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Tools for Analysis of the Microbiome

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Abstract

Over the past decade, it has become exceedingly clear that the microbiome is a critical factor in human health and disease and thus should be investigated to develop innovative treatment strategies. The field of metagenomics has come a long way in leveraging the advances of next-generation sequencing technologies resulting in the capability to identify and quantify all microorganisms present in human specimens. However, the field of metagenomics is still in its infancy, specifically in regard to the limitations in computational analysis, statistical assessments, standardization, and validation due to vast variability in the cohorts themselves, experimental design, and bioinformatic workflows. This review summarizes the methods, technologies, computational tools, and model systems for characterizing and studying the microbiome. We also discuss important considerations investigators must make when interrogating the involvement of the microbiome in health and disease in order to establish robust results and mechanistic insights before moving into therapeutic design and intervention.

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Authors and Affiliations

  1. Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 1954, Houston, TX, 77030, USA

    Jessica Galloway-Peña

  2. Department of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA

    Jessica Galloway-Peña

  3. Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Sciences Center, Houston, TX, USA

    Jessica Galloway-Peña & Blake Hanson

  4. Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health at Houston, University of Texas Health Sciences Center, 1200 Pressler St. RAS E739, Houston, TX, 77030, USA

    Blake Hanson

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  1. Jessica Galloway-Peña
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  2. Blake Hanson
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Correspondence to Jessica Galloway-Peña.

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Galloway-Peña, J., Hanson, B. Tools for Analysis of the Microbiome. Dig Dis Sci 65, 674–685 (2020). https://doi.org/10.1007/s10620-020-06091-y

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