Fecal Phage Dark Matter and Other Stories of The Human Virome Part II

Question 1

What did the Craigslist Roomates Fecal Matter Study find?

Answer 1

It found that people who cohabitate share about 25% of the viruses in their viruses just by virtue of living in the same space.

Question 2

What are some lessons from human viromes?

Answer 2

Most unknowns in human gut microbiota are viral however host associated viral diversity is often lower than other ecosystems.
Temperate viruses appear more common.
Most difference between individual are the viruses which appear to be stable over time.

Question 3

What is a virome?

Answer 3

is the community of viruses living in a particular environment.
Uncultured viromes can be generated with sequencing.

Question 4

Virome: Persistent viral infections

Answer 4

Effects on human health.
Interactions with immune system and other pathogens.

Question 5

Virome: Acute viral infections

Answer 5

Effects on human health
interactions with immune system and other pathogens

Question 6

Virome: novel viruses

Answer 6

Association with disease.
Virus characterization (demonstrates pathogenic isolate and study in vitro)
Epidemiology

Question 7

Virome: novel bacteriophage

Answer 7

Effects on bacterial community structure and metabolic potential.
Identification of genes that may affect human health.

Question 8

Virome: Bacteriophage with pathogenic potential or antibiotic resistance genes

Answer 8

Effects on the bacterial community structure and metabolic potential
Association with health and disease

Question 9

Commensal bacteriophage

Answer 9

Effects on bacterial community structure and metabolic potential
Association with health and disease

Question 10

Human endogenous retroviruses

Answer 10

Definition of integration sites and gene expression.

Question 11

What is the common response to immunosuppressants?

Answer 11

Total viral load goes up

Question 12

Important hallmark of healthy immune system?

Answer 12

Specific microbial immunity in compartments.

Question 13

Describe the main highlights of temporal response of human viriome to immunosuppressan and antiviral therapy

Answer 13

Vitrome-drug interactions were measured in cohort of organ transplant recipients.
The structure of the viriome is strongly affected by immune modulation and antivirals.
The total viral load increases markedly at the onset of therapy
A potential application of the virome state predicting immune strength is reported.

Question 14

___ represent the largest region of unkown sequence space on Earth

Answer 14

Viromes

Question 15

How many uncultured viral sequences lack homology to sequences in databases?

Answer 15

Most, 70-90%

Question 16

Human microbial communities have incredib _______ _________

Answer 16

metabolic diversity

Question 17

Most viral reads and contains have no contains have no ____ ___ to any database

Answer 17

hits to any database.
Gut: 70.5% of the reads had no hit to any database.
Cystic Fibrosis Sputum: 80% of the reads had no hits to any database.

Question 18

What was the first sequenced uncultured virome? What environment did it come from? When was it?)

Answer 18

It was sequenced in 2002 by Forest Rower at SDSU from seawater samples collected off the CA coast.

Question 19

The first human meta genome was a ___

Answer 19

virome

Question 20

What is the most ubiquitous gene in the universe?

Answer 20

Tranpossasses are the most abundant and ubiquitous genes in nature.

Question 21

Why should the viral component receive far greater attention and describe how explorations can yield to a more complete picture?

Answer 21

Potential for discovery
-Most sequences have no homology to anything known.
Canaries
-In dynamic microbial systems changes in the presence and abundance of phase are more dramatic than changes in microbes.
Specificity
- Phage can be quite specific to particular microbial hosts; following their presence through time may dive a more accurate picture than taxonomic genes.
Vast majority of viruses are uncultured study then using meta genomics.

Question 22

Viromes are the ___ between you and the person next to you

Answer 22

variation

Question 23

Most of the metabolic variation in human gut is coded by what?

Answer 23

viruses

Question 24

Phages may encode genes important for both ___ and ___ hosts

Answer 24

bacterial and human

Question 25

What will characterizing the function of even a few unknown sequences do?

Answer 25

It will improve annotation and analysis of the 70% of unkown sequences in the viral meta genomes.

Question 25

What will characterizing the function of even a few unknown sequences do?

Answer 25

It will improve annotation and analysis of the 70% of unkown sequences in the viral meta genomes.

Question 26

What are some important lessons from human viromes?

Answer 26

Mot unknowns in human gut microbiota are viral; however host-associated viral diversity is often lower than other ecosystems.
Temperate viruses appear more common
Most differences between individuals are the viromes which appear to be stable over time.

Question 27

Temperate Phage Life Cycle: Lysogeny

Answer 27

Protection against superinfection.
Expansion of the bacterial hosts’s niche by
-Enhanced carbohydrate utilization.
-Antibiotic resistance
-Production of toxins
-Modification of host gene expression.

Question 28

Temperate Phage Life Cycle: Lysis

Answer 28

Constant diversity dynamics
Destruction of niche competitors
Phage shunt and bacterial turnover

Question 29

Temperate Phage Life Cycle: Infection

Answer 29

Mobilization of genes (HGT)
Pressure on host for diversification of the phage receptor.