Genome Diversity in Space - After Midterm

Question 1

• Holistic Approaches

Answer 1

• approaches in which we view the parts of something as tightly interconnected and understandable only be reference to the whole; can’t really look at the parts by themselves; need a reference
• Genomics uses holistic approaches, since it looks at how genes and gene elements interact with each other

Question 2

*Biological Communities and why we study them

Answer 2

• A biological community is an interacting group of species in a common location
• We study biological communities
  1) to see how humans have impacted the biological communities and catalog diversity and improve conservation efforts to kind of try and undo what we did
  2) Because biological communities impact human health and society
• we want to preserve species that are important for global balance
• we want to do bioprospecting and bioremediation to try and find organisms that make natural products that could be helpful to us
  3) To better understand the world

Question 3

*Approaches to Studying Biological Communities

Answer 3

1) Field observation
- Cons associated with filed observation is that it is time-intensive and you can easily miss microbes, which are often a vital part of a community
2) Lab study
- This involves collecting samples and looking at the microbes
- The con associated with this is the “great plate anomaly”; 60-99% of microbes are unculturable
3) Metagenomics
- Involves taking the environmental DNA to tell us about the diversity of a biological community

Question 4

Metagenomics

Answer 4

• the simultaneous analysis of all genomes in a sample
• While I’m sure it can be used for many things, we’ll be discussing it in terms of studying biological communities
• The first step is to take a sample of environmental DNA: DNA from a variety of source available in a specific environmental sample
• you collect the sample, extract the DNA, and then do either targeted sequencing or whole genome sequencing on all of the genomes in the sample

Question 5

*Targeted Sequencing

Answer 5

• Targeted sequencing is a type of sequencing sometimes done when sequencing environmental DNA for metagenomic studies
• It involves zooming into one region of the genome (marker region) and PCR amplifying it
• The markers are then sequenced via next generation sequencing
• We then take all the sequences for the markers for all the different genome and try to align them to the databases to find matches to figure out which organisms the DNA belong to
• The marker you use will differ depending on the type of organisms you’re looking at (prokaryotes, fungi, animals, etc)
• Different groups will need different markers not just because some genes are only found in one group, but because we need to use a gene that has a “just right” level of diversity, meaning it evolves fast enough for there to be differences in the gene between different species, but slow enough that it will be identical in different individuals of the same species

Question 6

• Whole Genome Sequencing

Answer 6

• A type of sequencing sometimes done when sequencing environmental DNA for metagenomic studies
• Involves fragmenting and sequencing ALL the DNA in the environmental sample
• Once we have put together and separated out the different genomes, we can align them to the database to ID known organisms
• Something that we can do with WGS that we can’t do with targeted sequencing, however, is build contigs of new organisms that might be in your community
• Separating out the different genomes is difficult
• As an analogy: if doing a regular genome assembly is like trying to put together a puzzle without knowing what the picture looks like, then this is like trying to put together multiple puzzles with the pieces all mixed up, not knowing any of the pictures
• The main reason people choose to do WGS instead of targeted sequencing is to be able to annotate genes to get a sense of what genes are present in the sample and to get a sense of the functional diversity present
• WGS can tell us “who’s there” and “how many of them are there,” but it can’t tell us “what are they doing”

Question 7

• iClicker: Which Scientist will have to generate the most sequence reads to answer their research question?
• Scientist A who wants to find out how many different bacterial species are present on the surfaces in the hospital she works in
• Scientist B who wants to understand the metabolic pathways and biochemical reactions that allow bacteria to break down organic material in the compost bin
• Scientist C, who is interested in the bacterial genus Prevotella and want so know if people with different diets have different distributions of Prevotella species in their guts

Answer 7

Scientist B, because if you want to look at biochemical reactions you’re going to have to look at the products of different genes, meaning you will have to look at information across the entire genome; not just marker based sequencing

Question 8

• Species richness

Answer 8

• number of different species in a community (usually used for microbes)
• measure species richness by counting the sequences that align in the database and the number of sequences that didn’t align with the database (new species) and add the numbers together

Question 9

*rarefaction

Answer 9

• A technique used by researchers to know when they have accurately estimated the species richness
• Continue collecting samples until you reach the point where you stop getting new species
• In practice, scientists usually do the sampling informatically, by taking a big sample, sequencing lots of it, and then looking at subsets of that larger sample until they don’t get any new species
• A rarefaction curve can be used to show the diminishing gains in species richness with each additional sample (it levels out, kind of like a logarithmic graph)

Question 10

• OTU

Answer 10

• Operational Taxonomic unit
• used when a species is unknown, splitting sequences into groups based on how different they are
• OTUs are used as a “proxy” for microbial species
• We use a general rule for determining OTUs (species)
• If there is less than a 3% difference in 16S sequence between individual microbes, we consider them to be the same species
• if there is less than a 6% difference in the 16S sequence, we consider them to be in the same genus

Question 11

• Microbial relationships with their host

Answer 11

• Mutual symbiosis: host and symbiont both benefit
• pathogenic symbiosis: microbes benefit, host is harmed
• commensal symbiosis: microbe benefits, host is unharmed, but doesn’t benefit either

Question 12

• Human Microbiome

Answer 12

• we have more bacterial cells in our body than we do human cells
• while the percentage of the genome shared between two humans is roughly 99.5-99.9%, the percent microbiome shared between two humans is only 60-80%
• 99% of our non-human DNA in the microbiome is unknown
• In addition to bacteria and archaea, there are also viruses in there
• microbes in our microbiome interact with one another too

Question 13

*dysbiosis

Answer 13

• alterations in the human microbiome associated with disease
• We can see these differences by doing an MWAS: microbiome-wide association study