Wednesday February 5th 2020



The winning submission will receive a pre-clinical, Gastrointestinal SHIME® study, including sample processing, strain-level ID and functional characterisation of the microbiome with the CosmosID platform.

ProDigest and CosmosID today announced the launch of a new scientific challenge programme where the winning abstract submission will win a pre-clinical gastrointestinal study with a comprehensive, end-to-end microbiome characterisation workflow. The winner’s novel microbiome-based therapeutic will be investigated in ProDigest’s SHIME® in vitro gastrointestinal simulator for its impact on the gut microbiota activity and composition. The modulation of the gut microbiota will be assessed by sequencing and analysis with CosmosID’s industry-leading microbiome analysis pipeline.

“The gut microbiota is gaining increasing attention as a target for the modulation of host-related conditions. Phages, live biotherapeutic products, antibodies, … are all facing different challenges when reaching the colon. Understanding their mechanism of action is key to the further development of those compounds towards clinical applications” said Massimo Marzorati, CEO of ProDigest and professor at Ghent university. “We look forward to combining the ability of the SHIME to accurately recreate the gut microbiota with the power of CosmosID’s taxonomic and functional microbiome analysis platform. This synergy should provide a deeper understanding into the compositional and functional mechanics driving gut microbiome-related therapeutic effects.”


Manoj Dadlani, CEO of CosmosID, commented: “Scientific competitions have a long and successful history of inspiring exciting new approaches, and we believe this program will do the same for the pharmaceutical industry. We are pleased to be working closely with our colleagues at ProDigest to foster innovation in the development of novel microbiome-based therapeutics.”

ProDigest’s SHIME® technology platform is an established, validated in vitro simulator of the gastrointestinal tract. It can recreate the proximal-distal segmentation of the gut microbiota along the colon for 4 parallel runs and is thus ideally suited for assessing the impact of various therapeutics on a diseased gut microbiota. The CosmosID bioinformatics platform combines the world’s largest curated reference database of microbial genomes with proprietary analysis algorithms and machine learning tools to accurately and rapidly identify & characterise microorganisms within a metagenomic sample. By generating high-quality, standardised NGS data at CosmosID’s CLIA & GLP facility, new insight can be gained from studies utilizing metagenomics.

Researchers may enter the Gut Microbiome Therapeutic Innovation challenge by submitting a short abstract proposing a project that would make use of the ProDigest and CosmosID technologies. Abstract submission opens on February 5, 2020 and closes at midnight PST on March 31, 2020. A committee from ProDigest and CosmosID will select the winning abstract based on research creativity, scientific impact, and innovation. For full contest details and terms, please visit:

More information about offerings from ProDigest and CosmosID will be available at the Microbiome Drug Development conference taking place February 5-6, 2020 in London at The Tower Hotel where attendees can learn more during the following presentations:

Wednesday, February 5, at 9:15 am
Arne Materna, CosmosID
Accelerating Microbiome Discoveries Using Shotgun Sequencing and Strain-Level Bioinformatics

Wednesday, February 5, at 1:00 pm in Stream A
Massimo Marzorati, ProDigest
The Role of the Ileal Microbiota in Drug Stability and LBP Activity

About CosmosID

CosmosID®, based in Rockville, MD, provides solutions unlocking the microbiome through the use of Next-Generation Sequencing (NGS) and industry-leading bioinformatics solutions to achieve rapid identification and characterisation of microorganisms for pharmaceutical R&D, molecular diagnostics, public health, food safety, agriculture, and environmental applications. CosmosID’s 11+ years of expertise enables end-to-end support of microbiome studies including study design, sample collection, sample preparation, NGS, bioinformatics and interpretation support. Available online, CosmosID’s cloud-based metagenomics application offers user-friendly access to the world’s largest curated database for microbial genomics and independently validated to return metagenomic analyses at strain-level resolution with industry-leading sensitivity and precision. To learn more please visit

About ProDigest

ProDigest is a CRO focused on preclinical gastrointestinal research. At the centre of each project is the SHIME technology, the Simulator of the Human Intestinal Microbial Ecosystem. This unique in vitro gastrointestinal simulator accurately recreates the physiology of the host as well as the gut microbiota along the various regions of the colon. Food and pharma products can then be investigated for a multitude of research questions, ranging from delivery strategy and stability to functional and compositional modulations of the gut microbiota and the impact on the gut barrier. The SHIME provides mechanistic information that funnels product development and complement clinical findings. ProDigest’s expertise covers the investigation of prebiotics, probiotics, live biotherapeutic products, phages, APIs and other orally administered compounds. More information available at