CosmosID is the top performer in Janssen's Mosaic Strain Challenge and precisionFDA's CFSAN Pathogen Detection Challenge

Source: PRnewswire

 

Rockville, MDCosmosID a bioinformatics provider and NGS service laboratory announced that the company’s cloud-based bioinformatics platform for microbiome analysis has received the highest score in the strain-level microbial profiling category of the Mosaic Community Challenge and for strain-level microbial identification in the precisionFDA Pathogen Detection Challenge.
 
The Mosaic Community Challenge: Strains #1 is the first of three Mosaic Community Challenges  powered by DNAnexus, which is sponsored by Janssen Research & Development, LLC through its Janssen Human Microbiome Institute. The challenge aims to benchmark and improve computational methods in strain-level microbiome characterization. CosmosID bioinformatics received the highest score in microbiome profiling.
 
CosmosID also participated in the precisionFDA CFSAN Pathogen Detection Challenge, also powered by DNAnexus, and again took the lead in strain identification by correctly identifying the highest number of culture negative and spiked-in samples and overall outperforming other contenders in strain-level detection and identification of microbes in metagenomic samples. This challenge was organized by the Food and Drug Administration Center for Food Safety and Applied Nutrition (FDA CFSAN) to help improve bioinformatics pipelines for detecting pathogens in samples sequenced using metagenomics.
 
CosmosID led both challenges demonstrating highest scores for sensitivity (recall) and precision. “Most algorithms available today achieve robust sensitivity by trading off specificity and precision, effectively accepting false positive calls.” explained Manoj Dadlani, CEO of CosmosID. “Our machine learning based algorithms keep false positives under control and have grown smarter with each of the tens of thousands of datasets analyzed from a wide variety of sample types. This is how our bioinformatics continuously improve and achieve industry leading sensitivity without sacrificing precision.”
 
“We are committed to offering our customers a solution that combines class-leading accuracy with actionable results.” said Dr. Nur Hasan, CSO of CosmosID. “The clinically informative and actionable unit in microbiology is a strain, not a species. For this reason, our team has invested years of curation into the largest, most comprehensive microbial reference database. The databases structure follows the phylogenetic hierarchy of all represented microorganisms, which enables reliable microbial identification, down to strain-level.”
 
Helping the community to improve and standardize the complex metagenomic workflow is an important part of CosmosID’s vision. CSO Dr. Nur Hasan and VP of Products Dr. Arne Materna both serve as expert advisors in an ISO working group defining standards for pathogen sequencing, and the company has a track record of embracing metagenomics challenges. In 2017, CosmosID published an internal benchmark of its cloud based bioinformatics, and co-hosted The Metagenomics MVP Challenge v1.0 with the National Institute of Standards and Technology (NIST) and the Association of Biomolecular Research Facilities (ABRF). Most recently, CosmosID contributed to a more standardized metagenomics workflow with an update to its cloud platformenabling researchers to analyze datasets from microbiome standards free of charge. 
 
“Consistent with our vision, CosmosID is not only addressing the need for accurate and easy to use bioinformatics,” said Manoj Dadlani. “We provide customers access to best practices along the entire metagenomic sequencing workflow through our NGS Service Laboratory. We are proud to offer shotgun metagenomics and isolate sequencing services starting at $99 for 3 Million reads per sample and a turnaround time as fast as five days. Our offering leads the microbiome field with best-in-class accuracy and accessible pricing allowing CosmosID customers to sufficiently power their studies.
 
Manoj Dadlani will speak more about CosmosID software and NGS laboratory services, including CLIA and HIPAA compliance, at today’s Microbiome Drug Development Summit in Boston, MA.

Here’s a webinar about the Mosaic Community Challenge!

Zymo Research and CosmosID to Deliver Integrated Solution for Accurate Microbiome Analysis

Zymo Research and CosmosID announce their partnership to provide microbiome researchers with an integrated end to end solution for accurate microbiome analysis.

 

The partnership combines Zymo Research’s complete microbiomics product portfolio from sample collection/preservation, mock microbial community standards, nucleic acid isolation, and library preparation with the largest curated microbiome database maintained and powered by CosmosID. The combined technologies of both companies allow for comprehensive and simple service for multi-kingdom microbiome analysis, not limiting the identification to only bacterial constituents of microbial communities, but also covering other microbial kingdoms such as fungi.

 

“The partnership between CosmosID and Zymo Research is a perfect match for our customers.” said Manoj Dadlani, CEO of CosmosID. “CosmosID is powered by the largest database of microbial genome information which enables strain level resolution of bacteria, archaea, protists, fungi, viruses and even unknown microorganisms and Zymo Research’s pipeline has proven it can consistently prepare samples that accurately reflect microbial compositions.”

 

“The synergy of this partnership is very exciting because of the tremendous value we collectively bring to our customers by combining Zymo Research’s portfolio of products designed from collection to conclusion for accurate and reproducible microbiome measurements with CosmosID’s multi-kingdom strain-level resolution and industry leading sensitivity and precision,” said Ryan Kemp, Director of Nucleic Acid Solutions at Zymo Research. “Combined, our metagenomics solution has become both the most powerful and simplest collection to conclusion solution available.”

 

As a part of the first stage of the partnership CosmosID and Zymo Research are tackling the challenge of bias and irreproducibility in the field of microbiomics head-on. Microbial composition profiling powered by Next-Generation sequencing has become routine, however, these techniques are complex and can suffer from significant bias from collection to analysis. By adding defined and controlled Microbial Community Standards to a workflow or even within microbiome samples, researchers can assess, improve, and compare bias and errors in the metagenomics workflow.

 

Completing the first stage of this collaboration, CosmosID will release an update to its widely used cloud-based bioinformatics platform for microbiome analysis during this year’s ASM Microbe conference in Atlanta. The update introduces new, user friendly tools to analyze internal microbiome standards from Zymo Research and to automatically assess the quality of analyzed sequence data.  Data generated using the sophisticated yet streamlined pipeline for the analysis of Zymo Research microbiome standards can be conveniently interpreted – free of additional charge – via CosmosID’s user-friendly Cloud-based bioinformatics platform.

 

Both companies will present the integrated solution for microbiome research to the public at the ASM Microbe conference (booths 1309 and 2931) in Atlanta from June 7-11.

 

About CosmosID

CosmosID®, based in Rockville, Maryland, is a genomics big data company focused on rapid identification of microorganisms for molecular diagnostics, public health, food safety, agriculture, and environmental applications. The CosmosID platform uses proprietary sequence analysis algorithms to accurately profile all microorganisms in a metagenomic sample employing next-generation DNA sequencing. CosmosID was founded in 2008 by Dr. Rita Colwell, former director of the National Science Foundation and currently Distinguished University Professor at the University of Maryland and Johns Hopkins University Bloomberg School of Public Health. To learn more please visit www.cosmosid.com.

 

About Zymo Research

Zymo Research Corp. is a privately held company based in Irvine, California, USA. Since its inception in 1994 it has been serving the academic and biopharmaceutical scientific communities by providing innovative DNA and RNA purification products. Zymo Research is the first company to develop microbiomics solutions based on new rigorous standards for microbiome analyses and has been leading the initiative to improve reproducibility and accuracy in the field by developing the first commercially available microbiome (mock microbial community) standards. For more information, please visit: www.zymoresearch.com or visit us at ASM Microbe, booth 2931, in Atlanta from June 7-11, 2018. Follow Zymo Research Corp. on FacebookLinkedInTwitter, and Instagram.

 

All trademarks are the property of their respective owners. Zymo Research Corp., the stylized logo, the tagline "The Beauty of Science is to Make Things Simple", ZymoBIOMICS are trademarks of Zymo Research Corp. and are registered with the USPTO.

CosmosID at ASM Microbe 2018

This year we are at ASM Microbe in full force!

Come by booth #1309 and see our latest sequencing and metagenomic software developments.

 

PRESENTATIONS

Jun. 8, 2018, 11:00 AM - 11:45 AM (Exhibit Hall, Industry Showcase B)

CosmosID is co-hosting a workshop with iGenomX and Phase Genomics entitled "Advanced tools for NGS library prep, sequencing based microbiome analysis and Hi-C powered metagenomics

 

Jun. 9, 2018, 3:25 PM - 3:30 PM (Lounge and Learn 1, Building A, Level 4)

Syn-006, A Novel Beta-Lactamase, Mitigates Carbapenem-Mediated Gut Microbiome Dysbiosis in A Porcine Model

 

 

POSTERS (Exhibit and Poster Hall, Building B, Halls B2-B5)

Jun. 8, 2018, 11:00 AM - 1:00 PM

FRIDAY - 250 - Development and Evaluation of A Metagenomic Approach for the Diagnosis of Bloodstream Infections in Oncology Patients

 

Jun. 8, 2018, 11:00 AM - 1:00 PM

FRIDAY - 868 - Metagenomic Characterization of Microorganisms in An Advanced Water Treatment Facility

 

Jun. 9, 2018, 11:00 AM - 1:00 PM

SATURDAY - 425 - Use of Next-Generation Sequencing and Cloud Analytics to Identify Organisms and Detect Resistance Markers Directly from Urine Specimens 

 

Jun. 10, 2018, 12:45 PM - 2:45 PM

SUNDAY - 633 - Syn-006, A Novel Beta-Lactamase, Mitigates Carbapenem-Mediated Gut Microbiome Dysbiosis in A Porcine Model

Extensive Academic Study shows CosmosID's “Best in Class Accuracy” and “Unrivaled Detection Resolution”

The fast-growing field of metagenomics enables rapid identification and unbiased characterization of the microbial communities associated with different biological specimens, based on high-throughput DNA sequencing coupled with robust bioinformatics. While all steps of this multistep process (sample collection to data analysis) are important in achieving high identification accuracy and maintaining the proper biological representativeness of the community, bioinformatic analysis of complex metagenomic datasets represents one of the most critical and challenging steps...

Babies Get Their Smarts From...Their Gut?

Babies Get Their Smarts From...Their Gut?

In the daunting, demanding, 24/7 job that is raising a baby, parents love to claim how aspects of their child is a reflection of their contribution, i.e. their looks, athletics, and smarts. While this debate amongst partners has the ability to get rather heated, their contributions may not be as significant as they’d like to believe. There is no denying that parents have an impact in child development, both through nature and nurture, in aspects such as cognitive functionality. However, recent research published in Biological Psychiatry brings about evidence that those baby smarts that you or your partner claim to be responsible for, may actually be influenced by  the baby’s own gut microbiome.

Manipulated Tadpole Microbiomes Experience 'Jump' in Parasite Susceptibility Later In Life

Manipulated Tadpole Microbiomes Experience 'Jump' in Parasite Susceptibility Later In Life

Frogs, from children chasing them in the outdoors to being the center point in fairytales, have a more involved role in our daily lives than you may give credit for. As part of our ecosystem, they contribute through the consumption of many ‘pest’ insects, which I’m sure is a role we all appreciate. However, much like the fairytale “The Princess and the Frog”, these amphibians have more to offer than what meets the eye.

Fiber: Not Just For Your Gut

Fiber: Not Just For Your Gut

Do you eat enough fiber? If not, you might not just feel it in your gut! The importance of a high fiber diet has been well documented throughout the years by researchers and nutritionists alike citing many benefits that contribute to improved bowel function. From fiber tablets to high fiber grain, proprietors have pounced on this healthy gut craze creating a large specialized market with fiber supplementation in the spotlight. This movement has undoubtedly provided intestinal relief to thousands if not millions. However, much like fiber’s effect on bowel function, the health benefits doesn’t stop in the gut.

Gut Bacteria: A Future Love Potion?

Gut Bacteria: A Future Love Potion?

You’ve seen it in TV shows, movies, plays, and especially soap operas; silly fantasies in which one is able to create a concoction capable of inducing their victim into uncontrollable infatuation. This concept however, much to the dismay of many, has not been turned into reality. In truth, the emotion of love and it’s development is one that science has little explanation to offer, so the idea of a “love potion” seems out of reach. Despite this fact, studies into the universe of infinite possibilities (also called the gut microbiome) have unlocked the door to correlations between gut bacteria and their impact

Are Microbes the Future of Environmental Protection?

Are Microbes the Future of Environmental Protection?

Oil spills, and the environmental damage they cause, are one of the most dangerous and detrimental events to occur on Earth. The aftermath felt by affected ecosystems is almost irreversible, with practically no living organism capable of withstanding such pollution to their environment. As you may remember the Deepwater Horizon spill that occurred in 2010, the scope of devastation in which the Gulf of Mexico was exposed to was unfathomable, leaving thousands of organisms with unlivable conditions. What’s worse yet is the inability of human response to the containment and deterrence of these spills in an efficient manner, thus exponentially increasing the damage inflicted on the environment. However, researchers from the Lawrence Berkeley National Library have conducted studies into the microbial contribution to oil degradation and the possibilities it may present, specifically to the Deepwater Horizon event of 2010.