MetaHIT project analyzed this many base pairs of DNA- compared to what previous amount?
5. Environmental genomics is also known as

1. a genes from the most abundant reads
2. b gut
3. c Metagenomics
4. d MetaHIT project studied 577 Gb, whereas previous metagenomic studies only did 3 Gb microbe DNA from fecal samples of 33 people
5. e Top down is when selection pressure on host results in a microbial group selection in the gut as well as the host immune system and intermicrobial dynamics playing a role in the gut. Bottom up selection (99% of genes in our body are encoded in our gut) - genome interactions influence phenotype of cells, selection of cell phenotype results in selection of specific genomes

5 Multiple Choice Questions

1. 1. Single gene - many microbes with mixed 16S sequences. 2. Metagenomics-sequencing many genes from many microbes
   1. 1 Gb = x Mb = x bp
   2. 2 ways to look at diversity in body
   3. We are born with/without microbes
   4. Solexa sequencing
2. 500 bp, 42.7%
   1. Most prevalent genes in the MetaHIT found in x% of all individuals
   2. Composition of the minimal gut genome and metagenome
   3. Most contigs in the Solexa reads of the MetaHIT project were this long, x% of solexa reads assembled into contigs greater than 500 bp
   4. Selection pressure in the gut is dominated with which two divisions of bacteria
3. Bacteroides uniformis
   1. This species of bacteria most abundant in gut
   2. Minimal core genome is around # genes
   3. Solexa sequencing
   4. 2 ways to look at diversity in body
4. 577 Gb. 200 fold more sequence data than previous experiments. Allowed them to predict 3.3 million unique genes. There are only 25K genes in human genome - so there are 99% microbial genes, 1% human genes in our body.
   1. MetaHIT project analyzed this many base pairs of DNA- compared to what previous amount?
   2. MetaHIT project analyzed how much DNA? Allowed them to predict x unique genes.
   3. MetaHIT project sampled how many individuals?
   4. MetaHIT project - what was it? What did it set out to do?
5. colon with 10^11 to 10^12 cells/ml
   1. Environmental genomics is also known as
   2. Highest density of microbes is in x. - xcells/ml.
   3. This species of bacteria most abundant in gut
   4. Minimal core genome is around # genes

5 True/False Questions

1. We are born germ free but by adulthood - # abundant bacterial species in the gut → 1150

   True        False

2. MetaHIT project - what was it? What did it set out to do? → 124 europeans - healthy, overweight, and irritable bowel syndrome

   True        False

3. Minimal core genome is around # genes → Metagenomics

   True        False

4. MetaHIT project found that there is a x repertoire that is likely required for proper gut functioning → consortium of 13 partners spanning 8 countries and 21.2 million Euros. Set out to fully analyze the gut genome.

   True        False

5. This new type of sequencing uses reversible chain termination and chemoluminescence → Solexa sequencing

   True        False