Posts in category Microbial & Environmental Genomics

Ocean Sampling Day 2018

J. Craig Venter Institute (JCVI) scientists, led by Lisa Ziegler Allen, PhD, are collaborating with Kelly Goodwin, PhD (NOAA), Brian Palenik, PhD (UCSD), and Maitreyi Nagarkar (UCSD) to participate in this years’ Ocean Sampling Day on June 21. The team, which also includes Sarah Schwenck and Ariel Rabines from JCVI, is sampling the water off the pier at Scripps Institution of Oceanography (SIO).

Ocean Sampling Day participant sites since 2014.

Ocean Sampling Day (OSD) is an international effort to simultaneously sample the world’s oceans in one day, with the first such event happening in 2014. Following the success of the first event, the OSD consortium has held an event each year since, with continued long-term support from the EMBRC ERIC infrastructure.

Ocean Sampling Day 2014 with local Girl Scout groups.

JCVI Global Ocean Sampling Program

JCVI has a long history of ocean and environmental sampling, beginning in 2003 with a pilot study in the Sargasso Sea. This led to a two-year effort where JCVI scientists circumnavigated the globe, covering a staggering 32,000 nautical miles, visiting 23 different countries and island groups on four continents. Millions of new genes and nearly 1000 genomes for uncultivated lineages of microbes, as well as a more comprehensive understanding of marine microbiology through community datamining resulted from this historic project. JCVI has been engaged continually in these efforts since, culling the oceans, rivers, lakes, soil, and air to learn about the distinct microbial communities that inhabit each.

J. Craig Venter Institute Makes Strides in Microbial Analysis of Artwork which May Lead to Better Preservation Techniques

Through the Leonardo da Vinci DNA Project, researchers at J. Craig Venter Institute (JCVI), led by Karen Nelson, PhD, began taking environmental samples from different pieces of aging artwork with the aim of understanding which microbial species are present on varying surfaces and how these communities affect preservation efforts. This area of research also has broader forensic archaeological implications. JCVI hopes to use these methods to study Renaissance period artwork in the near future.

The speakers and participants of the Leonardo da Vinci DNA Project May 2018 Conference.

This past week the Leonardo DNA Project team met in Florence, Italy where they held public lectures on the overall progress of the project and to plan next steps. Findings from the microbial analysis component of the project, for which JCVI is responsible, were presented by Manolito Torralba.

One-hundred forty-two art surface samples were catalogued, the first of which was taken in December of 2015 and the second group in May of 2017. Each work sampled had on average three sites tested. The base materials for the works includes stone, wood, canvas, metal, and plaster—some of which were painted on.

Artwork sampled in May of 2017 from a private collection.

Using a statistical modeling process, principle coordinate analysis (PCoA), researchers have shown that samples from the same substrate, or base material, cluster and that there is some overlap between stone/marble and wood microbial communities.

JCVI researchers report that oil degrading species are present on canvas areas in deteriorated states. Additionally, oxidase positive organisms, which may be responsible for further breakdown in the art, are in high abundance on painted surfaces.

Additional samples from May of 2017. In total, there were 96 swab samples collected at this time (48 DNA and 48 RNA).

Future aims of the microbial analysis component of the project include 1) expanding they types of art being sampled to include fresco, painting on animal hides, other stone types, and glass; 2) confirming the presence of oxidase positive elements through metagenomics and metatranscriptomics sequencing; 3) identifying fungal species using molecular markers; and 3) using genomics to identify authenticity and geographical origin of works of art.

Project Background

The Leonardo DNA Project’s broad aims are to conclusively determine if the remains purported to be those of Leonardo da Vinci at Amboise Castle are his, by comparing DNA profiles to those of known relatives. Additionally, it will look at genetic markers using whole genome sequencing from Leonardo’s remains to better understand his extraordinary talents and visual acuity through genetic associations. Also, using novel informatics approaches researchers will create three dimensional images of Da Vinci using the genome sequence data.

Funding for this project provided by The Richard Lounsbery Foundation.

BioVision Alexandria 2018

The BioVision Alexandria conference convened at the Bibliotheca Alexandrina, in Alexandria, Egypt this past April. The Bibliotheca Alexandrina is a commemoration of the Ancient Library of Alexandria and an attempt to rekindle the global cultural and scholarship role of the library.

Dr. Nelson delivering the keynote address at BioVision Alexandria.

With this backdrop, BioVison joined scientific and other leaders spanning disciplines to meet and listen to presentations on the most pressing challenges relating to poverty and human health. Among the distinguished participants was JCVI president, Karen Nelson, PhD, and senior scientist at JCVI and associate professor at the American University in Cairo, Ahmed Moustafa, PhD.

In 2015, through the United Nations Department of Economic and Social Affairs (UN DESA), a set of seventeen sustainable development goals (SDGs) was outlined and adopted by the international community. In keeping with these targets, BioVision’s theme this year was “New Life Sciences: Towards SDGs.”

Dr. Nelson meeting with BioVision conference participants.

In her keynote speech, Dr. Nelson spoke broadly about the impact of genomics and advances in microbiome research that may have significant impact on our ability to achieve and sustain these goals. Dr. Nelson also met with next-generation scientists, MS and PhD students from the Middle East and Africa and discussed topics from scientific and technical to career advising and opportunities.

Dr. Karen Nelson and attendees of her lecture at the American University in Cairo.

Other conference topics included open data, precision medicine, drug discovery, environmental genomics, synthetic biology, as well as the supporting framework provided through policy and economic reforms. The conference also focused on the need to foster scientific discovery in developing countries. Of the 25 represented nations in the speaking lineup, about half were developing countries.

After the conference, Dr. Nelson visited the American University in Cairo (AUC) in New Cairo where she gave a public lecture on genomics and health. The lecture went over the history of genomic technologies and discoveries and the envisioned future role of genomics in clinical diagnosis and therapeutics.

During her visit to AUC, Dr. Nelson met Dr. Yehia Zakaria Gad, the head of Ancient DNA in the Egyptian Museum. They discussed several potential venues of collaboration between JCVI and the Egyptian Museum.

Dr. Nelson also joined Dr. Hassan El-Fawal, Dean of AUC’s School of Sciences and Engineering, and graduate students from the engineering and sciences departments for a discussion on the critical role of bridging communications between scientists and engineers to advance improvements to the quality of human life.

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.

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

What Does It Really Mean to Be a Scientist?

In the spring of 2016, JCVI partnered with Del Lago Academy to provide internships for some of its students.

Junior Stephanie Mountain shares about her experience and what her time at JCVI taught her:

Being an intern at JCVI was an amazing experience I will never forget. I learned so much through this internship that I would have been unable to learn in school. I learned a lot about coding and the importance of using computers to analyze data that is generated in the lab. Through my classes at Del Lago I had a good amount of hands on lab experience, but this internship was completely different than anything else I had done previously. It exposed me to the opposite side of scientific research, the kind that isn’t in the lab. I had very minimal computer skills at the start, but now I know how to run command prompt, a little bit on two coding languages, R and Perl, and how to use the Mothur program to run data analysis.

Stephanie with her JCVI mentors, Drs. Zhong and Zhu, and her Del Lago teacher Marc Kibler.

Stephanie with her JCVI mentors, Drs. Zhong and Zhu, and her Del Lago teacher Marc Kibler.

It was really fun to work with my mentors and “help” them analyze their data. Granted, they probably could have done everything much faster and with less problems than me, but it helped me see what happens in a day of the life of a researcher. Before this internship, I wanted to be a scientific researcher, but in my mind that meant doing strictly wet lab stuff. Now, I know that being a scientific researcher means a lot more than I had previously though. All of the computer stuff I did was really fun and cool, and it kind of surprised me how much math was involved in all of the computer things. I’m definitely going to take some computer science classes in college if I get the opportunity to. The math associated with computers seems really challenging and fun, and a lot less like a black box where I press buttons and the computer gives me stuff I want.

Overall, this internship has been eye opening to a new side of scientific research I didn’t know existed. All of the things I learned were really interesting and new. I now know that I really would love to be a scientific researcher in the future.

Junior Janine Vasquez worked with Dr. Orianna Bretschger, Dr. Sofia Babanova, and Jason Jones to research the development of microbial fuel cells for wastewater treatment. One big part of that research…pig poop!

I first want to thank everyone for allowing us to have the privilege to work with JCVI. I learned so much throughout this internship and I was able to get a lot of hands-on experience. During this internship, I learned the process of collecting data, running tests and analyzing the results. Our project was to run COD tests to see how different amounts of NaCL would affect the COD readings.

When we first arrived at the farm at San Pasqual, I did not know what I would be doing. When I found out that one of my tasks was to blend pig feces, I was really surprised. At first it was hard because I was still getting used to the smell but after a while, I surprisingly was not bothered by the fact that I was blending pig feces in a blender. I really enjoyed getting the experience of working in the farm and the lab. Some of my friends who also worked in a lab setting only got one side of the experience. Anabel and I were able to experience more than one working setting and I found that interesting.

One thing that I felt was kind of challenging was actually meeting new people. I am not really a social person but I tried to get out of my comfort zone; in the end, I got to meet great people. This internship really made me think about my future. I’ve always had this mindset that people in this industry only work in labs all day and I realized that is not true. I was actually relieved to find out that projects like these have you working in all kinds of places because I like trying different things and working in different work settings. This experience made me realize that this is something that I may want to do in the future.

JCVI is committed to helping youth pursue careers in science. To join our efforts, please contact Education Manager Amani Rushing at

JCVI’s Global Voyage of Discovery Continues

Global Ocean Sampling Expedition Planned for 2016

Over the past 12 years, JCVI’s Global Ocean Sampling (GOS) Expedition has continued to explore all of the world’s oceans, along with major inland seas such as the Baltic and Mediterranean.  The research team maintains ongoing sampling in the waters off of California and in extreme conditions such as Antarctica and the Amazon River.  JCVI’s effort is the largest marine microbial study to date, quantifying both the taxonomic and functional diversity of microbes within these environments, and examining how both the natural environment and humans shape these communities.

Planned 2016 route for the Sorcerer II Global Ocean Sampling Expedition

Planned 2016 route for the Sorcerer II Global Ocean Sampling Expedition

The scientific goals and ideas on the first Sorcerer II Expedition sprung from the sequencing and analysis of Methanococcus jannaschii by Dr. Craig Venter and his research team after the organism was isolated from a hot, deep-sea vent in the Pacific.  M. jannaschii is from the Archeal branch of life and is also known as an autotroph, in that it makes all it needs for survival from carbon dioxide, nitrogen, and hydrogen in water. Dr. Venter and the team continue to believe that the unknown and unseen world in the oceans is vital to understanding diversity on the planet and potentially holds the key to solving growing environmental issues.

The deck of the Sorcerer II is equipped with scientific tools including advanced water filtration and communications systems.

The deck of the Sorcerer II is equipped with scientific tools including advanced water filtration and communications systems.

Past GOS efforts have been funded by The Gordon and Betty Moore Foundation, the Beyster Family Foundation Fund, Life Technologies, and additional anonymous donors. To date, the GOS team has analyzed billions of DNA sequences and discovered over a billion new genes, 1700 unique protein families, and assembled dozens of whole genomes for uncultivated microbes.  The GOS data are freely available to the public and have resulted in follow-on research across several fields by scientists worldwide.   The GOS team utilizes a shotgun metagenomics technique to examine the presence and possible role of microbes in open ocean ecosystems.  JCVI has ongoing research internally and with international collaborators to characterize the unexplored microbiomes of marine, estuarine, freshwater, and terrestrial environments around the world.

Highlights of past and present expeditions:

  • The Gordon and Betty Moore Foundation was a significant funder of the first phase of the GOS Expedition from 2004-2006. To date, there are 41 publications from this phase, and an evaluation of the scientific impact of their support shows that these publications have been cited over 2700 times.
  • During the J. Robert Beyster and Life Technologies Foundation 2009-2010 Research Voyage of the Sorcerer II Expedition, aquatic samples were collected by filtration from over 300 aquatic environments in 12 nations and international waters, resulting in over 1100 possible metagenomic samples. The data generated has fostered collaborative projects between JCVI and institutions in eight nations and formed the focus of nine postdoctoral projects and five graduate student theses. The expedition extensively cataloged the microbial diversity and function of nearly all global oceans and marginal seas, and has further developed a mechanistic understanding for the distribution of microbes and function that can be applied to all aquatic environments.
  • In 2014, JCVI embarked on a sampling expedition of the Amazon River and its tributaries, which contains 1/5th of the Earth’s river flow. Long recognized for the biodiversity of visible organisms, the Amazon is understudied with regards to the diversity of microorganisms and the goal of this effort is to continue to increase our understanding of the biological diversity of Earth.
  • Since 2008, JCVI scientists have traveled to the continent of Antarctica. As one of the most untouched regions on the planet and home to the world’s largest marine ecosystem, Antarctica and the Southern Ocean are invaluable to JCVI research involving climate change. Major objectives of the fieldwork are to understand how changes in micronutrient availability, temperature, and pCO2 impact growth, community composition, and nutrient utilization in Southern Ocean phytoplankton.  Recently JCVI researchers in collaboration with Scripps Institute of Oceanography uncovered a series of complicated relationships among marine microbes in their fight for important resources, like vitamin B12, that has critical consequences for coastal Southern Ocean food webs. Scientists at J. Craig Venter Institute, Scripps Institution of Oceanography and Other Collaborators, Publish Paper Outlining New View of Microbial Relationships in Southern Ocean Phytoplankton Blooms.

2016 Global Sampling Expedition Addresses Plastic Pollution & Environmental Policy

The planned 2016 GOS Expedition, led by Chris Dupont, Ph.D., Assistant Professor, combines the basic science approaches of previous expeditions with applied science. The team plans to study the wide variety of marine protected areas (MPAs) found throughout the Caribbean Sea, the Florida Straits, the Gulf of Mexico, and the Sea of Cortez. The goal is to profile the ecosystem health of the MPAs and the impact to them by fishing, pollution, habitat degradation and climate change. With dramatic differences in the levels of protection of various MPAs, JCVI researchers will assess the conservation strategy of each MPA then evaluate the outcomes of those strategies on a microbial level, with the goal of making policy recommendations for better ocean preservation.

Chris also proposes to examine the microbes found on plastic pollution in the ocean.  Plastic is the most common type of marine litter in the world, and it is wreaking untold havoc on marine ecosystems. This pollution, currently 50 million metric tons per year, has been examined by JCVI researchers and collaborators in preliminary studies, and they have found that these plastics harbor microbes that are not normally found to be abundant in the ocean. With 100 million tons of plastic in the “Great Pacific Garbage Patch”—visualize Texas covered with plastic and floating in the Pacific Ocean, —there is a real and timely need to address the declining health of our oceans. Chris hopes that this research will not only further characterize what microbes are found on plastic pollution, but will also provide the genomic information necessary for building designer microorganisms for the biological degradation and recovery of plastic waste

Exploring the microbes of the oceans is even more exciting and promising than it was when JCVI launched the Sorcerer II Expedition from Halifax, Nova Scotia in August 2003. Each JCVI expedition has led to new discoveries that have deepened our understanding of the world’s waters.  What else will we discover in the coming months and years?  Whatever it may be, count on JCVI being at the forefront of the discovery.  There are many ways that you can support the next phase of discovery and help JCVI scientists find solutions to these environmental challenges.   For more information about our GOS expeditions, as well as details on partner opportunities for our 2016/2017 voyages, please contact Katie Collins,

June Grant Update

Congratulations to our JCVI Principal Investigators for the several successful grants that were awarded or that we received notification of in the month of June. All of the following PIs received official confirmation of awards to be made to them. Christopher Dupont, John Glass, Granger Sutton, Daniel Gibson, Charles Merryman, Rembert Pieper, Richard Scheuermann, Christopher Town, Reed Shabman, Orianna Bretschger, Sanjay Vashee and Sarah Highlander to the sum of $6,365,099. The topics of these awards ranged from synthetic approaches to studying the human microbiome, vaccine development, protein modeling, studies on tuberculosis strain diversity, and immune profiling.

Of notable mention are the awards to be made to Sanjay Vashee $1,879,282 from the NSF (BREAD supplement that will allow for an extension of the current program focused on developing a synthetic vaccine for Bovine pleuropneumonia), Reed Shabman from DHS ($1,135,654; The development and validation of sequence subtraction databases to improve virus discovery through next generation sequencing – special acknowledgement to Tim Stockwell and Derek Harkins for their contributions to this proposal), and to Chris Town from NSF ($883,704; Federated Plant Data Base Initiative for Legumes).

A sincere Congratulations to the team.

JCVI Scientist Tackles Global Sanitation Challenges

Orianna Bretschger received her B.S. in Physics and Astronomy at the University of Northern Arizona. After a five- year career in aerospace and consulting, she completed a Ph.D. in Materials Science at the University of Southern California. Eager to focus her efforts on alternative energy and sustainability, she joined the J. Craig Venter Institute in 2008. Over the course of her research tenure, Dr. Bretschger has established a productive team of researchers dedicated to understanding the fundamental mechanisms associated with extracellular electron transfer (a process that enables microbes to respire solid surfaces, i.e., “breathe rocks”) and applying that understanding to technology development for bioremediation, bioenergy, and water recycling.

Dr. Bretschger and team at White Labs with JCVI constructed reactor.

Dr. Bretschger and team at White Labs with JCVI constructed reactor.

Bretschger’s research group has secured over $11M of external funding from diverse resources including NASA, The State of California, The San Diego Foundation – Blasker Science and Technology Award, the National Science Foundation, the Office of Naval Research, Synthetic Genomics Inc. and the Roddenberry Foundation. Her publications have drawn over 800 citations and most recently includes an article in Nature Communications, which describes a novel metatranscriptomic method for understanding metabolic relationships in highly diverse (over 400 species) microbial communities and new findings related to how microbes share electrons. The approach developed by her team can now be applied to many different environmental samples and begins to unravel the complex interactions that exist in our sediments, soils, oceans and fresh water resources. These studies will shed new light on how our changing environment will impact ecosystem function.

Reacter installation at San Pasqual High School

Reacter installation at San Pasqual High School

Her applied projects include the development and integration of microbial fuel cell systems that can remove contaminants from wastewater and transform the waste into direct electrical energy. Bretschger’s most recent awards include a $5M grant from the Roddenberry Foundation to demonstrate her microbial fuel cell technology as a sustainable sanitation approach to address the sanitation and related public health impacts in Latin America.  Further, a recent award from SPAWAR Pacific will test her technology at an S.E.R.E training base outside of San Diego and demonstrate its effectiveness for providing cost-effective water recycling and wastewater treatment to our militaries forward operating bases.

UABC and JCVI teams showing local elementary student how to do titrations while testing water quality in Baja MX.

UABC and JCVI teams showing local elementary student how to do titrations while testing water quality in Baja MX.

Bretschger has developed methods for how to apply her technology for the removal of medications and other toxic personal care products from wastewater; and is developing new methods for addressing the removal of nitrogen and phosphorous from agricultural waste streams (two big factors in creating ‘dead zones’ in our coastal waters).

Growing up in the Southwest, access to water has always been paramount in Bretschger’s life.  She lived through periods without access to plumbing and running water, and therefore knows first hand some of the basic challenges families face.  One third of the world’s population has no access to sanitation, resulting in high child mortality rates and a critical lack of public health and safety. Today, Bretschger directs a lab of nine researchers and five interns (high school through master’s level students) and conducts collaborative work throughout San Diego and across the International boarder. Her installations can be seen at the San Pasqual High School Agricultural center and previously at White Labs. Bretschger believes her team is poised to have a real impact on the global sanitation crisis, she just needs more funding “ to go faster and to go bigger.” Her Roddenberry funded efforts will lead to the installation of improved sanitation systems at a school in San Quintin, Mexico over the next two years, and she hopes to expand these efforts globally to begin addressing the critical sanitation needs for nearly 2.6 billion people world-wide.

Zoo in You Exhibit Now Open

Did you know trillions of microbes make their homes inside your body? In fact, these microorganisms outnumber our human cells 10 to 1, “colonize” us right from birth, and are so interwoven into our existence that without each other, none of us would survive! Thanks to new sophisticated technology and the cutting-edge research of the Human Microbiome Project, we are just starting to discover what these microbes are up to and how they affect us. And now in Zoo in You: The Human Microbiome, a new 2,000 square foot bilingual traveling exhibit created in partnership between JCVI and the Oregon Museum of Science and Industry (OMSI), and funded by a SEPA grant from the NIH, visitors can now explore this fascinating and complex world inside us that is our microbiome—a dynamic, adaptable, and delicately balanced ecosystem like any other found in nature.

A few of the Zoo in You components including “Weather Reports” and “Microbes in the Family”

A few of the Zoo in You components including “Weather Reports” and “Microbes in the Family”

The exhibition features 15 interactive, free floating hands on components that are designed to focus on three overarching topic areas to educate and inform visitors on the concept that our bodies are complex ecosystems that we are just starting to understand and explore.  Through these exhibit components museum goers will “meet the microbes” to learn about the organisms which live on and inside us from the moment we are born, to understanding the importance of the dynamic and delicately balanced human microbiome in “balanced ecosystems”, and lastly visitors will “explore the microbiome” to learn the importance of scientific research to increase our understanding of human health.

Zoo In You introduction component “Meet the Microbes”

Zoo In You introduction component “Meet the Microbes”

There are numerous interactive, hands on activities for visitors.  Such activities include “Weather Reports” where guests will have the opportunity to interact with green screen technology to give a weather report on the climate conditions of your nose, gut or skin.  They also will be able to build a DNA Puzzle where they race against the clock to assemble a DNA strand and participate in a hand washing contest.   Participants can challenge each other in exhibit components such as “Microbes in Balance”, a large touch screen video game to see if they can keep their “health-o-meter” in balance and in “Microbe Mirror” a motion sensing activity where visitors come face to face with their full body reflection and control the changes in their microbiome as they react to everyday occurrences.  Throughout the exhibit components feature contributions by JCVI Scientists Dr. Karen E. Nelson, Dr. Hernan A. Lorenzi, and Dr. Ramana Madupu including “Stories & Choices” an activity where visitors listen to the scientist interviews and make choices based on various fun questions which relate to microbiome research.

The Zoo in You exhibit is now on display at the Oregon Museum of Science and Industry (OMSI) in Portland, OR through July 2015, it will then travel to Science Works Hands-On Museum in Ashland, OR October through December 2015.  It will begin its national tour at the Reuben H. Fleet Science Center in San Diego, CA in partnership with JCVI.