We have a diverse group of researchers in the lab that include undergraduate volunteers, graduate students (MS & PhD), post-docs, and visiting scientists.
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Our lab offers research and training opportunities for students (undergraduate, MS, PhD), postdocs, and scientists.
Lab Training & Methods
Learn how to build the tools that we use to explore diverse ecosystems.
To celebrate a century of phage exploration, we invite you to get intimate with 30 diverse phages in this premier phage field guide. In these 404 pages you'll learn who these phages are, where on Earth they've been found, who their close relatives are, how their genomes are structured, and how they trick their hosts into submission. Researchers who have devoted their lives to phage also recount their experiences in pursuit of their quarry.
The book is available in electronic (PDF) format for free. It can be downloaded as a high-resolution (323 Mb) or lower resolution (75 Mb) file. For optimal viewing, display the pages with the two-page view that includes the cover.Electronic Book Downloads
For millennia, coral reefs have flourished as not only one of the planet's most magnificent ecosystems, but also as its most biodiverse. However, since the 1980s the corals have been struggling. Both coral bleaching and disease have spread globally. During recent research expeditions to the remote Line Islands, microbial ecologist Forest Rohwer and his colleagues found that the large-scale changes to the reefs in recent decades are the work of the microbes as they respond to various human impacts.
Coral Reefs in the Microbial Seas is the first book to recount this story, complete with introductions to the coral reef ecosystem, 21st century metagenomic research tools, and the coral's microbial and viral partners. An engaging book, its science is liberally spiced with artistic illustrations and playful stories from the research expeditions.Book Downloads
Professor Arzu Ozkal from the Art Department, in collaboration with Professor Anca Segall and Professor Forest Rohwer from the Biology Department are all joining forces this semester under the Art Alive Program at SDSU. The class brings Graphic Design and Biology students together to illustrate both the beauty and complexity of biology through art and research. Throughout the semester, students have been working together to create beautiful and effective infographics from microbiome research publications on topics ranging from coral reef diseases to the microbial composition of breast milk. The class will culminate in a “living” art instillation that will be presented at the San Diego Microbiome Group Annual Symposium on May 13th. These pieces will convey complex biological processes or ideas such as the induction of prophages or the effects of coral-algal interaction on the host microbiome.
Fresh faces at SDSU’s Viral Information Institute are bringing diverse backgrounds and fearless experimentation to the fast-moving world of microbial research.
The recent publication by Ben Knowles & Cynthia Silveira in Nature is featured by SDSU
Awesome science of the week
Jeremy Barr's article featured at the Tree of Life website
New research reveals that bacteriophages use slow, staccato movements to hunt bacteria on cell surfaces.
Bacteriophages (phages) are viruses that infect and kill bacteria. Being inanimate, phages rely on diffusion to search for bacterial prey. Here we demonstrate that a phage that adheres weakly to mucus exhibits subdiffusive motion, not normal diffusion, in mucosal surfaces. Supporting theory and experiments revealed that subdiffusive motion increases bacterial encounter rates for phages when bacterial concentration is low. To the best of our knowledge, no other predator has been shown to effectively use a subdiffusive search mechanism. Mucosal surfaces are vulnerable to infection. Mucus-adherent phages reduce bacterial infection of lifelike mucosal surfaces more effectively than nonadherent phages. These findings provide a basis for engineering adherent phages to manipulate mucosal surface microbiomes for protection from infection and other purposes.
Being a marine microbial ecologist, Dr. Forest Rohwer sees a coral reef as a finely-tuned community in which the microbes and viruses are major players. Recognizing their importance, he pioneered the use of metagenomics as a means to characterize these previously inscrutable organisms and to investigate their role in coral reef health and disease.
For his scientific contributions, he has received numerous awards including the prestigious Young Investigators Award of the International Society of Microbial Ecology and the Marine Microbiology Initiative Investigator Award from the Gordon and Betty Moore Foundation.Linda Wegley Kelly, PhD
Drs. Wegley Kelly and Rohwer have been working together since 2001. She has directed research projects on everything from fluorescent-labeled phage to large-scale metagenomic from deep mines, salterns, and coral reefs to ammonium oxidizing Archaea.
Linda's research group mostly works on coral-associated microbes. She uses a combination of large-scale DNA sequencing (e.g., metagenomics), analytical chemistry, and microbiology to study how the coral holobiont changes in response to local and global stressors. Linda recently showed that shipwrecks cause devastating outbreaks of algal-microbial mats the kill kilometers of coral reefs in the iron-poor parts of the central Pacific.
Coral reefs worldwide are in decline. The dramatic rise in incidences of coral disease over the last two decades has been instrumental in this process. We have hypothesized that most of these diseases are actually opportunistic infections instigated by anthropogenic stressors. Our research is focused around understanding the interactions between the microbial world and coral reefs, and how these systems change following perturbation.Human Research
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.
Our mission is to interest high school students in the study of the Phage Virus and attract them to the field of science in the future. We will do this by sharing the most interesting aspects about the phage virus along with an educational foundation, a fun art contest, and an in-depth field trip. Additionally, 3-5 motivated students will be offered a summer internship at our lab researching the Phage Virus.