Sign-up to Apply for a Sampling Kit / Aplica AQUÍ para tu kit

SARS-CoV-2 In the SARS-CoV-2 Detection in the Urban Environment Project we are collecting samples from surfaces around San Diego to test for traces of the virus and investigate if it is possible to contract the virus from public spaces.

En el Proyecto de Muestreo de SARS-CoV-2 en el Ambiente, queremos saber si el virus está presente en en ambiente de tu casa y de los espacios públicos en San Diego.

*A Google account (e.g., Gmail or G Suite) is required to participate (Gmail Account Signup) with a secure, convenient way to access the Sample Collection portal without having to create an account for our website. We respect your privacy! We do not store your login credentials and we never have access to your password.

*Necesitas una cuenta de Google (ej., Gmail o G Suite) (Crea una cuenta de Gmail) para un acceso seguro y conveniente a nuestro Portal de Toma de Muestras. Respetamos tu privacidad! No guardamos tus datos de registro y no tenemos acceso a tu clave.

Principal Investigators

  • 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 Dr. Wegley Kelly and Dr. 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.


  • CoralCoral Research
    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.

  • CFHuman 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.

  • Phage OutreachPhage Outreach Program
    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.


  • Life in Our Phage World book coverLife in Our Phage World
    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 BookCoral Reefs in the Microbial Seas
    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

The 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.

Lab News & Events

Phage-encoded elements and the ecology and evolution of marine disease pathogenesis

Mar 06, 2020

In a new book chapter from the Rohwer lab, published in the book Marine Disease Ecology, Little*, Rojas*, and Rohwer shed light on the abundance and functional role of bacteriophage integrated in the genomes of bacteria that live in association with marine animal hosts. These prophages were shown to be more prevalent in host-associated pathogens than non-pathogens existing in the same animal holobionts. Additionally, a comparison of the prophage-encoding genes between the two groups, found that in disease-causing bacteria these are enriched for carbohydrate and nitrogen metabolism, virulence factors, and membrane transport. The chapter reviews what is known about prophages in the context of marine diseases.

News Article

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome

Jul 25, 2019

Recent work published in the journal Gut Microbes, Boling et. al. examined the effects of 117 commonly consumed foods, plant extracts, and additives on the growth and prophage induction capacity of bacterial species representing the two major phyla of the human gut.  The research was enabled by the development of two novel experimental techniques – one to mass-analyze bacterial growth curves, and another to quantify induced prophage with flow cytometry.  These studies show that the compounds tested differentially affect bacterial growth, and likely human gut microbiome composition.  Several prophage inducing agents were also identified including stevia, uva ursi, and propolis.  Antiviral compounds were also identified. The methods and results present novel tools toward the eventual landscaping of the human gut microbiome.

A link to the full, open access paper can be found below.

News Article