This unique book officially defines microbiome statistics as a specific new field of statistics and addresses the statistical analysis of correlation, association, interaction, and composition in microbiome research. It also defines the study of the microbiome as a hypothesis-driven experimental science and describes two microbiome research themes and six unique characteristics of microbiome data, as well as investigating challenges for statistical analysis of microbiome data using the standard statistical methods. This book is useful for researchers of biostatistics, ecology, and data analysts. Presents a thorough overview of statistical methods in microbiome statistics of parametric and nonparametric correlation, association, interaction, and composition adopted from classical statistics and ecology and specifically designed for microbiome research. Performs step-by-step statistical analysis of correlation, association, interaction, and composition in microbiome data. Discusses the issues of statistical analysis of microbiome data: high dimensionality, compositionality, sparsity, overdispersion, zero-inflation, and heterogeneity. Investigates statistical methods on multiple comparisons and multiple hypothesis testing and applications to microbiome data. Introduces a series of exploratory tools to visualize composition and correlation of microbial taxa by barplot, heatmap, and correlation plot. Employs the Kruskal–Wallis rank-sum test to perform model selection for further multi-omics data integration. Offers R code and the datasets from the authors’ real microbiome research and publicly available data for the analysis used. Remarks on the advantages and disadvantages of each of the methods used.

This unique book addresses the statistical modelling and analysis of microbiome data using cutting-edge R software. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of R for data analysis step by step. The data and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter, so that these new methods can be readily applied in their own research. The book also discusses recent developments in statistical modelling and data analysis in microbiome research, as well as the latest advances in next-generation sequencing and big data in methodological development and applications. This timely book will greatly benefit all readers involved in microbiome, ecology and microarray data analyses, as well as other fields of research.

Microbiome research has focused on microorganisms that live within the human body and their effects on health. During the last few years, the quantification of microbiome composition in different environments has been facilitated by the advent of high throughput sequencing technologies. The statistical challenges include computational difficulties due to the high volume of data; normalization and quantification of metabolic abundances, relative taxa and bacterial genes; high-dimensionality; multivariate analysis; the inherently compositional nature of the data; and the proper utilization of complementary phylogenetic information. This has resulted in an explosion of statistical approaches aimed at tackling the unique opportunities and challenges presented by microbiome data. This book provides a comprehensive overview of the state of the art in statistical and informatics technologies for microbiome research. In addition to reviewing demonstrably successful cutting-edge methods, particular emphasis is placed on examples in R that rely on available statistical packages for microbiome data. With its wide-ranging approach, the book benefits not only trained statisticians in academia and industry involved in microbiome research, but also other scientists working in microbiomics and in related fields.

Compared with other research fields, both microbiome and metabolomics data are complicated and have some unique characteristics, respectively. Thus, choosing an appropriate statistical test or method is a very important step in the analysis of microbiome and metabolomics data. However, this is still a difficult task for those biomedical researchers without a statistical background and for those biostatisticians who do not have research experiences in these fields. Graduate students studying microbiome and metabolomics; statisticians, working on microbiome and metabolomics projects, either for their own research, or for their collaborative research for experimental design, grant application, and data analysis; and researchers who investigate biomedical and biochemical projects with the microbiome, metabolome, and multi-omics data analysis will benefit from reading this work.

This unique book addresses the bioinformatic and statistical modelling and also the analysis of microbiome data using cutting-edge QIIME 2 and R software. It covers core analysis topics in both bioinformatics and statistics, which provides a complete workflow for microbiome data analysis: from raw sequencing reads to community analysis and statistical hypothesis testing. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of QIIME 2 and R for data analysis step-by-step. The data as well as QIIME 2 and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter so that these new methods can be readily applied in their own research. Bioinformatic and Statistical Analysis of Microbiome Data is an ideal book for advanced graduate students and researchers in the clinical, biomedical, agricultural, and environmental fields, as well as those studying bioinformatics, statistics, and big data analysis.

The Food Forum convened a public workshop on February 22-23, 2012, to explore current and emerging knowledge of the human microbiome, its role in human health, its interaction with the diet, and the translation of new research findings into tools and products that improve the nutritional quality of the food supply. The Human Microbiome, Diet, and Health: Workshop Summary summarizes the presentations and discussions that took place during the workshop. Over the two day workshop, several themes covered included: The microbiome is integral to human physiology, health, and disease. The microbiome is arguably the most intimate connection that humans have with their external environment, mostly through diet. Given the emerging nature of research on the microbiome, some important methodology issues might still have to be resolved with respect to undersampling and a lack of causal and mechanistic studies. Dietary interventions intended to have an impact on host biology via their impact on the microbiome are being developed, and the market for these products is seeing tremendous success. However, the current regulatory framework poses challenges to industry interest and investment.

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.