Rohwer Wegley-Kelly Lab

The Lab

Rohwer Lab

Lab Members
We have a diverse group of researchers in the lab that include undergraduate volunteers, graduate students (MS & PhD), post-docs, and visiting scientists.

Join the Lab
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.


Life in Our Phage World book cover

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

Sampler (3 Mb)
Low-resolution (75 Mb)
High-resolution (323 Mb)

Hardcover Book Purchases

Buy at Amazon
Buy at Barnes & Noble
Buy at Powell's

Forest Rohwer - Coral Book

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

Sampler (1.5 MB)
Buy at Amazon

NOAA Summer 2017 Field Expedition

Jul 24, 2017

Each year, a microbiologist from the lab spends a month on a ship called the Hi’ialakai as part of the National Oceanic and Atmospheric Administration (NOAA) Coral Reef Monitoring Program. A month is a long time to live aboard a 224 ft ship with 50 other scientists and crew members, but the time passes quickly thanks to early morning wakeups, long days of diving, and late nights in the lab.

This past May, I met the ship in Guam after it traveled from Hawaii southwest to the Northern Line Islands, then north to Wake atoll and finally, east across the International Dateline. After a few days at Guam, we spent the month traveling north up the Marianna island chain to Saipan. Each island had unique underwater inhabitants from bumphead parrotfish to small black tip reef sharks and the reefs ranged from Porites rus colonies as far as the eye could see to murky, algae flats.

Each island had a unique history as well. The Marianas were key in the Pacific theater during WWII and the war scars were still evident 73 years later. The islands from Guam to Saipan were occupied by Japanese soldiers after the bombing of Pearl Harbor and most of 1944 consisted of bloody battles between Japan and America for control of the islands. Technological advances allowed American planes, warships and beach landing vehicles to outmaneuver the Japanese defenses and the Marianna islands were in American control by the end of 1944. Although much time had passed, I still saw unexploded torpedoes overgrown by coral, the entombed bombs now part of the reef matrix. Tanks sat rusted in the Saipan lagoon where the unexpected deep water surprised the American soldiers as they drove over the reef crest and the jungle crept over the entrances to limestone pillboxes that once housed cities of Japanese soldiers. One of our small boats broke down for the third year in a row on the eerie banks of Tinian, the island that housed the atomic bomb en route for Hiroshima.

The grey beaches lined with soldiers in the black and white footage of the Pacific War are now beautiful white sand beaches lined with five star resorts and shopping malls. The bloody history of the islands may be covered by casinos and hotels, but the influence of the war can be seen in coral reefs around the world. After WWII ended, surplus ships were turned into large-scale fishing outfits with new technologies and the fish populations began to decline quickly. Grazers, especially herbivorous fish, eat the fleshy algae which maintains a balanced coral reef ecosystem, from the viruses to sharks, and the removal of grazers leads to the algae flats that I observed on the trip. The war for the Marianas might be long over, but the battle to save its coral reefs has just begun.

-Emma George

All image credit to the NOAA - Coral Reef Ecosystem Program (


Living art takes over the SDMG

May 23, 2017

The Art and Microbiology class, lead by Professor Arzu Ozkal, Professor Anca Segall and Professor Forest Rohwer, presented their final art pieces at the Annual San Diego Microbiome Group Symposium held at UCSD. The graphic designer and biology student pairs put the final touches on their project after multiple rounds of critique and improvements throughout the semester, culminating in these presentations to members of the SDMG.


Along with the art, members from the Rohwer lab presented posters pertaining the their research alongside the art pieces. The “living art” was intended to display a non-trivial scientific idea or phenomenon while possessing both artistic and design elements allowing individuals who are not deeply involved with the projects to understand the research. The scientific ideas presented ranged from how common foods and sweeteners which we consume everyday effect the lifestyle of bacteriophages in our gut to displaying how the exudates produced by macro algae on coral reefs can negatively impact the health of corals, even when they are not in direct contact.


These living art pieces will continue to run throughout the summer and samples will be collected to be sequenced on the Oxford Nanopore Technologies minION Sequencer. This novel sequencing technology has allowed researchers to process and sequences samples in the field at a reduced cost. The art pieces will hopefully show the shift in microbial communities associated with the phenomenon that are being tested. Stay tuned for the results!


The Learning Glass helps to connect researchers to the public

May 23, 2017

Students Kevin Green, Brandi White, Adam Barno, and Douglas Naliboff participated in Molecular Biology 610 last semester taught by Dr. Nicholas Shikuma. There they learned how to successfully write grants as well as presented their work via the Learning Glass, an online instructional tool developed by Dr. Matt Anderson in the Physics Department at SDSU to better teach students who participate in online classes. The students had to give a 2-3 minute “chalk-talk”, using the Learning Glass, on their research aimed at students who have a semester of introductory biology under their belt.


Microbiology and Art Join Forces

Apr 04, 2017

Spring 2017

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.

Going Viral

Jun 27, 2016

Fresh faces at SDSU’s Viral Information Institute are bringing diverse backgrounds and fearless experimentation to the fast-moving world of microbial research.

News Article

"Piggyback the Winner" published

Mar 16, 2016

The recent publication by Ben Knowles & Cynthia Silveira in Nature is featured by SDSU

News Article

The aesthetics of coral reefs

Nov 18, 2015

Awesome science of the week

News Article

The story behind the paper by @JeremyJBarr on phage using mucus to hunt prey

Oct 22, 2015

Jeremy Barr's article featured at the Tree of Life website

News Article
Read more news stories

Principal Investigators

Forest Rohwer, PhD

Forest RohwerBeing 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

Linda Wegley-KellyDrs. 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.

Research Areas

Coral Research

CoralCoral 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

CFWe 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.

Related Websites

Outreach Education

Phage Outreach Program

Phage OutreachOur 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.

Media Galleries

© 2015, All Rights Reserved.
Rohwer Laboratory, San Diego State University.

Design by Big Rose Web Design

Lab Info
North Life Sciences Biology Bldg
San Diego State University

PDF: Lab Directions
Map: 32.777818, -117.071543

Forest Rohwer, PhD
Professor of Biology
SDSU Dept. of Biology