The Breitbart lab studies viruses and bacteria in a wide range of environments. Here are descriptions of just a few of our many current projects.  To see recent publications on each of these topics, click here



MERA: An innovative, beach water quality investigation that considers human behavior, water pollution, and risk of illness. Learn more on the MERA website (


Only 10% of the world’s household wastewater is properly treated and disinfected prior to flowing into rivers and ultimately, coastal beaches. Since this wastewater contains millions of pathogens, swimming and playing at beaches polluted by wastewater can greatly impact your health. In total, millions of cases of illness occur each year due to playing at contaminated beaches and this costs the global community 12 billion USD annually. Despite scientific advancements, government beach management approaches rely on outdated compliance practices that do not accurately identify public health risks. This innovative investigation will advance local management practices, serve as an example from a tropical region, as well as contribute to our global achievement of the 2030 Agenda for Sustainable Development. The Investigation MERA research team is composed of anthropologists and natural scientists, from a variety of backgrounds, from Universities, private laboratories, governmental institutions, as well as non-governmental non-profit organizations from the United States of America and Costa Rica. Together, we will execute a holistic beach water quality investigation that will consider human behavior, water pollution, and risk of illness at a Costa Rican beach. Our ultimate goal is to improve beach management and ensure the protection of public health.


by Allison CohenVector-Enabled Metagenomics   (Image by Allison Cohen)

Many dangerous plant and animal viruses are transmitted by insect vectors. The whitefly-transmitted begomoviruses are among the most damaging and emergent plant pathogens worldwide. Through this NSF-funded study, we have significantly expanded current knowledge regarding the diversity, evolution, and biogeography of these plant pathogens through the application of a novel approach examining begomoviruses directly from their whitefly vector (Bemisia tabaci). Whiteflies feed on a very wide range of plants and are highly mobile, being able to fly short distances and capable of traveling up to a few kilometers when assisted by the wind. Our approach, known as vector-enabled metagenomics (VEM), leverages the sampling ability of whiteflies with a sequence-independent approach (metagenomics) that allows us to recover novel viruses. VEM effectively integrates over space and time, enabling rapid and efficient description of the begomoviruses circulating in whiteflies within a given region, and provides advantages over standard methods by enabling the identification of viruses infecting native vegetation, newly emerging viruses that are not yet widespread in crops, and viruses that have more mutualistic interactions with their hosts. We have also used VEM to examine other insect vectors (e.g., mosquitoes), other virus types (e.g., RNA viruses), and top insect predators (dragonflies). The application of VEM provides an effective molecular surveillance system capable of recognizing introduced and emerging viruses of great societal importance for agriculture and public health.

cartoonmyaAToL: ACCESS DNA Viruses: A Comprehensive Survey of Circular Eukaryotic Single-Stranded DNA Viruses in Invertebrates and Fungi to Bridge Gaps in a Tractable Branch of the Viral Tree of Life
(Image by Allison Cohen)

The impacts of viruses on the biosphere and the evolution of cellular organisms are undeniable; however, we have only scratched the surface of viral diversity, as entire taxa have not been explored for the presence of viruses. While it is clearly critical to understand the evolutionary relationships among these biological entities, construction of a universal tree of life for viruses is challenging due to rampant gene exchange and the lack of universally conserved genetic markers. This project, funded through NSF’s Assembling the Tree of Life program, aims to construct an understudied and tractable branch of the viral tree of life: that of circular eukaryotic single-stranded DNA (CESS) viruses. CESS viruses are the smallest known viruses, yet they include pathogens with devastating impacts on agriculture and health worldwide. Recently, environmental sampling has uncovered a diversity of CESS viruses that are only distantly related to these pathogens and we have shown that they infect a wide range of hosts, including insects and fungi. This project is systematically testing previously unexplored hosts to discover, sequence, and classify their CESS viruses. Tree and network based approaches applied by collaborator Siobain Duffy at Rutgers University will then determine how all CESS viruses are related to one another, providing a framework for classifying the CESS viral tree of life.

Peppers and poopViral Indicators of Fecal Pollution

Fecal pollution in aquatic systems is a growing problem worldwide and has devastating impacts on human and environmental health. Although many government agencies mandate the use of bacterial indicators to identify fecal pollution, it is well known that these indicators poorly correlate with risk of disease and contamination events.Therefore, a paradigm shift in predicting health risks from fecal pollution is needed. Our recent work has demonstrated the potential of pepper mild mottle virus (PMMoV), an ornamental pepper virus that dominates human feces, as a bioindicator of fecal pollution in coastal waters. We are currently using PMMoV as a conservative tracer to test novel wastewater treatment techniques, as well as for tracking virus removal in both the United States and in the developing world.

OLYMPUS DIGITAL CAMERADisease in Marine Animals
New diseases in marine animals are emerging at an increasing rate, yet methodological limitations currently hinder characterization of viral infections. As global climate change intensifies, we are seeing severe disease outbreaks on an unprecedented scale. Our lab is using viral metagenomics (virus particle purification followed by shotgun sequencing) to attack the critical first step of identifying potential pathogens responsible for causing diseases in a marine animals. We are currently studying chronic infections in sea turtles, investigating the causes of mortality events in captive and wild marine mammals, and rapidly responding to explore potential causes of large scale disease outbreaks. Identifying and sequencing viruses that are potential pathogens enables the development of rapid and inexpensive diagnostic tests. Further research on these pathogens determines the association of a virus with the disease in question, determines the transmission mechanism and environmental reservoirs of the virus, and develops steps to treat active infections and/or prevent further exposure and spread.

PhageIllustration1Marine Phage Diversity

Over the past two decades, marine virology has progressed from a curiosity to an intensely studied topic of critical importance to oceanography. At concentrations of approximately 10 million viruses per milliliter of surface seawater, viruses are the most abundant biological entities in the oceans. The majority of these viruses are phages (viruses that infect bacteria). Through lysing their bacterial hosts, marine phages control bacterial abundance, affect community composition, and impact global biogeochemical cycles. In addition, phages influence their hosts through selection for resistance, horizontal gene transfer, and manipulation of bacterial metabolism. Recent work has also demonstrated that marine phages are extremely diverse and can carry a variety of auxiliary metabolic genes encoding critical ecological functions. Our research examines the spatiotemporal variability in marine viral abundance and diversity at the Bermuda Atlantic Time-series Study Site and exploring under-studied viral groups (single-stranded DNA phages) and hosts (e.g., copepods).

marine scientistsMarine Biodiversity Observation Network

As part of a large consortia led by Dr. Frank Muller-Karger, we are creating a demonstration Marine Biodiversity Observation Network (MBON) to observe and monitor changes in marine biodiversity within three US National Marine Sanctuaries (NMS): Florida Keys, Flower Gardens Bank, and Monterey Bay. Our lab will be focusing on microbial diversity, with the goal of linking these critical microorganisms at the base of the food chain with the diversity of higher trophic levels (measured using eDNA techniques) and environmental conditions assessed by remote sensing and in situ measurements. These time series of biodiversity and environmental observations will help construct conceptual and forecast models of the inter-relations between human dimensions, climate and environmental variability, and ecosystem structure at multiple trophic levels. Results will enable scientists and sanctuary managers to assess ecosystem integrity, advance protection of marine resources, and promote conservation.