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Breakthrough microbiomics platform offers cost-efficient imputed whole-genome metagenomics and strain-level analyses

Clinical-Microbiomics, a specialized microbiome analyses provider and developer of advanced bioinformatics tools, announces a new metagenomics platform for microbiome systems biology that significantly reduces the cost of comprehensive whole-genome metagenomics profiling by imputation from shallow sequencing, and enables de novo strain-level microbiome profiling.   

The platform is built on knowledge learned from an unprecedented collection of more than 2000 deep-sequenced human gut samples and the pioneering metagenomics species (MGS) concept (Nielsen et al., Nature Biotechnology, 2014). The MGS concept relies on de novo species identification and captures up to 80% of the microbial diversity in the samples compared to most reference-based methods that capture just 25% of the diversity at species level.

“By leveraging our vast collection of deep-sequenced human gut samples we can impute the microbiome composition from a 40 times lower sequencing depth without significant reduction in quality compared to deep-sequenced shotgun metagenomics. Imputed metagenomics is ideal for comparative studies normally associated with high costs for sequencing, which alternatively would rely on inferior 16S metagenomics due to cost concerns. With imputed metagenomics you get the full shotgun metagenomics picture of the microbiome including its functional potential, but at a fraction of the sequencing cost”, says Martin Santini, CEO of Clinical-Microbiomics.

The microbiome metagenomics platform further allows for a suite of advanced analyses, which enable detailed insights of the microbiomes in pre-clinical and clinical projects. From regular deep-sequencing shotgun metagenomics, we can obtain de novo strain-level resolution of the microbiome, assess growth dynamics, colonization and persistence probabilities, and integrate microbiome data with an array of other -omics and clinical data.

“This framework significantly reduces the cost of high-resolution microbiomics and at the same time boost the insight we can gain from a broad range of microbiome studies aimed at disease etiology, microbiome interventions and therapeutics. With this platform we can move from standard association studies to mechanistic associations and with the strain-resolution we can learn much more about microbiome ecology and evolution. Importantly, the platform allows us to custom-tailor the analyses to our clients’ needs”, adds Henrik Bjørn Nielsen, CSO of Clinical-Microbiomics.

About Clinical-Microbiomics
Clinical-Microbiomics is a contract research organization specialized in microbiome metagenomics. Through state-of-the-art sequencing and development of tailor-made bioinformatics analyses, we assist partners across industries to extract key biological insights from microbiome research.

Our proprietary bioinformatics platform and continuous innovation pipeline provides our partners with revolutionizing capabilities to analyze and interpret microbiome metagenomics data, including integration of big data, such as metabolomics, metatranscriptomics and clinical data.

Contact information
Martin Santini, CEO


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