News

Time Since Death? Ask the Microbes

As many microbiologists can attest, microbiome research is not for the squeamish. From swabbing roadkill carcasses to isolating the DNA present in human waste samples, microbiome researchers aren’t afraid to get dirty – they probably even enjoy it. Yet, it’s hard to imagine that Dr. Nathan H. Lents and his team from John Jay College of Criminal Justice, City University of New York, enjoyed their probing of 21 decomposing cadavers. As part of study published recently in PLOS ONE, Lents and his team collected and analyzed bacteria from the ears and noses of cadavers as the corpses decomposed over the course of weeks.

 

You may not know that the forensic techniques used currently to identify how long someone has been dead are still not very precise. As such, death investigations, which often include identifying what’s known as the postmortem interval (PMI), or the time that has elapsed since a person has died, provide limited answers to critical questions. That’s what inspired the researchers to analyze the “necrobiome” – the community of microorganisms found on a dead body.

 

As described in the publication, the research team sampled skin microbiota from the noses and ears of decomposing cadavers to see if they could gain microbiological clues that can eventually be used to help more precisely identify times of death when dead bodies are found. Specifically, the researchers noted the importance of analyzing the cadavers as they decomposed, as it enabled them to take stock of which microorganisms took over the sampled parts of the body, and at what times. They are hopeful that this proof-of-concept study will lead to the realization of reliable microbial indicators that will enable forensics experts to better determine time since death.

 

It’s also important to note that the team relied on next-generation sequencing and metagenomic analysis of the necrobiome samples to capture the most comprehensive and accurate information for their research. While this study is certainly novel, it joins a growing number of publications that are focused on leveraging metagenomic DNA sequencing and analysis techniques to improve forensic investigations. Bacteria may now often be the culprits, causing deaths through infections, but as this and other studies show, they may soon be helping convict human murderers instead.

Rita Colwell Talks About Cholera and Women in Science on "Naturally Speaking" Podcast

The University of Glasgow in Scotland featured our founder, Rita Colwell, in an insightful podcast on the impact of her work on water quality and changing opportunities for women in science.  

Click here to listen to the podcast!

Announcing A Deep Sequencing Gut Microbiome Kit!

We are incredibly excited to announce that in a partnership with The BioCollective we will be offering an affordable gut microbiome kit based on all of the DNA in your sample. Most microbiome analysis kits only give you a limited peek at what is in your sample DNA. They are based on something called 16S analysis - looking at only one or a few genes. Instead of doing this, we actually sequence the DNA of the entire sample which, as you can imagine, gives us much more information. And with this extra information we are able to tell you things like which strains of bacteria we find and we can also identify viruses, fungi, parasites and even antibiotic resistance and virulence factors, all important components of the microbiome. 

The kit will have an introductory price of $299 (regular price: $499). Please click here to sign up for yours! We will send you a kit with detailed instructions on how to send your samples for analysis. 

If you've ever been wondering what your gut microbiome looks like or maybe you want to establish your baseline microbiome before making some dietary changes or athletic pursuits, this is a great time! 

CosmosID Founder Dr. Rita Colwell to Receive an Honorary Degree from Notre Dame

Congrats, Dr. Colwell, on your 62nd honorary degree!

Rita Colwell, a molecular microbiologist whose research focuses on global infectious diseases, water and health, will receive a doctor of science honorary degree at the University of Notre Dame’s 171st University Commencement Ceremony on May 15 (Sunday). She joins six previously announced honorary degree recipients.
— http://news.nd.edu/news/65958-renowned-microbiologist-rita-colwell-to-receive-notre-dame-honorary-degree/

CosmosID partners in new Center of Excellence for Sustainable Water Reuse, Food & Health, with a 10M$ Award by the USDA to the UMD School of Public Health

Rockville, MD – April 6, 2016 - In today’s world of severe droughts and dramatic changes in climate, the shortage of clean water has become a major challenge. To support the improvement of community water sources, the USDA Water for Agriculture Challenge program has awarded a $10M four year grant to the University of Maryland, College Park, School of Public Health and its collaborating partners, one of which is CosmosID, to launch a new Center named CONSERVE: A Center of Excellence at the Nexus of Sustainable Water Reuse, Food and Health. Agriculture Secretary Tom Vilsack, said “the grants we are announcing today are the latest of many steps USDA has taken to help communities who are struggling with water quality”.

The multidisciplinary team, led by Dr. Amy R. Sapkota at the University of Maryland, College Park, School of Public Health, will dedicate its efforts to developing innovative, safe, and sustainable ways to irrigate food crops in variable climates. “We are running out of water in our key food production regions,” Dr. Sapkota, an environmental microbiologist, said. “We need to act now to figure out how to shift water usage patterns and successfully reuse water to sustainably and safely grow our food.”

The University of Maryland, College Park, School of Public Health selected CosmosID to join their team based on the capability of CosmosID to provide a rapid, accurate, and actionable platform for metagenomic microbial identification and characterization. CosmosID Founder and Chief Scientific Officer, Dr. Rita Colwell, is a world leader in water-related research and a distinguished microbiologist. Dr. Colwell was awarded the 2010 Stockholm Water Prize by the King of Sweden for outstanding water-related achievements. “The University of Maryland has a long history of excellent work in water research,” said Dr. Colwell. “CosmosID has partnered with the Orange County, CA, Water District and organizations in Europe and the Middle East to develop methods for water reuse. Therefore, it’s exciting to be part of this effort developed by the University of Maryland because water reuse is a major challenge globally. This award by the USDA to the University of Maryland, College Park, School of Public Health is recognition of the strength of the formidable team clearly highly qualified to meet this challenge headed by Dr. Sapkota, an outstanding scientist.”

Contact:
Jon Ryan, 703-995-9879

Jon.ryan@cosmosid.com

www.cosmosid.com

 

About CosmosID:

CosmosID is a genomic big data company focused on rapid identification of microorganisms for infectious disease diagnostics, public health surveillance, food safety monitoring, pharmaceutical discovery, and microbiome analysis for health and wellness. Using patented methods and curated databases of more than 65,000 microbial genomes, including bacteria, viruses, fungi, parasites, and antibiotic resistance and pathogenicity markers, CosmosID provides ultra fast identification of pathogens and commensal flora to sub-species or strain level, comprehensive profiles of microbial community resistance and virulence, and highly sensitive relative abundance predictions for all microorganisms in a sample.

CosmosID, the Microbial Metagenomics Company, Expands into Hip-Hop Music Production

Rockville, MD, April 1, 2016 - CosmosID today announced the expansion of their genomic big data company into the music production sector. CosmosID provides rapid identification of microorganisms for infectious disease diagnostics, public health surveillance, food safety, pharmaceutical discovery, microbiome analysis, and now music production, with a focus on the hip-hop industry.

Manoj Dadlani, CEO, said of the expansion, “It seemed like the logical next step for our company.”

The debut song under the CosmosID label can be found here.

Founder Rita Colwell, former director of the National Science Foundation and pioneer in the field of microbial ecology, sees this as a surprising move for the company she started based on the need for rapid identification of microbes using modern DNA-based techniques. “It was not part of my original vision for this company”, said Colwell, “and I am a Beethoven, Bach, Mozart, and Vivaldi fan. But I have always tended to be a visionary. So, if one considers the microbial DNA sequence to be a fascinating symphony, this next step is a natural.”

Chris Mason, known for his study of the microbes in the New York City subway system and for his emphatic support of the hygiene hypothesis, where he once encouraged rolling babies like sushi on the subway floor, said, “No doubt - DNA is music. Mixing the metagenome of uptown and downtown trains is just as beautiful as when DJ Danger Mouse blended the Beatles White Album and Jay-Z’s the Black Album to make the Grey Album. In fact, this was even highlighted last year at TEDMED. I am totally onboard to collaborate with them on the music front. Get this hygiene hypothesis to your metropolis.

DJ LMNOP, leader in the music industry, commented “Just because you think you’re on top of the world with your fancy algorithms and amazing databases … does not mean you can just suddenly one day decide to produce music and expect to be successful with no experience in this field. This field will break you. Good luck to them.” DJ LMNOP later announced the expansion of his company into the microbiome therapeutics space.

This new direction will allow CosmosID to expand and collaborate with leaders in the music production field. “It should open new doors and opportunities and lead to our growth as a company,” said Dadlani.

Email jon.ryan@cosmosid.com for additional information.

 

CosmosID raises $6 Million in Series B Funding

Rockville, MD - January 27, 2016 -  CosmosID, the leading genomic big data company focused on microbiome research, outbreak investigations, and infectious disease diagnostics, using next-generation DNA sequencing, announced $6M in Series B funding. The company will expand its engineering capabilities, enhance clinical applications, undertake research and development to improve linkage of the DNA genetic code to actual biological traits (genotype to phenotype), such as antibiotic resistance, and develop new products directed at monitoring, predicting, and preventing disease outbreaks.

The funding round was led by the Applied Value Group (AVG), a private investment firm chaired by Bruce Grant (former head of Arthur D. Little North America and Chairman of Tele2, the second largest Swedish telecom carrier). As Vice Chairman of CosmosID, Mr. Grant said, “We invest in small and medium-sized companies that can significantly create economic value for their customer base through innovation in radically improving cost and time efficiency for customers. AVG has achieved that in an array of industries from high tech to manufacturing. Among all of our current 25+ investments there is no one that will revolutionize the speed and cost efficiency for their customers like CosmosID. And much more importantly the outstanding accuracy in diagnosis will save a multitude of lives"

The power of the CosmosID platform is its ability to identify all microorganisms (bacteria, viruses, fungi, and parasites) and characterize their attributes (e.g. antibiotic resistance, virulence, etc.) in a single, universal, rapid analysis. The company has analyzed over 20,000 biological samples that range from human, animal, plant, water, and soil. Chris Mason, Associate Professor in Genetics from Weil Cornell Medical School said, “I have explored the microbiome of everything from the NY subway to outer space and the software analysis component is critically important. CosmosID provides a robust tool for the quantification and detection of microorganisms and antimicrobial resistance markers and we are actively using it for onsite in situ diagnostics.”

CosmosID began generating revenue in 2015, with customers in the pharmaceutical, probiotics, microbiome research, and food safety markets. Later this quarter, they will announce new partnerships with some major players in the genomic space.

Key to long-term growth, the company is evaluating the clinical utility of its broad range pathogen detection system in partnership with 15 leading research hospitals in the United States and Europe. A single CosmosID analysis detects multiple organisms and accurately identifies pathogens and their virulence and antibiotic resistance genes, all within a clinically relevant time(<24 hours), whereas legacy assays normally take days to weeks. CosmosID will be used to detect disease causing agents where legacy assays perform poorly, such as co-infections (i.e., gonorrhea/chlamydia), polymicrobial infections (i.e., pneumonia, cystic fibrosis, urinary tract and prosthetic joint infections etc.) and infections caused by difficult to detect microbes (chronic wound and respiratory infections, and meningitis/encephalitis).

CosmosID also provides rapid screening for multi-drug resistant organisms (MDROs), also known as super bugs, including Clostridium difficile, Staphylococcus aureus, and Carbapenem-resistant Enterobacteriaceae. These organisms are prevalent in healthcare associated infections (HAIs). HAIs are recognized as the most frequent adverse event encountered in health care, and can result in prolonged hospital stays, long-term disability, antimicrobial resistance, unnecessary death, and major increases in healthcare costs. The technology developed by CosmosID will help improve patient outcomes, shorten the length of hospitalization, allow better therapy selection, and ultimately reduce the total cost of care. George Watts, co-director of the Genomic Center at University of Arizona said “CosmosID can provide the resolution necessary for genomic sequencing of pathogens to become a reality in the shift to precision medicine.”

With better food safety monitoring, CosmosID will help reduce foodborne illness outbreaks. CosmosID’s platform provides identification of bacteria and/or viruses needed to detect causative agent(s) of food-borne illnesses, such as the recent Chipotle E. coli and norovirus and Blue Bell ice cream Listeria outbreaks. The Food and Drug Administration recently awarded CosmosID a contract to facilitate faster and more accurate identification of both common and novel foodborne pathogens.

CosmosID offers its genomic analysis software platform in the cloud, on an appliance/server (for high volume, high confidentiality environments), and as a one-stop solution to handle study design, DNA sequencing, and high quality microbiome analysis. CosmosID’s algorithms, interface, and database also can be run on a laptop, without an internet connection, an ideal solution for investigating outbreaks in remote areas, such as the Ebola situation in Africa.

Rita Colwell, Founder and Chair, says, “As a pioneer in the field of microbial ecology, I am very familiar with the need to understand microbial community structure and function. CosmosID developed an accurate, reproducible system that provides actionable identification of bacteria, viruses, fungi, and parasites, literally within minutes, using DNA sequencing. The CosmosID platform represents a major development in microbiology and achieves my major objective.  I am very proud of CosmosID and its outstanding achievement and momentum.”

Rita Colwell is a Distinguished University Professor at the University of Maryland at College Park and at Johns Hopkins University Bloomberg School of Public Health. She was the 11th Director of the National Science Foundation and recipient of the 2006 National Medal of Science of the United States and the 2010 Stockholm Water Prize. Dr. Colwell is a member of the National Academy of Science.

“The next phase of the genetic revolution is in microbiology and we are excited to be a leading company innovating in this space. By analyzing huge amounts of data, we are able to make actionable decisions to improve health and well-being,” said Manoj Dadlani, CEO. “CosmosID’s solution is scalable, portable, and does not require bioinformatics skills to rapidly identify microbes”

Manoj Dadlani is a Cornell University graduate in biological engineering and served as head of the US branch of Applied Value Management Consulting. He subsequently transitioned to the investment side of the Applied Value Group, which is the lead investor in CosmosID.

An example of a real-world application of CosmosID’s capabilities is found in a recently published paper in the Proceedings of the National Academy of Sciences http://www.pnas.org/content/113/3/722.abstract. Ashok Chopra, the study’s lead said “CosmosID’s unbiased metagenomic analyses helped us uncover how multiple strains, with varying virulence, of a flesh eating bacterium called Aeromonas hydrophila can crosstalk in developing devastating necrotizing fasciitis. Since these strains belonged to the same species, routine clinical diagnostic methods will never to be able to identify this mono-species polymicrobial infection. The precise strain level identification that CosmosID provides could revolutionize clinical microbiology, directing physicians towards improved and more effective treatment options.”

The scientific advisory board of the company includes the global thought leaders Vint Cerf, one of the fathers of the internet and Chief Internet Evangelist for Google, Richard Roberts, Nobel Prize laureate and Research Director of New England Biolabs, and Eric Haseltine, former Director of Science and Technology of the National Security Agency and former executive vice president, Disney Imagineering, and outstanding technical experts.

Other notable investors incude Bert Nordberg (Chairman of Vestas Wind Systems and former CEO of Sony Ericson), Kristian Tear (VP, Head of EMEA of Logitech and former COO of Blackberry), and Mark Rosenblatt (a leading tech investor).

For additional information, please contact Jon Ryan, jon.ryan@cosmosid.com

About the CosmosID Technology

CosmosID has the most rapid and accurate metagenomic microbial identification platform in the field today. Using patented methods and curated databases of more than 65,000 microbial genomes, including bacteria, viruses, fungi, parasites, and antibiotic resistance and pathogenicity markers, CosmosID provides ultra fast identification of pathogens and commensal flora to sub species or strain level, comprehensive profiles of microbial community resistance and virulence, and highly sensitive relative abundance predictions for all microorganisms in a sample.

Unique to the CosmosID system and currently not offered by any other metagenomic analysis tool is a statistical probability value for identifications made for every sample. Other features of the CosmosID system include functional analysis and virtual panels that allow clients to tabulate microorganisms and specific genes linked to hospital infections and foodborne outbreaks. CosmosID’s platform analyzes data produced from commercially available sequencers, including Illumina, Thermo Fisher, Pacific Biosciences, and Oxford Nanopore platforms.

Unlike traditional taxonomic methods for microbial classification, CosmosID employs proprietary phylogenetic identification, which captures strain relationships at the DNA level, in addition to accurate identification to species and/or strain. “Historically, microbial taxonomy was constructed from phenotype and, as a classification system, proved cumbersome and time consuming,” says founder and Chairman, Rita Colwell. “I established CosmosID to provide rapid, accurate, and reliable microbial identification and classification based on genome sequencing.”

A closer look at the interaction of "flesh-eating" bacterial strains in a case of necrotizing fasciitis

Necrotizing fasciitis (NF) is a serious skin infection caused by "flesh-eating" bacteria. Interactions of multiple strains of bacteria in a mixed infection can have more devastating consequences than previously anticipated. Progression of necrotizing fasciitis caused by infection with multiple strains of Aeromonas hydrophila significantly differed when compared to infection caused by single strain alone.

A study, “Cross-Talk among Flesh-Eating Aeromonas hydrophila Strains in Mixed Infection Leading to Necrotizing Fasciitis" published today at: www.pnas.org uncovered the interaction of four strains of A. hydrophila isolated from the same patient by using our (CosmosID’s) GENIUS bioinformatics package. In a mouse model, GENIUS differentially detected individual strains using strain-specific genetic markers and demonstrated the selective dissemination of a less virulent strain to peripheral organs in the presence of other toxin producing virulent strains. The results were independently validated using luciferase and kanamycin-marked strains. The study underscores the critical need for strain level identification for better understanding of the dynamics of mixed infection.

 

The Gut Microbiome Photoshoot

Here at CosmosID, we can tell you a lot about your gut microbiome.  We can identify what bacteria, viruses, fungi, and parasites are lurking (and thriving!) in there and in what quantity.  We can profile the antibiotic resistance and virulence genes present in the organisms.  We can even tell you how your intestinal flora compares to other intestinal flora the world over.

The one thing we can't do is show you what your gut microbiome actually looks like.  Now, the Sonnenburg Lab at Stanford University has just published a study unveiling some never before seen images of gut microbes.