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Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data

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Abstract

The human microbiome plays critical roles in human health and has been linked to many diseases. While advanced sequencing technologies can characterize the composition of the microbiome in unprecedented detail, it remains challenging to disentangle the complex interplay between human microbiome and disease risk factors due to the complicated nature of microbiome data. Excessive numbers of zero values, high dimensionality, the hierarchical phylogenetic tree and compositional structure are compounded and consequently make existing methods inadequate to appropriately address these issues. We propose a multivariate two-part zero-inflated logistic-normal model to analyze the association of disease risk factors with individual microbial taxa and overall microbial community composition. This approach can naturally handle excessive numbers of zeros and the compositional data structure with the discrete part and the logistic-normal part of the model. For parameter estimation, an estimating equations approach is employed that enables us to address the complex inter-taxa correlation structure induced by the hierarchical phylogenetic tree structure and the compositional data structure. This model is able to incorporate standard regularization approaches to deal with high dimensionality. Simulation shows that our model outperforms existing methods. Our approach is also compared to others using the analysis of real microbiome data.

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Funding

This work was supported by NIH grants: R01GM123014, R01GM123056, P01ES022832, UG30D023275, R01CA127334, P20GM104416, K01LM011985 and R01LM012723 and EPA grant RD-83544201.

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Authors and Affiliations

  1. Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, 1 Medical Center Drive, Lebanon, NH, 03756, USA

    Zhigang Li, Anne G. Hoen & A. James O’Malley

  2. Children’s Environmental Health and Disease Prevention Research Center at Dartmouth, Hanover, NH, USA

    Zhigang Li, Margaret R. Karagas, Juliette C. Madan & Anne G. Hoen

  3. Department of Epidemiology, Geisel School of Medicine at Dartmouth, 1 Medical Center Drive, Lebanon, NH, 03756, USA

    Zhigang Li, Margaret R. Karagas, Juliette C. Madan & Anne G. Hoen

  4. Department of Biostatistics, University of Florida, Gainesville, FL, 32611, USA

    Zhigang Li

  5. Phillips Exeter Academy, Exeter, NH, 03833, USA

    Katherine Lee

  6. Division of Neonatology, Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH, USA

    Juliette C. Madan

  7. The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine at Dartmouth, 1 Medical Center Drive, Lebanon, NH, 03756, USA

    A. James O’Malley

  8. Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA

    Hongzhe Li

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  1. Zhigang Li
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  2. Katherine Lee
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Correspondence to Zhigang Li.

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Appendix

Appendix

Comparison of selected genera under two randomly selected reference genera: Akkermansia and Anoxybacillus. Results for Akkermansia being the reference genus is also presented in Sect. 4.

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Li, Z., Lee, K., Karagas, M.R. et al. Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data. Stat Biosci 10, 587–608 (2018). https://doi.org/10.1007/s12561-018-9219-2

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  • DOI: https://doi.org/10.1007/s12561-018-9219-2

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