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  • Moving metagenomics from lab to clinic

    I have been working on microbiome research at Washington University in St Louis for the last 2-3 years and wanted to introduce myself. My lab has released microbiome power/sample size calculations and tests of hypotheses open source software developed for translational clinical microbiome research.

    Our paper describing it provides a link to software that a statistician in your lab could use free of charge. This paper is at:

    This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups), and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches such as bootstrapping and permutation testing, in that this model is able to retain more information contained in the data. This paper details the statistical approaches for several tests of hypothesis and power/sample size calculations, and applies them for illustration to taxonomic abundance distribution and rank abundance distribution data using HMP Jumpstart data on 24 subjects for saliva, subgingival, and supragingival samples. Software for running these analyses is available.


    You (or your colleagues doing microbiome research) are more than welcome to use this software on your own to develop microbiome protocols and run statistical analyses. We think this software will be very important for translational clinical use of microbiome technology.

    We have a second paper that analyzes taxonomies through the analysis of taxonomic trees. This paper (and a link to software) can be found at

    PLOS Collections PLOS Collections bring you expert research from active researchers across the field. Covering a connected body of work and evaluated…


    We are currently extending this second paper to define microbiome cores and identify subgroups of samples with distinct microbiome cores using statistical criteria.

    If the software seems useful and you need technical help running the software for power/sample size calculations or for designing a study, performing data analysis, writing a statistical analysis section for a grant, or other statistical help, we can discuss our helping you. Feel free to call anytime (1-314-704-8725). If I am busy I will call you back as soon as possible.

    Bill Shannon
    Washington Univ. in St Louis
    BioRankings LLC

  • #2
    That is such a thoughtful offer BillShannon, I am sure that it has helped many scientists.

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