New Method for Genome-wide Engineering of Viruses

Researchers at JCVI have been developing synthetic genomics assembly methods since 2000, addressing fundamental biological questions. Together, with researchers at Oregon Health and Science University, Johns Hopkins University School of Medicine, Synthetic Genomics, Inc., and Vir Biotechnology, Inc. (formerly TomegaVax, Inc.), the team has made another major advance in this field.

Building upon past advancements, a protocol has been developed whereby we are able to engineer genome variants of large DNA viruses by breaking the original genome up into smaller, overlapping pieces, that can then be independently modified, and then reassembled back into full-length virus genomes.

This allows for quick assembly of genome variants that can be used to understand the function of genes and gene combinations in viruses. Previous genetic systems for large DNA viruses, such as herpesviruses and poxviruses, required you to make one change at a time, making the new system significantly more efficient.

In our study, we used herpes simplex virus type 1 (HSV-1) and human cytomegalovirus (HCMV), both members of the herpesvirus family. Herpesviruses can cause a range of diseases and symptoms, including cold sores, congenital birth defects, and cancer.

Fluorescence microscopy shows an HSV-1 genome engineered to express a fusion of viral protein VP16 and fluorescent protein Cerulean. Image by Peter Grzesik with assistance from The Johns Hopkins University Integrated Imaging Center.

Herpesviruses have extremely large genomes. HCMV is about 230,000 base pairs, the largest genome of any virus known to infect humans, and carries over 100 genes. Many of the functions of these genes are not yet known. We believe that our system will allow for a combinatorial approach to herpesvirus genetics that was not possible previously.

Rapid engineering of herpesviruses could also lead to new therapeutics and vaccines. For most herpesviruses, there are no effective vaccines. Improved genetics may allow us to rationally design and attenuate the virus, which would lead directly to vaccine strains.

Herpesviruses could be developed as delivery systems for gene therapy. Herpesviruses could also be developed to treat cancer as oncolytic viruses, which are viruses that attack cancer cells. An HSV-1-based oncolytic virus has already been approved by the FDA to treat melanoma and rapid engineering strategies could help generate oncolytic viruses to treat other cancers.

We believe this method to assemble and engineer virus genomes will be applicable to many different viruses and help expand our understanding of the basic biology of other viruses that are difficult to work with currently.

You can read more about this in the two original papers, and a just published commentary.

Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods

Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination

Commentary: Synthetic genome engineering gets infectious

JCVI Launches New Internship Partnership with Smithsonian Science Education Center

Are you passionate about science education? If so, we have a unique hands-on opportunity for you to be a part of real teams of scientists and educators. This opportunity doesn’t require any previous lab experience, and is open to undergraduate and graduate students in the United States.

The internship will be split between the J. Craig Venter Institute (JCVI) and the Smithsonian Science Education Center (SSEC). At JCVI you will participate in cutting-edge research. This will dovetail into curriculum enhancement previously developed at the SSEC, which aligns with the U.N.’s Global Sustainability Development Goals (SDGs).

This is an excellent opportunity for both science majors who may be interested in pursuing a path in education, and for education majors looking to gain valuable experience in a professional laboratory.

Space-fill drawing of the outside of one Zika virus particle, and a cross-section through another as it interacts with a cell. Image courtesy David Goodsell.

What will do you?

At the JCVI, you will work on a part of a larger project geared towards the development of rapid tests for virus genes that suppress host antiviral defenses. The project, which will focus on the mosquito-borne Zika Virus Disease, will use synthetic biology techniques to help scientists identify virulent strains.

At the SSEC, you will work with curriculum developers and experts in the field of global science education to support the development and rollout of the SSEC’s curriculum module “Zika!,” which helps students understand mosquito-borne diseases through inquiry-based science education methods.

The outcomes of this internship will lead to not only a better understanding of current research being done in the field, but will also result in the development of effective ways to communicate scientific research to the public.

Apply on our website today!

The 2017 JCVI Summer Internship Program

JCVI’s long-running internship program just concluded its summer 2017 session with a well-attended poster symposium held in both its Rockville and La Jolla locations. Eighteen of our interns presented their research in a session open to all JCVI faculty and staff. Montgomery College professors and staff attended, as well to support our Genomic Scholar Program (GSP) Interns in Rockville.

2017 Rockville Interns

2017 Rockville Interns

This past session was one of our most competitive yet, with over 1700 unique candidates applying to the program. A total of 20 interns took part in the program, 10 at each campus. Of the entire intern cohort, eight were part of our Genomic Scholar Internship Program (GSP), which is a 15-month long internship focused on helping community college students transition successfully into a four-year university. This year, the GSP was excited to include a bioinformatics intern into the program for the first time. Four of our GSP interns successfully completed their internship and are continuing their undergraduate careers at various universities, including Georgetown University, University of Maryland and UC Davis. Our remaining GSP cohort will be staying on throughout the academic year as they continue their studies at local universities.

2017 La Jolla Interns

2017 La Jolla Interns

JCVI strives to prepare future scientists by exposing them to multiple facets of scientific research as well as the professional working environment. During our summer internship program, interns not only conduct their own research project and present their findings to the JCVI community, but also are involved in a variety of professional development activities. Our interns participate in a weekly journal club, which exposes them to current scientific literature. There they present and discuss a scientific journal article selected by JCVI mentors. JCVI also holds a weekly intern-only seminar series, where our cohort has the opportunity to learn more about JCVI research, talk with graduate students and learn about different career options in the field of science.

Hands-on informatics training with Rockville interns

Hands-on informatics training with Rockville interns

If you are interested in JCVI’s internship program, please check our website for additional information and updates about our upcoming 2018 summer session.

Scientist Spotlight: Brett Pickett, Ph.D.

The son of a dentist, Brett Pickett grew up in Salt Lake City, Utah focused initially on a career in the family business (his siblings are hygienists and an oral surgeon). Brett believed from an early age that he would follow in his father’s footsteps. He enrolled in Brigham Young University committed to dental school. It was not until Brett’s zoology major was canceled that he became a student of microbiology, where he began researching antibiotic resistance genes in gut microbiota. Dental school was out. Brett received his B.S. in microbiology and continued his studies at the University of Alabama at Birmingham (UAB).

Brett Pickett

While working in UAB’s bacteria pathogenesis labs, Brett’s path would take another detour as he encountered West Nile, Hepatitis C, and Dengue viruses in his work. He also began to cultivate an interest in computers, technology, and statistics as it related to biological data. These experiences have led to him to his current field of research: viral bioinformatics.

In 2010, Brett moved to the University of Texas Southwestern Medical Center at Dallas to begin his postdoctoral research with Dr. Richard Scheuermann (presently the Director of JCVI La Jolla). Working with Richard, Brett began to shift his focus on how a virus behaves to examining how the human host is responding to being infected. While at UT Southwestern, Brett worked with Richard and his team to identify and develop new statistical, analysis, and visualization tools for the National Institutes of Health (NIH)-funded Viral Pathogen Resource Bioinformatics Database (ViPR). In 2012, Brett moved his family to La Jolla to be a part of JCVI’s informatics team. During this time, his work focused on enhancing the Virus Pathogen Resource and Influenza Research Database bioinformatics resource centers.

Brett stepped away from JCVI for a brief period to work at Thomson Reuters. There he analyzed “-omics” data with pathway analysis and network-building tools, together with drugs and protein target information to better understand viral infection, differences between pathogenic and commensal bacteria, oncology, and other therapeutic areas. This experience allowed him to gain a better understanding of human genetics, disease profiling, and biomarker identification before returning to research at JCVI in 2016.

At JCVI, Brett continues to work on cutting-edge science. He appreciates “the access to collaborators to solve big problems,” and Brett’s efforts are addressing the world’s biggest health challenges. He recently received funding from the US Agency for International Development (USAID) to develop a method for differentiating antibodies against Zika and other closely-related viruses in human patients.

Brett lives in San Diego with his wife and five children. When he is not in the lab, Brett enjoys golf, waterskiing, playing the piano, and visiting the beach with his family. His children, ranging in ages from 1-11, want to be scientists or doctors when they grow up. While there may be no dentists in this generation either, it is clear Brett’s children will have inspirational and accomplished footsteps in which to follow.

Summer 2016 Intern Program

Interns in both Rockville, MD and La Jolla, CA participated in our summer 2016 internship program at the J. Craig Venter Institute (JCVI). A total of 19 interns were hired for the summer 2016 program, selected from 578 applicants. Of the 19 interns, six interns were part of the Genomic Scholar Program (GSP) that is a transition program focusing on the leap from a community college to a four-year college using a combination of activities including undergraduate research experience with mentoring and professional development. The interns were mentored by JCVI faculty and research scientists. Mentors design a research project for each intern depending on their education and prior research experience.

GSP interns Emily Samuels, Rolande Tra Lou, Erica Ngouajio, Raja Venkatappa (mentor), Claudia Najera, Kat Rocha, Tayah Bolt (from La Jolla) and Kenya Platero gather at JCVI Rockville's poster session.

GSP interns Emily Samuels, Rolande Tra Lou, Erica Ngouajio, Raja Venkatappa (mentor), Claudia Najera, Kat Rocha, Tayah Bolt (from La Jolla) and Kenya Platero gather at JCVI Rockville’s poster session.

The involvement of fellows in individually focused research projects was designed to stimulate interest in biomedical research as well as to develop independent critical thinking and communication skills with other team members. In addition to research activities, throughout the summer interns participated in professional development activities that included:  education on the importance of documenting research activities and maintaining accurate laboratory records,  responsible conduct of research, the art of reading scientific literature (interns participated in weekly science journal clubs that aimed to teach how to dissect and interpret scientific literature), and scientific presentations. All the interns participated in JCVI internal presentations and presented their summer research as a poster.

Summer 2016 Interns gather for a picture in the courtyard at JCVI La Jolla.

Summer 2016 Interns gather for a picture in the courtyard at JCVI La Jolla.

A brief summary of 2016 interns summer research projects and their mentors are listed below.

Intern Name(s) Research Project Mentor(s)
Roshni Bhattachara Structural implications of unique substitutions found in a paralysis-associated enterovirus D68 clade Richard Scheuermann
Christopher Henderson Assessment of the Contribution of Ascertainment Cohort to the Genetic Architecture of Alzheimer’s Disease Nicholas Schork
Nathan Lian and Anthony Kang Experimental Validation of ChIP-Seq Identified Centremeres Philip Weyman
Rohith Kodukula The Oral Microbiome of Caries in Children: A Study on Twins Andres Gomez
Ian Lamb Identifying Bacterial Antibiotic Resistance Markers in gut microbes Manolito Torralba
Stephanie Mountain Hydrogen peroxide tolerance variation among different isolates of Acinetobacter baumannli Mark Adams and Meredith Wright
Kathryn O’Nell Cell-Type Clustering in Cortical Brain Cells via differential Expression Analysis of Single Nuclei Richard Scheuermann
Josefa Rivera Identifying new promoter elements in Phaeodactylum tricornutum Vincent Bielinski, Philip Weyman, and Chris Dupont
Jennifer Tuman Pan-Cancer Analysis of Somatic Mutations in DNA Damage Repair Genes Alexandra Buckley  and Nicholas Schork
Ben Grimes Using Synthetic Biology Methods to Engineer Herpes Simples Virus-1 and Mycoplasma mycoides subspecies capri Genomes Suchismita Chandran and Sanjay Vashee
Nicolette Maragh Technical Improvements of Sample Preparation for Proteome Analysis Yanbao Yu
Claudia Najera (GSP fellow) Using Synthetic Biology to Engineer Herpes Simplex Virus Type 1 Lauren Oldfield and Sanjay Vashee
Erica Ngouajio (GSP fellow) Developing a method to optimize sequencing of the Zika virus genomic termini Kari Dilley and Reed Shabman
Tayah Bolt (GSP fellow) Reduction of GUS Activity in Phaeodactylum via Episomal hpRNA Expression Philip Weyman
Alexandra Rocha (GSP fellow) Fibronectin and LRG1 protein interactions in T1D patients Rajagopala Venkatappa
Emily Samuels (GSP fellow) Cloning and Expression of proteins in Zika Virus and Legionella pneumophila in E. coli Keehwan Kwon
Rolande Tra Lou (GSP fellow) Filovirus-human protein-protein interaction Reed Shabman and Rajagopala Venkatappa
Carolina Hatanpaa Constructing a Novel Hidden Markov Model for a tRNA Binding Domain Architecture in the Minimal Cell Granger Sutton and David Haft

Scientist Spotlight: Anna Edlund, Ph.D.

Although Sweden is synonymous with Ikea, Volvo, meatballs and ABBA, the country has had a significant impact on science and discovery as far back as the 17th Century. Scientist Anna Edlund, Ph.D. who recently joined JCVI is another Swede pushing the boundaries of discovery in her new role as Assistant Professor, Department of Genomic Medicine.

Anna Edlund, Ph.D.

Anna Edlund, Ph.D.

Anna grew up in the middle of nature on a horse farm in the northern part of Sweden. Inspired by her country’s natural beauty and wilderness, she grew to care a great deal about the environment. During her first years at Södertörn University College she studied ‘green ecology’ and population genetics while she kept her job as a ranger for the Swedish Environmental Protection Agency working in a National park. Dr. Janet K. Jansson first introduced Anna to microbiology during an undergraduate course, and she immediately became fascinated with the unexplored world of microbes – she could not resist becoming a microbiologist. Anna finished her studies at the Karolinska Institute with a Master’s in microbiology and molecular biology. Under the guidance of Dr. Jansson, she pursued her Ph.D. studies in microbiology at the Swedish University of Agricultural Science in Uppsala. Between 2002 and 2007, she studied marine biology specifically exploring the microbial life in sediments of the Baltic Sea. She continued her education in marine microbial ecology as a Postdoctoral Scholar at Scripps Institute of Oceanography at the Center for Marine Biotechnology and Biomedicine, and ultimately returned to Sweden as an Assistant Professor at the Department of Systems Ecology at Stockholm University.

Anna’s trajectory changed in March 2012 when she returned to California at the invitation of Dr. Jeff McLean, a former JCVI scientist and pioneer in the human oral microbiome. As a Project Scientist and Postdoctoral Fellow at UCLA’s School of Dentistry and JCVI, Anna turned her focus from studying bacterial ecological functions in the marine environment towards understanding the role of the oral microbiome in human health.

As a scientist at JCVI, Anna’s research focuses on the complex human oral microbiome and how bacterial gene expression and signaling molecules orchestrate the development of both health and disease associated communities. Anna joined the team at JCVI to work with world-leading experts in microbiology in an environment where most of her time can be spent doing research.

Recently, Anna received a three-year award of $750,000 from the National Institute of Dental and Craniofacial Research (NIDCR) to investigate oral pathogen virulence within complex oral biofilm communities. Her goal is to deepen our knowledge of the molecular processes of oral biofilms during stress and disease-like conditions (e.g. pathogen invasion, low pH). She hopes her findings will lead to improvements in treating and preventing oral diseases.

Research Impact: Accelerating Efforts to Contain and Prevent the Zika Virus (ZIKV)

The rapidly developing Zika virus (ZIKV) outbreak has research groups, government agencies, and industry is all striving to develop a response plan to contain and ultimately prevent ZIKV spread. Currently JCVI is working with both private and public sector funders to sequence and analyze historical and current ZIKV strains. Work at JCVI is geared toward developing sensitive ZIKV diagnostics, significantly increasing the number of ZIKV genomic sequences available, and performing cutting-edge analysis on current and future sequence data.  We expect these efforts to guide the rational design of ZIKV antivirals and vaccines to treat and prevent ZIKV-induced disease.   Here we highlight areas of ongoing ZIKV related work at JCVI.  In each area, additional funding would accelerate our efforts to understand and ultimately control ZIKV infection in the human population.

ZIKV

As of October 12, 2016 the Centers for Disease Control and Prevention reported 3,936 cases of ZIKV infection, with two Florida cities identified as the Ground Zero for local transmission.

ZIKV sequencing efforts at JCVI: 

  • JCVI, through an existing NIH funded grant, is working with the Biodefense and Emerging Infections Research Resources Repository (BEI Resources) to provide high quality sequence data for publically available ZIKV strains. These strains represent a collection of ZIKV isolates, ranging from the initial 1947 isolate from Uganda to 2015 isolates from Puerto Rico, Colombia, and Panama, Mexico, and Honduras. JCVI is providing the gold standard annotated reference sequence for all strains available from BEI and will continue this effort as BEI obtains additional ZIKV isolates.
  • Shortly after the recent Zika virus outbreak emerged in eastern Brazil, Dr. Richard Scheuermann and his bioinformatics team at JCVI collaborated with software engineers at Northrop Grumman to develop a custom Zika website portal to provide genomic sequence and other data about Zika virus through the public Virus Pathogen Resource (ViPR). As of September 2016, the ViPR Zika portal contains 389 genomic and 2399 protein sequences representing the three major Zika lineages – East African, West African and Asian. To support comparative genomics analysis to investigate the evolution of virulence in the newly emerging outbreak isolates, Scheuermann’s group developed an algorithm for predicting the proteolytic cleavage sites that generate Zika mature peptides, and applied this method to produce a comprehensive record of all predicted mature peptides for all Zika genomic sequence in the ViPR database.
  • JCVI is currently working with collaborators in Colombia and Nicaragua to collect sera from patients suspected to harbor ZIKV and to sequence the viral genome from these patients.
  • JCVI was recently awarded NIH supplemental funding to work with Sanofi-Pasteur to screen and sequence human samples suspected to be positive for ZIKV. The majority of samples, provided by Sanofi, are from children and adolescents from the Americas and the South Pacific where mosquito transmitted viruses are common. Over the upcoming year, JCVI anticipates screening both retrospective and prospective human serum samples for ZIKV, with the assumption that many of these samples are from individuals infected with other viral diseases (e.g. Dengue Virus).

Toward the development of a rapid ZIKV diagnostic:

  • Brett Pickett recently received funding from the US Agency for International Development (USAID) to develop a method for detecting antibodies against Zika virus in human patients. A bioinformatics analysis performed previously at JCVI uncovered regions of Flavivirus proteins that differentiate between 10 species of viruses—including Zika. Custom peptide arrays will be constructed to identify immunodominant epitopes in human serum, which we will then optimize as an ELISA-based diagnostic for use in developing countries.
  • To distinguish between ZIKV and other viral diseases, we are developing a highly sensitive and specific ZIKV diagnostic PCR assay.
  • Our assay is sensitive, and we have demonstrated the ability for the assay to identify ZIKV from diverse geographical regions. Future work seeks to move this technology from the laboratory to the field.

Next generation vaccine technology at JCVI can be applied to ZIKV:

  • JCVI has previously coupled synthetic biology for the rapid generation of an Influenza vaccine.
  • Currently, JCVI is using both synthetic biology and vaccinology to develop a universal vaccine for the common cold in partnership with Synthetic Genomics (A company founded by Dr. Venter) and private funders
  • The established vaccine technology at JCVI and our ability to rapidly identify and sequence ZIKV would allow the institute to pursue novel ZIKV vaccine platforms.

Mosquito genomic sequencing:

  • JCVI is currently sequencing the genome of a mosquito that is known to harbor ZIKV and is present in the Americas.
  • Determining the genomic sequence of this mosquito will help research groups identify develop targeted approaches to impair ZIKV replication in the mosquito host.

Current efforts to combat Zika virus involve CLIA-approved methods to detect viral genetic material. In addition, there are multiple players currently developing a vaccine including GlaxoSmithKline, Sanofi, and Onovio Pharmaceuticals. Ensuring that any vaccine doesn’t cause any neurodevelopmental problems further complicates these efforts. Vector control departments around the United States are currently spraying to eradicate adult and larval mosquitoes. While these endeavors serve to prevent virus infection and spread through mosquitoes, they have negatively affected bee populations and organic crops—potentially increasing public acceptance of sterile GMO mosquitoes.

One of the key questions that arose as a result of the Zika outbreak in the western hemisphere is if the virus has mutated to become more virulent, causing more severe neurological pathology than previously circulating strains.  Comparative genomics analysis using sequences and analysis tools in ViPR has identified both nucleotide and amino acid substitutions in the outbreak lineage that warrant further investigation to determine if they are responsible for the apparent increased virulence of the new outbreak strain.  With the detection of mosquito-borne transmission in Puerto Rica and the continental US, there is now a critical need for more funding for further research into the genomic determinants of virulence and for accelerated development of targeted diagnostics, therapeutics and vaccines. Donate today!

Genomic Workshop for Native American College students

A Genomic Science Workshop was held  last week (May 24-26, 2016) at the J Craig Venter Institute Rockville campus for a group of ten Native American college students.  The students participated in two full-day intensive training activities learning how to study the “microbiome” of natural water sources. Each student had the chance to perform hands-on lab work including DNA isolation from an environmental water source, PCR of the 16S ribosomal RNA gene, and gel electrophoresis. Individual computer workstations were provided for the computer lab sessions for students to follow along.  The group was introduced to basic Linux command-line analysis and the popular 16S analysis package QIIME. Overall, the workshop provided the students a foundation of knowledge and tools to identify and classify microbial populations in environmental water sources, and enabled the students to participate in water quality analysis and monitoring efforts of their homeland reservations.

Collage from Maize Cell Genomics Workshop for Undergraduates

Collage from Genomic Workshop for Native American College students

The workshop students were welcomed by JCVI President Karen Nelson and Rockville Campus Director Rembert Pieper. Informal discussion panels were also held to provide networking and research career development opportunities with invited guest speakers including Science Education Directors from the Howard Hughes Medical Institute (HHMI), and Native research scholars from the National Institute of Health (NIH). The students were also presented with a preview of the astronaut microbiomes as an application of human microbiome study. Workshop students also had the opportunity to visit the US Capitol and the National Museum of the American Indian.

The workshop was funded by the National Science Foundation through a Maize Cell Genomics grant and was organized by Agnes Chan (JCVI; co-PI), in collaboration with the Cold Spring Harbor Laboratory (CSHL; PI Dave Jackson, Outreach Educator Joslynn Lee), the University of Wyoming (UW; co-PI Ann Sylvester), Montana State University (Mari Eggers), and the Little Big Horn College (LBHC; John Doyle).  LBHC is a tribal college located in the Crow Reservation, MT. The NSF Maize project has established a long-term outreach relationship with LBHC, and has organized a number of training workshops for Native students previously at LBHC, UW, and CSHL. Participants for the 2016 workshop included Native students recruited from the LBHC, Montana State University, Fort Lewis College, and Northern Arizona State University.

The PIs of the Maize Genomics Project would like to express sincere thanks to instructors from JCVI including Hernan Lorenzi, Yongwook Choi, Vivek Krishnakumar, Stephanie Mounaud,  the JCVI Information Technology team, the Administrative Assistant team, and all colleagues for their generous assistance, support, and patience for a successful outreach educational workshop.

To find out more information on workshop schedule, notes, and manuals, please visit the Maize Cell Genomics project web site at http://maize.jcvi.org/cellgenomics/2016_pcr.php.

Ongoing Zika virus work at JCVI

The rapidly developing Zika virus (ZIKV) outbreak has research groups, government agencies, and industry all striving to develop a response plan to contain and ultimately prevent ZIKV spread. Currently JCVI is working with both private and public sector funders to sequence and analyze historical and current ZIKV strains. Work at JCVI is geared toward developing sensitive ZIKV diagnostics, significantly increasing the number of ZIKV genomic sequences available, and performing cutting-edge analysis on current and future sequence data. We expect these efforts to guide the rational design of ZIKV antivirals and vaccines to treat and prevent ZIKV-induced disease. Here we highlight two areas of ongoing ZIKV related work at JCVI.

Zika virus

This is a digitally-colorized transmission electron micrograph (TEM) of Zika virus, which is a member of the family Flaviviridae. Virus particles, here colored red, are 40 nm in diameter, with an outer envelope, and an inner dense core. Image credit: CDC/ Cynthia Goldsmith

JCVI/BEI Resources/NIAID: JCVI, through an existing NIH funded grant, is working with the Biodefense and Emerging Infections Research Resources Repository (BEI Resources) to provide high quality sequence data for publically available ZIKV strains. These strains represent a collection of ZIKV isolates, ranging from the initial 1947 isolate from Uganda to 2015 isolates from Puerto Rico, Colombia, and Panama. JCVI is providing the gold-standard annotated reference sequence for all strains available from BEI and will continue this effort as BEI obtains additional ZIKV isolates. A list of the ZIKV isolates sequenced by JCVI are found here: https://www.beiresources.org/Organism/118/Zika-virus.aspx

JCVI/Sanofi-Pasteur/NIAID: JCVI was recently awarded NIH supplemental funding to work with Sanofi-Pasteur to screen and sequence human samples suspected to be positive for ZIKV. The majority of samples, provided by Sanofi, are from children and adolescents from the Americas and the South Pacific where mosquito transmitted viruses are common. Over the upcoming year, JCVI anticipates screening both retrospective and prospective human serum samples for ZIKV, with the assumption that many of these samples are from individuals infected with other viral diseases (e.g. Dengue Virus). To distinguish between ZIKV and other viral diseases, we are developing a highly sensitive and specific ZIKV diagnostic assay. After confirming ZIKV positive samples, JCVI will perform whole genome sequencing and sequence analysis to understand the evolution of the virus over time and geographical location. We hope that results from this collaborative work will significantly increase our understanding of the origins of the ZIKV outbreak in the Americas and lay the groundwork for future collaborations with NIAID and Sanofi.

Unlocking the Mysteries of the Microbiome

In the early 2000s, JCVI researchers pioneered in the exploration of the human microbiome, the community of microbes that live in and on the human body. Originally while at The Institute for Genomic Research (TIGR, now part of JCVI) Drs. Craig Venter and Hamilton Smith were awarded a grant from DARPA to examine the microbes found in the human gut.  This work was carried out by researchers at JCVI and published in 2006 in Science.  While this team had previously published 16S surveys of the human body, this paper in which the researchers found more than 60,000 microbial genes was the first metagenomic description of microbes resided anywhere on the human body.  Ten years since this seminal publication, our scientists continue to pave the way for a broader understanding of these vast microbial populations.

fragment recruitment plot

Visualization of ocean microbial data collected on JCVI’s Global Ocean Sampling Expedition (GOS). The Sorcerer II circumnavigated the globe for more than two years, covering a staggering 32,000 nautical miles, visiting 23 different countries and island groups on four continents.

On May 13, 2016, Drs. Craig Venter and Karen Nelson were present at the White House for the launch of the National Microbiome Initiative (NMI).  The NMI will invest $121 million in new microbiome studies in fiscal years 2016 and 2017.  The goals of the project are to supplement fundamental research, develop new technologies and engage more people in this area of research.

Today we know that the human body is host to more than 1 trillion microbes. Thanks to continued advances in genome sequencing technologies and metagenomic analysis JCVI scientists are providing a deeper understanding of these microbes across a variety of fields. JCVI researchers know that translating the role of the microbiome in the development of health and disease in humans is essential.  We believe that eventually the screening of the human microbiome will be a routine part of medical care, leading to prescribed diets and preventive measures personalized to an individual.

JCVI currently has several dozen microbiome studies underway.  In this issue of Amplifier, we are highlighting some of our most exciting and cutting edge work unlocking the mysteries of the human microbiome.

The Effects of Long-Term Space Travel on the Microbiome of Astronauts

On March 1, the world celebrated the safe return of NASA astronaut Scott Kelly after 340 days in space.  Researchers are fascinated to learn more about the impact of long-term space travel on the human body, and JCVI scientists are excited to be a part of the process.  During a mission to space, astronauts are subject to many stressful conditions (g-forces, radiation, microgravity, anxiety, etc.) that can have a negative impact on their health. For example, astronauts lose muscle mass, bone density, and experience a wide range of health problems with everything from their vision to their gastrointestinal tract. Several studies have demonstrated that space travel also affects the astronauts’ immune systems (for example the reactivation of latent viruses like Herpes Simplex Virus 1 and Epstein Bar virus) and have shown some evidence suggesting that stool microbes change after space flight.

JCVI researchers want to determine how the composition of the astronauts’ microbiome changes during long-term space missions (six or more months), and to evaluate potential risks to astronaut health from changes in the microbiome. We are also interested in how the microbiome of astronauts interacts with other factors such as the microbial communities that inhabit the International Space Station (ISS). To accomplish this, we will monitor the astronauts’ health status, environmental stress, and exposure to space conditions. The skin, tongue, nose and gut of each astronaut will be sampled at multiple time points before, during, and after the mission to the ISS. By sampling the microbiome of astronauts on earth while in peak physical health and during subsequent space flight, we will be able to define signatures of human response to a variety of relevant aspects of space travel. Astronauts will also sample different surfaces and the water supply during their stay at the ISS to correlate crew microbiomes with the microbes living at the ISS. We will also assess changes in the astronauts’ immune function and stress levels throughout the mission by analyzing their saliva and blood for metabolic markers. Finally, we will correlate the microbiome and immune function data collected with other measured metadata including astronaut health and hygiene as well as environmental factors such as temperature, humidity and environmental factors.

This research program is being led by Dr. Hernan Lorenzi.

The Gut Microbiome and Human Evolution

Who we are, where we come from and how we came to be as we are, are questions that have always fascinated biologists. The reasons to answer these questions are multiple, but one critical aspect centers on understanding what makes us human. To start addressing these issues JCVI scientists are exploring the gut microbiome of non-human primates, our closest living relatives, and of populations that most faithfully reflect the lifestyles of early hominids: hunter-gatherers. The goal of this project is to establish an evolutionary baseline to shed light on the host-microbe factors that impacted health and disease in modern and western human populations.

Our scientists have shown, in several recent publications, that the gut microbiome of wild gorillas, is strongly shaped by the external environment, namely by diet. Specifically, we showed that gut microbes adapt to different dietary stimuli, probably providing gorillas with energetic plasticity when preferred feeding resources are seasonally and temporally absent. Interestingly, we also suggested that, in conditions in which gorillas exploit high-energy diets, their gut microbiomes resembles those of humans. This fact has critical implications to understanding the evolutionary origins of obesity and inflammation in modern human populations from a microbe perspective. Along these lines, our most recent publication on the gut microbiome of central African hunter-gatherers, traditional agriculturalists and western humans shows evidence that transitions to agriculture and industrialization, and giving up hunting and gathering could have radically changed our gut microbiomes for good. This observation is vital considering that traditional hunter-gatherers, whose microbiomes resemble those of wild gorillas, do not show symptoms of modern inflammatory disease. These observations highlight the potential impact of gut microbes in human evolution.

The research team consists of  Drs. Andres Gomez and Karen Nelson.

Solving Crimes with Your Microbial Signature

In January 2016, JCVI received a two-year, $962,500 award from the United States Department of Justice to design and build an open-access microbiome database for the forensic science community. The Forensic Microbiome Database (FMD), the first of its kind will be populated with several thousand microbiome datasets and associated metadata available from the public domain. The database will be based on established procedures for database development designed at the JCVI, incorporating expansive sets of data and metadata that relate to forensic evidence.

The goals of this project are to: provide a host location and continuous monitoring of the database; define well-structured standard operating procedures for data generation and searching against and uploading data into the FMD; and test the utility of the FMD by sequencing a range of samples obtained geographically for querying and proof of concept against the database. The foundation of this project will serve for future enhancements of the FMD and utility for forensic casework. The research team expects this will become the community resource for analysis of microbiome data and for attributing weight to microbial forensic evidence.

The research team consists of Rhonda Roby, Lauren Brinkac, Toby Clarke, Andres Gomez, Karen Nelson, Harinder Singh, and Shibu Yooseph,

Using the Microbiome to Advance Wound Therapies

Chronic wounds are wounds that fail to heal after 4 months of proper wound care and management.  It is a major public healthcare burden that affects an estimated 1% of the US population and costs $25 billion per year. Common chronic wounds are leg, foot, and pressure ulcers occur in adults especially the elderly with diabetes, vascular diseases, or specific body locations under prolonged pressure. According to the Centers for Disease Control and Prevention, approximately 12% of U.S. adults with diabetes had a history of foot ulcer and 11% of U.S. nursing home residents had pressure ulcers. In addition to the economic burden, from the perspective of patients chronic wounds can also lead to loss of function (e.g. amputation), decreased quality of life, and increased rate of mortality.

At JCVI we are interested in deciphering not only the microbial communities present in chronic wounds but also their potential impacts and relationship with the wound healing outcome, for working towards more effective clinical strategies of wound healing. In collaboration with George Washington University, we are conducting a study to analyze chronic wounds. Samples are selected from patients enrolled in the Wound Etiology and Healing biospecimen and data repository (WE-HEAL). We will analyze the chronic wound microbiome at the molecular level, and attempt to identify biological indicators that can be used to predict the healing outcome to further advance wound therapies and management.

This project is being led by Dr. Agnes Chan.

Metagenomic Epidemiology of Antibiotic Resistance in Infectious Diarrhea

Genes that encode antimicrobial resistance (AMR) to antibiotics have been detected in environmental, insect, human and animal metagenomes and the sum of these are known as “resistomes.” While metagenomic datasets have been mined to characterize the healthy human gut resistome, directed metagenomic sequencing has not been used to examine the spread of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate AMR elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple AMR in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia.

Sarah Highlander, Ph.D. and her team are characterizing the microbial composition and its component AMR transfer elements (such as plasmids and transposons) by metagenomic sequencing of stool samples from pediatric patients from Colombia who are suffering from diarrhea. Our goal is to assess whether groups of species/strains associate with specific mobile genetic elements and whether their presence is enhanced or amplified in diarrheal microbiomes. This work could potentially identify clonal complexes with enhanced resistance and potential pathogenesis.

For more information on how you can support or human microbiome research program at JCVI, please contact development@jcvi.org.