Fecal Phage Dark Matter and Other Stories of The Human Virome Part II Flashcards
What did the Craigslist Roomates Fecal Matter Study find?
It found that people who cohabitate share about 25% of the viruses in their viruses just by virtue of living in the same space.
What are some lessons from human viromes?
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.
What is a virome?
is the community of viruses living in a particular environment.
Uncultured viromes can be generated with sequencing.
Virome: Persistent viral infections
Effects on human health.
Interactions with immune system and other pathogens.
Virome: Acute viral infections
Effects on human health
interactions with immune system and other pathogens
Virome: novel viruses
Association with disease.
Virus characterization (demonstrates pathogenic isolate and study in vitro)
Epidemiology
Virome: novel bacteriophage
Effects on bacterial community structure and metabolic potential.
Identification of genes that may affect human health.
Virome: Bacteriophage with pathogenic potential or antibiotic resistance genes
Effects on the bacterial community structure and metabolic potential
Association with health and disease
Commensal bacteriophage
Effects on bacterial community structure and metabolic potential
Association with health and disease
Human endogenous retroviruses
Definition of integration sites and gene expression.
What is the common response to immunosuppressants?
Total viral load goes up
Important hallmark of healthy immune system?
Specific microbial immunity in compartments.
Describe the main highlights of temporal response of human viriome to immunosuppressan and antiviral therapy
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.
___ represent the largest region of unkown sequence space on Earth
Viromes
How many uncultured viral sequences lack homology to sequences in databases?
Most, 70-90%
Human microbial communities have incredib _______ _________
metabolic diversity
Most viral reads and contains have no contains have no ____ ___ to any database
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.
What was the first sequenced uncultured virome? What environment did it come from? When was it?)
It was sequenced in 2002 by Forest Rower at SDSU from seawater samples collected off the CA coast.
The first human meta genome was a ___
virome
What is the most ubiquitous gene in the universe?
Tranpossasses are the most abundant and ubiquitous genes in nature.
Why should the viral component receive far greater attention and describe how explorations can yield to a more complete picture?
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.
Viromes are the ___ between you and the person next to you
variation
Most of the metabolic variation in human gut is coded by what?
viruses
Phages may encode genes important for both ___ and ___ hosts
bacterial and human
What will characterizing the function of even a few unknown sequences do?
It will improve annotation and analysis of the 70% of unkown sequences in the viral meta genomes.
What will characterizing the function of even a few unknown sequences do?
It will improve annotation and analysis of the 70% of unkown sequences in the viral meta genomes.
What are some important lessons from human viromes?
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.
Temperate Phage Life Cycle: Lysogeny
Protection against superinfection.
Expansion of the bacterial hosts’s niche by
-Enhanced carbohydrate utilization.
-Antibiotic resistance
-Production of toxins
-Modification of host gene expression.
Temperate Phage Life Cycle: Lysis
Constant diversity dynamics
Destruction of niche competitors
Phage shunt and bacterial turnover
Temperate Phage Life Cycle: Infection
Mobilization of genes (HGT)
Pressure on host for diversification of the phage receptor.
