Posts tagged microbiome

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

Zoo in You: The Human Microbiome Exhibit Opens in San Diego

On January 28, over 250 scientists, philanthropists and other STEM community notables, including JCVI CEO Council Member Reena Horowitz, came out to support the San Diego premier of the Zoo in You: The Human Microbiome exhibit at the Reuben H. Fleet Science Center. The Zoo in You is a new 2,000 sq. ft. exhibit funded by a SEPA grant from NIH in partnership with JCVI. Through May 8, 2016 visitors to the display can learn about our constant microbial companions, where they live, how diverse they are, and in what ways scientists are realizing just how important they are to our personal health.

Dr. Karen Nelson

JCVI’s President, Karen Nelson, Ph.D., spoke about JCVI’s passion for STEM education and dedication to encouraging STEM growth in San Diego.

JCVI at Zoo in You Opening

JCVI staff and friends came out to support the event (from left to right): Hernan Lorenzi, Katie Collins, Karen Beeri, Amani Rushing, CEO Council Member Reena Horowitz, Nicole Deberg, Mark Adams.

Thanks to new, sophisticated technology and the cutting-edge research of the National Institutes of Health’s Human Microbiome Project, the world is just starting to discover what the microbes in each of us are up to and how they affect us.

JCVI is taking other steps to help the San Diego community learn about the importance of their microbiomes. In addition to the exhibit, JCVI scientist Karen Beeri led a class of 23 girls in activities about microbes and DNA sequencing at Fleet’s Saturday Science Club for Girls on February 13. The girls toured the Zoo in You exhibit, made DNA bracelets, and used RNA decoders to decode the secret messages found in our amino acids.

Zoo in You: The Human Microbiome will be on display at Fleet until May 8, 2016. Check it out!

For more information about JCVI’s education initiatives, please contact Education Manager Amani Rushing at

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.

Guest Speakers Marlo Gottfurcht Longstreet and Dean Ornish Inspire Guests at JCVI‘s “Life at the Speed of Light” Gala

On October 18, J. Craig Venter Institute (JCVI) hosted our “Life at the Speed of Light” black tie gala featuring special guests Dean Ornish, MD, and Marlo Gottfurcht Longstreet. JCVI welcomed 200 community leaders, sponsors and supporters including Representative Scott Peters, Susan Taylor, Reena Horowitz, Linda Chester, Jack McGrory, Jessie Knight, Jr., Joye Blount, Wendy Walker, Randy Woods, Andrew and Erna Viterbi, Mary Ann Beyster, and JCVI Board Member Bill Walton and wife Lori.

Guests experienced our science first hand through various displays and had the opportunity to interact with many JCVI scientists to learn how advances in genomics are impacting our health and environment.

microbiome station

JCVI Scientists Manny Torralba and Stephanie Mounaud welcomed guests with a brief introduction to the palm microbiome by taking swabs and sharing aggregate population results midevening.

Following welcome remarks by J. Craig Venter, Ph.D., Founder & CEO of JCVI, Marlo Gottfurcht Longstreet shared her son Tanner’s battle with a Giloblastoma Brain Tumor. It is understood that the tumor developed as a result of a mutation in the TP53 tumor suppressor gene. Sadly, Tanner Jay Longstreet passed away in 2013 at the age of 11.

Marlo Gottfurcht Longstreet sharing her personal story about her son Tanner and ongoing work at the Tanner Project.

Marlo Gottfurcht Longstreet sharing her personal story about her son Tanner and ongoing work at the Tanner Project.

Personal tragedy turned mission for Marlo as she set out to do everything she could to better understand what afflicted Tanner, which gave rise to the Tanner Project at JCVI. Led by Nicholas Schork, Ph.D., the Tanner Project is what is referred to as an “N of 1” project – a single patient case study. Rather than go in for yearly checkups, the patient in the study is monitored daily so that any evidence of cancer can be detected at onset. The goal is to keep the study patient at what is referred to as stage 0. By closely monitoring the condition in this “N of 1” study, its application can be applied more broadly in personalized medicine – “N of 1 for everyone.”

Dr. Ornish discussed advances in personalized medicine and how simple behavioral changes can greatly affect patient outcomes. He addressed ideas presented in his most recent book, The Spectrum, suggesting diet and exercise are not all or nothing propositions. If today wasn’t a great food day, there is no reason tomorrow can’t be. This kind of thinking can greatly improve longevity and quality of life.

Dean Ornish speaking to gala attendees on advances in medicine.

Nobel Laureate Hamilton Smith (right) walks gala attendees through JCVI advances.

Rangers and the Re-Arrangers

The evening was rounded out with a delectable dinner, dancing, and gypsy jazz music by Seattle’s Rangers and the Re-Arrangers.

JCVI is grateful to its event sponsors – CapitalOne Bank, BioMed Realty, Synthetic Genomics, Inc., Human Longevity, Inc., Thermo Fisher Scientific, Gunderson Dettmer, ZGF, and Egon Zehnder – for their support. Thank you as well to our DNA gift bag sponsors: Way Better Snacks, GoodBelly, Kowalski Communications, La Jolla Playhouse, Lean & Green Café, and Travel Set Go.

JCVI remains committed to tackling today’s pressing medical and environmental concerns, and we continue to rely on your generosity to achieve our goals. For more information on funding needs and opportunities, please contact Katie Collins as

Thule, Greenland Year Two

Sequence data from the previous year allowed us to determine the overall microbial population in each site and this year we decided to focus on the Rich Lake site which seem to have representation of nearly all microbes found in the other sites. So lucky for us we only had to work on one site this year rather than six. This in itself had me excited to go back to Thule. After a five-hour flight on a military plane from BWI I finally arrived to Thule Greenland where we were greeted by the Colonel as well as other high ranking military officials at the hanger. Once I cleared the customs processing area, I arrived to the dorm where the other scientists were living. It was a little different from last year’s accommodations but nevertheless the luxuries of WI-FI, Internet and cable TV were all available. As I am anxious to get to the field and see the changes in the Rich Lake site, we were given some interesting news. That day was not a good day to travel to the site because a mother polar bear and her two cubs were spotted nearby not too long ago by military police. However, we managed to get other work done by preparing the schedule for the sampling, cultivation and other labwork.


The next few days consisted of preparing culture media, cultivation traps and diffusion chambers, and going out into the field (polar bear spray in hand; yes it’s a real thing!). We were extra careful in the field since there was quite a bit of fog in the area that did not seem to go anywhere and fog happens to be the same color as polar bears. The fog did however make it a bit easier to sleep since most of the sunlight was covered and when there’s 24 hours of daylight from mid-April until September, a little fog can still serve a purpose.

Rich Lake Site

Rich Lake Site



JCVI Hosts South African Scientists to Share Microbiome Research Techniques

Two scientists from the University of Cape Town, South Africa have joined Dr. Bill Nierman’s lab for the next month as part of NIH’s Human Heredity and Health in Africa (H3Africa) Initiative, a training program designed to build out technical biological skills in the African research community. This training relates specifically to developing techniques around the area of microbiome analysis, a relatively new field in the biological sciences.

Microbiome analysis for the collaborative study is looking at entire community of microorganisms in the respiratory tract of South African infants to better understand how the microbiome is associated with infant pneumonia and wheezing episodes. The expectation is that the organisms that reside in the infant respiratory tract will provide protection from or a predisposition to the pneumonia or wheezing episodes.


The Nierman Group

The Nierman group left to right Sarah Lucas, Bill Nierman, Shantelle Claassen, Mamadou Kaba and Stephanie Mounaud (unpictured Jyoti Shanker and Lilliana Losada) welcomes visiting scientists Ms. Classeen and Dr. Kaba from University of Cape Town for a month long training in microbiome sequencing and analysis.

Mamado Kaba, MD, PhD and colleague Shantelle Claassen from the University of Cape Town will be working closely under the guidance of JCVI’s Stephanie Mounaud who is functioning as the project manager and coordinating the laboratory components of a similar project at JCVI studying the microbiomes of inafnts in the Philippines and also in South Africa. These studies are sponsored by the Bill and Melinda Gates Foundation. The training will focus initially on preparing samples for DNA sequencing on a modern DNA sequencing platform, the Illumina MiSeq instrument. Once the sequence reads are off the sequencer, the instructional focus will shift to analysis of the reads by means of an informatics pipeline that develop phylogenies, or family trees, of the microbes that are obtained from the infant respiratory tract so that the abundance and relatedness of the microbes can be established. The bioinformatics training will be provided by Jyoti Shankar, the statistical analyst working on the Gates Foundation Project.

Mamadou Kaba is a Wellcome Trust Fellow working in the Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town. Mamadou’s research interests include the molecular epidemiology of infectious diseases and the study of human microbiome in healthy and disease conditions. He has contributed in establishing a new research group conducting studies on how the composition of the upper respiratory tract, gastrointestinal, and the house dust microbial communities influences the development of respiratory diseases.

Prior to joining the University of Cape Town, Mamadou worked as Research Associate at the Laboratory of Medical Microbiology, Timone University Hospital, Marseille, France, where he studied the epidemiological characteristics of infection with hepatitis E virus in South-eastern France.

Shantelle Claassen is pursuing a Masters degree in the Division of Medical Microbiology at the University of Cape Town. She has completed a BSc (Med) Honours degree in Infectious Diseases and Immunology at the University of Cape Town, during which she examined the relative efficacy of extracting bacterial genomic DNA from human faecal samples using five commercial DNA extraction kits. The DNA extraction kits were evaluated based on their ability to efficiently lyse bacterial cells, cause minimal DNA shearing, produce reproducible results and ensure broad-range representation of bacterial diversity.

Mamadou and Shantelle are currently involved in an additional prospective, longitudinal study of which the primary objective is to investigate the association between fecal bacterial communities and recurrent wheezing during the first two years of life.

Amazon Expedition

Yesterday, JCVI expedition scientist Jeff Hoffman embarked from Manaus on a sampling expedition of the Amazon River and its tributaries, which contains 1/5th of the Earth’s river flow. In collaboration with scientists Dr. Guilherme Oliviera and Dr. Sara Cuadros from the Centro de Excelencia em Bioinformatica (CEBIO) of Belo Horizonte, Jeff is taking samples to characterize the genomes of microbes found along 2/3rds of the entire Amazon watershed, including inflowing rivers from Manaus to Macapa. Our collaborators at CEBIO will be sequencing the samples with a joint Brazil-USA effort on analysis. Long recognized for the biodiversity of visible organisms, the Amazon is understudied with regards to the diversity of microscopic organisms and this expedition will substantially increase our understanding of the biological diversity on Earth. This work continues, leverages, and complements previous and ongoing JCVI work characterizing the unexplored microbiomes of marine, estuarine, freshwater, and terrestrial environments around the world.

See a gallery of the expedition on Facebook. More pictures will be added throughout the trip.