lecture 2a) the human microbiome project (HMP)

Question 1

what is the HMP?

Answer 1

looks at the impact of genetics, ethnicity, origin and environment on human microbiome
measures the variability of the human microbiome

Question 2

why is the HMP important?

Answer 2

treatment strategies
outcome of treatment
noticing transient microbes

Question 3

what does the HMP look at?

Answer 3

genomes and necessary RNA
proteins
metabolic products

Question 4

do humans have a core microbiome?

Answer 4

depends on how it is acquired/transmitted

there are similarities between families, communities, ethnic groups etc

Question 5

what causes changes in microbiome?

Answer 5

correlated with changes in human health
unstable as tissue changes with age
influential factors such as genetics, socioeconomic background

Question 6

what allowed this project to develop new technological and bioinformatic tools?

Answer 6

vast data

culture independent sequence analysis (can now use DNA sequencing to culture more microbes at once)

Question 7

what are some of the ethical and social implications and other legalities to consider with the HMP?

Answer 7

participant level - selection process must be non-biased

broader society - ensure conclusions are exploited in the right way

Question 8

what type of sequencing is used in bacterial sequencing?

Answer 8

16S rRNA sequencing

Question 9

why is 16S rRNA sequencing used to sequence bacteria?

Answer 9

all bacteria have the 16S ribosome
same sequences are conserved therefore they are on all bacteria
highly variable regions (hypervariables) change quickly
close relatives may have same hypervariables

Question 10

what does VBNC stand for and what does it mean?

Answer 10

viable but not culturable
bacteria that are in a very low metabolic activity and dont divide but are alive and are able to be cultured once resuscitated

Question 11

what is the aim of 16S rRNA sequencing?

Answer 11

to determine what microbes are there

Question 12

once microbes that are present in the culture have been determined, how do we find out what they do?

Answer 12

metagenome sequencing

Question 13

what is the purpose of metagenome sequencing?

Answer 13

the vast majority of microbial biodiversity has been missed by 16S rRNA sequencing
can reveal the previously missed diversity of microbial life

Question 14

what kingdoms can metagenomics sequence?

Answer 14

bacteria

archea

Question 15

what did the 2010 catalog of genomes reveal?

Answer 15

178 microbial genomes
approx 5% genomes found to be unique
approx 2.5% of polypeptides found to be unique

Question 16

describe the steps involved in targeted isolation; partial and genomic sequencing

Answer 16

unusual cells from microbiome extracted
tag DNA with fluorescence
sequence to find out its abundance