Key microbial biomarker detection

BaseClear’s key microbial biomarker detection solution is based our proprietary bioinformatics pipeline that links clinical metadata with microbial taxonomic abundance tables. The state-of-the-art pipeline facilitates the identification of novel microbial biomarkers of diseases and personalised medicine applications and can enhance understanding of results in clinical trials. Partner with BaseClear to get more value out of your human microbiome research!

The human microbiome is intrinsically linked to health, with certain microbes associated with disease phenotypes in the literature. However the complexity of the microbiome hampers our ability to use microbes or microbial signatures to predict or detect disease. Metabolomics & biomarker analysis quantifies molecules produced by microbial community & hosts in sample such as blood, urine, faeces, tissues and cell cultures, thus providing a direct indication of the health of the community and how this microbial community interacts with its environment.

Microbial abundance tables from amplicon and shotgun sequencing can be jointly compared to metadata using advanced statistical methods such as dimension reduction, differential abundance analysis and machine learning. The strengths of these individual methods are most effective when used in parallel, and help to enhance the predictive power.

Benefits of our key microbial biomarker detection product

  • Successful detection of key microbes and microbial signatures linked to host phenotype
  • Enhanced predictive power through an ensemble of advanced methods
  • Computation of statistical value
  • Fully validated
  • Standardised end-to-end solution
  • State-of-the-art data visualisation with the BaseClear Microbiome Explorer

Microbial biomarker detection solutions

Disease diagnostics

Diseases that have microbes as a cause or sentinel in the disease process are candidates for the development of diagnostics based on key microbial biomarkers. Human microbiome samples from the skin, gut, vagina, nose or eye can be used to discover and identify key biomarker species. Robust correlations with metadata turn abundance tables into diagnostic tools that have the potential to reduce both the burden of disease and health care costs.

Personalised medicine

The microbiome is unique to each individual, and is dynamic. We all have different taxonomic diversity and key species in our gut, which affects the overall metabolic potential of the gut. Some drugs are metabolised by key microbes in the gut before they can be absorbed, reducing their efficacy. By identifying key microbes in the gut microbiome that affect drug absorption, patients’ individual microbiomes can be tested to better predict response to treatment. This enables to select the right treatment for each individual patient.

Mechanistic research

Examination of the mechanisms behind the interaction of the microbiome and the host offers valuable insights in how the microbiome is involved in disease. Whether the treatment is a new probiotic, prebiotic, or can be affected by the microbiome, the Key Microbial Biomarker Detection product can support clinical research by robustly explaining the mechanism and function of host-microbe interactions.

An overview of BaseClear’s analysis pipeline

  • 16S rRNA or whole genome sequencing taxonomic data is used as input
  • Data undergoes pre-processing including filtering, normalisation and transformation
  • In parallel, the following techniques are used:
    • Feature elimination and importance evaluation using Random Forest
    • Logistic regression using LASSO, ridge or elastic net regularisers, arranged by effect sizes
    • Biomarker validation using LEfSe (Linear discriminant analysis Effect Size) and filtered by LDA score
    • Differential abundance analysis filtered by p-value
  • This ensemble analysis results in selection of single biomarker microbes or a biosignature of multiple microbes.

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