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Grand Challenges is a family of initiatives fostering innovation to solve key global health and development problems. Each initiative is an experiment in the use of challenges to focus innovation on making an impact. Individual challenges address some of the same problems, but from differing perspectives.

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Challenges: Bacteriophage

Bacteriophage and the Physical Structure of the Microbiota

Paul Bollyky, Stanford University (Stanford, California, United States)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Paul Bollyky from Stanford Medical School in the U.S. will study whether filamentous phage – viruses that infect bacteria – direct structural changes in the lining of the intestines and thereby promote the growth of healthy bacteria to protect against disease. Phage are considered to be a potentially rich therapeutic resource for infectious diarrhea and environmental enteropathy, which are prevalent in developing countries, but much remains to be learned about them. They have shown that a phage of the genus inovirus directed the formation of bacterial biofilms, which have specific crystal-like properties. They will use their newly developed software package along with polarization microscopy to image intestinal bacterial populations and analyze the structure of biofilms in human specimens and mouse models, and study the effect of phage, bacterial infection, and diet. They will also measure inovirus from around 2000 stool samples from children in Bangladesh to determine whether the levels decrease in line with the severity of diarrhea, suggesting that this phage might be protective. The effect of these isolated phage on intestinal structure will also be analyzed in mouse models.

Bacteriophage Particles to Target the Intestinal Microbiome

Todd Parsley, SynPhaGen, LLC (Gaithersburg, Maryland, United States)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Todd Parsley of SynPhaGen, LLC in the U.S. will engineer phage-like particles to transfer genes into specific bacteria in the infant gut that program them to produce therapeutic proteins that protect against environmental enteric dysfunction, which is a major cause of morbidity and mortality in developing countries. Rather than employing bacteria-infecting phage to destroy bacteria, they will engineer safer particles, which are unable to replicate and do not kill the bacterial host. As proof-of-principle, they will modify the defective bacteriophage particles to carry a gene encoding the protein alkaline phosphatase, which keeps the gut healthy in multiple ways including neutralizing bacterial toxins, and program them to infect the bacterium Bacteriodes thetaiotaomicron. The activity of these particles will then be assessed in a mouse model of environmental enteric dysfunction.

Developing Bacteriophages to Eradicate Infant Shigella

Martha Clokie, University of Leicester (Leicester, United Kingdom)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Martha Clokie from the University of Leicester in the United Kingdom will develop a bacteriophage to destroy the diarrhea-causing bacterium Shigella, and study its effect on microbial populations in the gut. Shigella is a leading cause of death in children under five years old in the developing world but there are no effective vaccines due in part to the many different forms of the bacterium. Phage are viruses that can destroy specific bacteria, and are an alternative approach to vaccines. They will perform a longitudinal study in a mouse model of chronic Shigella infection using their collection of 46 lytic phage isolated from infants in Bangladesh that infect 200 clinical strains of Shigella. The effects of the phage will be evaluated both by sequencing to determine the quantities and types of bacteria in the gut, and by analyzing protein production in the bacteria and the mice, which will also reveal insight into the host immune response.

Editing the Newborn Gut Microbiome Using Engineered Phage

Srivatsan Raman, University of Wisconsin (Madison, Wisconsin, United States)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Srivatsan Raman of the University of Wisconsin-Madison in the U.S. will develop a platform for engineering synthetic phage - bacteria-infecting viruses - that can be easily reprogrammed to target specific bacterial species and that can be switched off to improve their safety for treating enteropathogenic diseases in newborns. Natural, so-called lytic phage have two main limitations when being considered as potential therapies: they cause death to bacteria by physically destroying them, which can release large concentrations of lethal toxins into the body, and the bacteria also evolve resistance to the phage, necessitating the identification of new phage, which is a lengthy process. They will focus on producing phage targeting enterotoxigenic Escherichia coli (ST-ETEC), which is one of the most common diarrhea-causing pathogens in infants in developing countries. They will use the Rosetta software to design thousands of proteins and test them for binding to specific bacterial receptors when incorporated into the T7 phage. They will also redesign a protein required for phage replication to make it unstable in the absence of a small molecule so it can act as an on-off safety switch in case of high toxin levels.

Integrated Systems Biology for Phage/Microbiome Modeling

Diane Joseph-McCarthy, EnBiotix (Cambridge, Massachusetts, United States)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Diane Joseph-McCarthy of EnBiotix Inc. in the U.S. will use a systems biology approach incorporating gene, protein and metabolic data to computationally model the complex interplay between specific microbes in the gut and the host response, and the effect of phage, to enhance our understanding of pathogenic diseases and identify new treatments. They will use a mouse model of enteropathogenic E. coli infection and measure the effect of treatment with phage on the genetic or molecular response of both the host and the resident bacterial populations, as well as the interactions between the two. These data will be incorporated with other publicly available data and modeling algorithms used to produce a visual interaction network that can generate hypotheses for experimental testing.

Phagocins: Precision Tools for Remodeling the Gut Microbiota

Ry Young, Texas A&M AgriLife Research (College Station, Texas, United States)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Ry Young III from Texas A&M AgriLife Research in the U.S. will engineer particles that resemble bacteria-infecting viruses (phage), but are functionally defective, for developing treatments that can more safely modify bacteria in the infant gut and thereby protect against disease and malnutrition. So-called lytic phage physically destroy the bacteria they infect and are considered to be potentially highly valuable for treating many childhood infectious diseases that are prevalent in developing countries and cause substantial morbidity and mortality. However, phage can randomly change their behavior by mutating their genome, and can transfer genes between different species, raising safety concerns. They will modify the defective prophage PBSX from the harmless bacterium Bacillus subtilis to produce phage-like particles - phagocins - that cannot replicate and that kill bacterial cells without lysing them. They will evaluate the ability of the phagocins to infect and kill a variety of bacteria, and optimize methods for their low-cost production.

Reversal of Virulence of Pathogenic E. Coli

Reza Nokhbeh, Advanced Medical Research Institute of Canada (Sudbury, Ontario, Canada)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Reza Nokhbeh from the Advanced Medical Research Institute of Canada in Canada will genetically engineer phage that infect pathogenic Escherichia coli bacteria to express proteins and short RNA molecules that block multiple bacterial functions and thereby stop it from colonizing the human gut and causing disease. Diarrheal diseases cause substantial mortality in children under five in developing countries, and there is an urgent need for new treatments. They will develop their approach to first target E. coli O157:H7 by incorporating genes and RNAs into the phage that promote bacterial cell death, slow growth, and block its ability to produce toxins and attach to host cells. The resultant phage will be tested in a mouse model of the infection.

Strategy for Development of Enteric Pathogen-Specific Phage

David Low, University of California Santa Barbara (Santa Barbara, California, United States)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

David Low from the University of California, Santa Barbara in the U.S. will engineer phage to selectively target and destroy several pathogenic bacteria to prevent enteric diseases in infants. Lytic phage infect bacteria and hold great promise as therapeutics for infectious diseases, but controlling their activity and preventing the development of bacterial resistance is challenging. They will engineer different versions of the T2 lytic bacteriophage that bind multiple different regions of the BamA protein found on the surface of several pathogenic bacteria, which will ensure they only infect these target bacteria. And, as the BamA protein is essential for bacteria survival, it is unlikely that it will be mutated to cause resistance. They will test the different phage for capacity to kill pathogenic E. coli and Shigella, and whether they cause resistance.

The Role of Phages in Infant Gut Microbiome Modulation

Jennifer Mahony, University College Cork (Cork, Ireland)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Jennifer Mahony and Douwe van Sinderen of University College Cork in Ireland, with Marco Ventura of University of Parma in Italy, will study how bacteriophage, which are viruses that infect and kill bacteria, affect both beneficial and pathogenic bacterial populations over time in the guts of infants from developing countries, which ultimately influence infant health and well-being. They will take fecal samples at 1, 2, 3 and 6-month time points from healthy children and those with gut disorders in Malawi, Sudan, Ethiopia or Nigeria, and identify the types and levels of bacteria and phage present by sequencing their DNA. These data will be combined with obtained dietary information to identify links between phage populations and the changes in bacterial populations in the gut. They are particularly interested in whether changes in the levels of beneficial bacteria caused by phage might make the gut more vulnerable to colonization by pathogenic bacteria such as enterotoxigenic E. coli (ETEC) and Shigella, which are a major cause of mortality in infants. In parallel, they will identify phage that can kill these pathogenic bacteria and may be developed into new treatments.

Toward Rational Remodeling of the Infant Gut Microbiota

Bryan Hsu, Harvard Medical School (Boston, Massachusetts, United States)
May 1, 2016
Grand Challenges Explorations> Bacteriophage

Bryan Hsu from Harvard Medical School in the U.S. will develop a mouse model carrying specific bacteria to mimic conditions in the infant gut for studying bacteria-infecting viruses known as phage, which could be valuable agents for treating infectious diseases and promoting child health in developing countries. Understanding how phage behave within the complex human gut is a critical step towards developing phage-based therapeutics that can safely modify resident bacterial populations. They will create a computational model to predict the effects of selected combinations of phage on bacteria dynamics in the mice, and then evaluate a phage-based therapeutic for treating a pathogenic Escherichia coli infection.

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