Data Generation

Therapeutic discovery begins with sound experimental design, detailing the precise clinical biospecimens vital for revealing microbiome-generated bioactives. We collect those biospecimens in our patient-friendly kits to ensure excellent preservation and efficient shipping to our laboratory in South San Francisco. Our propitiatory TracerMix™ reagents allows high-throughput quantitative sample handling and eliminates unreproducible results often “discovered” in big data. Samples then proceed through the first and only metagenomic platform to employ multiple confirmatory assays, leveraging both NGS and PhyloChip™ to identify and quantify the microbiome products that differentiate the disease state from the healthy state in the tissue under investigation.

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Data Processing

In addition to data generated in our lab, we include highly curated raw data from the public domain in our SGKnowledgeBase™. Appropriate AWS cloud processing pipelines are triggered for metagenomics, metatransciptomics, RNA-Seq, meta-metabolomics or hybridization data followed by extensive data mining with StrainSelect™ to determine the precise strains and Savant™ to reveal novel gene products from microbial dark mater, chromosomes of completely novel coding regions. The resulting quantitative profiles of the microbial bioactives are then statistically evaluated and connected into the first of its kind microbiome therapeutic database from which we nominate the top assay candidates.

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Nomination & Lead Prioritization

After data processing, potential therapeutic candidates are identified and categorized as strains, metabolites, or peptides and proteins. While administration of health-associated bacterial strains could potentially be used as therapies, Second Genome focuses on bioactive products derived from these strains that will have positive disease-modifying effects. These metabolites, peptides and proteins can be tested for activity in traditional pharmaceutical in vitro assays and further developed using classical drug development processes. Results of these in vitro assays are analyzed using machine learning models to improve subsequent nominations of therapeutic candidates.

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Classic Drug Development

Lead molecules identified through the Second Genome platform undergo classic drug development processes for further characterization in pre-clinical and IND enabling studies. Our ability to identify proteins, peptides and metabolites allows Second Genome to use standard manufacturing processes to help reduce technical and regulatory risk in drug development. Second Genome’s drug development approach allows us to identify tailored therapeutic solutions targeting precise disease mechanisms and populations in heterogenous diseases.

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Microbiome Technologies

Our world-class multi-disciplinary team has completed over 300 microbiome studies across industry, government, academia, nutrition companies, and pharma. Expert-built and validated bioinformatics generate the most insightful microbiome insights. These insights are the foundation of our microbiome drug discovery platform.

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Data Analysis Tools

Some of our tools that we’ve made available for collaborators and academic institutes. The tools can assist with organizing microbiome data by strain and by function.

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