Fecal Phage Dark Matter and Other Stories of the Human Virome (Part I)

Question 1

For every cell there are ____ viruses affecting it.

Answer 1

10

Question 2

Why do viruses exist? (one perspective)

Answer 2

Cellular life exists so that viruses have something to eat.

Question 3

How many viruses are there in the world?

Answer 3

There are 10^31 viruses in the world

Question 4

How many viral species on Earth?

Answer 4

At least 100 million viral species on Earth.

Question 5

What are important aspects of viruses?

Answer 5

Major predators on the planet
Determine which strains survive and control the number of microbes.
Most genetic diversity is viral.
Move DNA around planet
Important genes are evolving in viruses.

Question 6

What are microbes?

Answer 6

Microbes = collection of bacteria, viruses, fungi, and other microbes.

Question 7

What are human microbiomes correlated to?

Answer 7

Obesity, cancer, autoimmune disease, brain chemistry, and vaccine efficacy

Question 8

True or False: overwhelming number of viruses affect microbes.

Answer 8

True

Question 9

What are examples of ways the human virome works?

Answer 9

Persistent/latent infections, Transient infections with animal cell viruses.
Endogenous retroviruses (8% of human DNA).
Bacteriophage predators of bacteria and archaea

Question 10

What are holobionts?

Answer 10

Collection of all animal and human genes (includes environment)

Question 11

What makes holobionts different?

Answer 11

The main difference between holobionts are the viruses: Differently encoded in viruses and leads to diversity in microbes.

Question 12

What are bacteriophages?

Answer 12

Viruses that infect bacteria

Question 13

There are more bacteriophages on Earth than:

Answer 13

Stars in the Universe, Grains of sand on Earth, Atoms in the human body.

Question 14

Host-associated polymicrobial communities are powerful indicators of?

Answer 14

health and disease.

Question 15

What do probiotics and prebiotics do?

Answer 15

Shape the composition and activity of microbes by providing nutrients.

Question 16

What is the difference between probiotics and prebiotics?

Answer 16

Probiotics = live cultures
Prebiotics = fiber

Question 17

What does a fecal transplant do?

Answer 17

replenishes gut microbes after antibiotics. (First FDA approved fecal transplant has occurred).

Question 18

What does phage therapy do?

Answer 18

Targets bacterial killing and could target antibiotic resistant bacteria.

Question 19

When was phage therapy discovered and why is it important?

Answer 19

Discovered > 100 years ago and is at the forefront of molecular biology. CRISPER may be used to defend against phages.

Question 20

What is the current state of antibiotics?

Answer 20

No fundamentally new antibiotics have been discovered for 20 years. They are not profitable because resistance arises quickly. But bacterial infections are becoming increasingly lethal.

Question 21

What is a profitable industry?

Answer 21

Statins

Question 22

What is the difference between antibiotics and phage therapy?

Answer 22

Anitiobitics kill pathogens and are more general.
Phage therapy is specific to a subset of bacteria and doesn’t affect all members of genus and species.

Question 23

What is an unconventional form of antimicrobial treatment: phage therapy?

Answer 23

Bacteriphages are viruses that kill bacteria and since they are specific to bacteria and cannot infect human cells or cause disease, they are an ideal tool.

Question 24

What are the applications of phage therapy?

Answer 24

Because poor circulation makes it difficult to deliver the correct amount of antibiotics to an infected area, phage therapy can be used to increase the dosage of antibiotics. This also helps prevent pockets where bacteria that is resistant to the antibiotics pops up, because of prior insufficient dosage due to poor circulation.

Question 25

What are some experiments that have contributed to the phage therapy technique?

Answer 25

Experiments that helped determine DNA to be the genetic material (Hershey-Chase)
Francis Crick and Sydney Brenner’s experiment establishing the triplet nature of the genetic code.
Elucidation of transcription initiation and termination in archaea
Restriction- modification systems/CRISPR Cas9 genome editing.

Question 26

Where can we find phages?

Answer 26

Soil, sewage, food, water, everywhere!

Question 27

Describe the life and times of phages in nature

Answer 27

The circle of life: bacterial death and nutrient turnover.
Gene transfer
Drivers of bacterial evolution/diversity
Phages kill 30-40% cyanobacteria
Select for particular strains in antibiotics

Question 28

Describe the life and times of phages in terms of their applications?

Answer 28

Model system and tools for molecular biology
Model system for studying evolution
Phage therapy

Question 29

How do bacteriophages impart diversity?

Answer 29

Phages are even more personalized than bacteria.
Horizontal gene transfer
Co-evolution arms race

Question 30

What phage diversity is under explored and poorly understood?

Answer 30

Enterococcus phage

Question 31

What phage is well understood?

Answer 31

Mycobacterium phages due to Phage Hunters program.

Question 32

How are phages harvested?

Answer 32

1) Cultured bacteria are plated to create a bacterial lawn.
2) Phages are spotted onto specific plate regions.
Phage A, B C and D.
3) Plque formation indicates host susceptibility to Phage A

Question 33

Describe plaques from phages?

Answer 33

These are clear zones formed in a lawn of cells due to lysis by phage.
A cell is infected with a single phage and lysed, releasing progeny phage which can diffuse to neighboring cells and infect them, lysing these cells then infecting the neighboring cells and lysing them etc. .
It ultimately results in a circular area of cell lysis in a turbid lawn of cells.
This is a dynamic process.

Question 34

Describe the difference between small genomes and big genomes in phages

Answer 34

Small genomes = kill
Big genomes = more complex functions

Question 35

Describe how each plaque time corresponds to phage type.

Answer 35

Hazy and big plaques = Myoviridae (150 kB genome)
Clear and small plaques = Siphoviridae (50 kB genome)
Even smaller and clear plaques = Podoviridae (20 kb genome).

Question 36

Describe the role of taxonomy/ genomes in viruses.

Answer 36

Originally based on morphology (electron microscope) and nucleic acid content.
Now it is a combination of genome composition and morphology which is an major criterion for classification at the family rank., with the current taxonomy comprising 22 families grouping bacterial or archaea viruses.

Question 37

Which virus is most abundant in wastewater?

Answer 37

Tomato plant virus!

Question 38

Why is E. coli so prominent?

Answer 38

Historical reasons/ K12 patient room