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Gut microbiome, big data and machine learning to promote precision medicine for cancer

Abstract

The gut microbiome has been implicated in cancer in several ways, as specific microbial signatures are known to promote cancer development and influence safety, tolerability and efficacy of therapies. The ‘omics’ technologies used for microbiome analysis continuously evolve and, although much of the research is still at an early stage, large-scale datasets of ever increasing size and complexity are being produced. However, there are varying levels of difficulty in realizing the full potential of these new tools, which limit our ability to critically analyse much of the available data. In this Perspective, we provide a brief overview on the role of gut microbiome in cancer and focus on the need, role and limitations of a machine learning-driven approach to analyse large amounts of complex health-care information in the era of big data. We also discuss the potential application of microbiome-based big data aimed at promoting precision medicine in cancer.

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Fig. 1: Representation of a machine learning workflow.
Fig. 2: From big data to precision medicine: moving through the data science.

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Acknowledgements

This publication has in part emanated from research conducted with the financial support of AIRC Foundation for Cancer Research (AIRC IG grant number 18599, MFAG grant number 23681) and Science Foundation Ireland (grant number SFI/12/RC/2273).

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ColPortal: https://colportal.imib.es

GenBank and Gene Expression Omnibus: https://www.ncbi.nlm.nih.gov/gds

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Microbiome Learning Repo: https://knights-lab.github.io/MLRepo/

ML4Microbiome COST Action: https://www.cost.eu/actions/CA18131

ONCOBIOME Project: https://cordis.europa.eu/project/id/825410/it

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Cammarota, G., Ianiro, G., Ahern, A. et al. Gut microbiome, big data and machine learning to promote precision medicine for cancer. Nat Rev Gastroenterol Hepatol 17, 635–648 (2020). https://doi.org/10.1038/s41575-020-0327-3

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