Rohwer Lab

BioTools

Phage Proteomic Tree

Coral Microbes

Microbial dynamics

Pristine and human-impacted reefs

SCUMS

Viruses and Phage

Cystic fibrosis

Cystic Fibrosis viruses
We are currently investigating the dynamics of bacteria, phage, and eukaryotic viruses in the respiratory tracts of individuals with and without Cystic Fibrosis. Characterization of viral communities coupled with microbial transcriptomics and viral metagenomics will allow a better understanding of how the unique environment of the CF airway drives microbial and viral specialization and vice versa.

Viral discovery
Many diseases in humans have no known associated-etiological agents. These so called ailments of unknown etiology (AUE) range from rare, poorly described to well-characterized clinical conditions with efficacious therapeutic medicines capable of providing a complete cure. The inability to determine the etiology of diseases caused by infectious agents often hampers any preventive effort to control their spread.

Unfortunately, the determination of viral etiology of AUE is hindered by the lack of sensitive techniques to detect new viruses. These putative viruses can be notoriously difficult to detect in cell culture, or by the nucleic acid-based hybridization or serological methods. However, it is estimated that <1% of existing viruses have been cultivated. Culture-independent molecular methods have been proposed to genetically characterize viruses without prior in vitro replication or the use of virus-specific probes. The 16S profiling technique has been useful for the detection of AUE-associated bacteria but this approach cannot be applied to viruses as there is no single gene that is common to all viral genomes. To circumvent all these limitations, we are using a high-throughput 454 pyrosequencing and bioinformatics approach to analyze samples from diverse geographical sources and disease types.

Ongoing effort is focused on the following diseases:
* Lymphomas of unknown origin (Cameroon, Democratic Republic of Congo)
* Effect of malaria in viral acquisition during early childhood (Kenya, West Africa)
* Respiratory flu-like illness of unknown origin (USA)
* Liver-failure of unknown origin (USA)

Collaborators:
* Dr Nathan Wolfe, Global Viral Forecasting initiative
* Dr Rosemary Rocheford
* Dr Robin Ryder, UCSD
* University of Kinshasa
* Dr Rick Tullis, Aethlon Medical, Inc.

Oxygen Minimum Zones
Oxygen Minimum Zones (OMZ) are very unique regions in the ocean where the concentration of oxygen is extremely low, ranging from less than 20 µM to anoxia. These areas are typically situated between 100 and 1000 meters deep in the water column and are generally created due to high levels of respiration of organic matter that enters from the highly productive euphotic zone (Ulloa y Pantoja, 2008). Even though there is not great macrofaunal diversity in these areas, it is known that these zones host a great abundance of microorganisms and meiofauna (Levin, 2003). When it comes to viruses, their types as well as the role they play in this particular environment is still unknown. Elizabeth Dinsdale is currently leading research in the lab to look at the viral assemblages of various depths and areas within the OMZ off the coast of Iquique, Chile. Preliminary data from a cruise to the OMZ in June 2008 show that over 99% of the genetic information from these sites does not match anything in the existing databases. Efforts to understand the types of viruses present as well as the hosts they infect are underway. We are returning to the OMZ in August 2009 to continue investigating the viral assemblages of this unique ecosystem.