title: Toward Accurate and Quantitative Comparative Metagenomics.
abstract: Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized.
authors: Integrative Program in Quantitative Biology, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA.
authors: Stephen
authors: S
authors: Nayfach
authors: Gladstone Institutes, San Francisco, CA 94158, USA; Division of Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA. Electronic address: kpollard@gladstone.ucsf.edu.
authors: Katherine S
authors: KS
authors: Pollard
mesh_terms: D002965:Classification; D019295:Computational Biology; D006801:Humans; D054892:Metagenome; D056186:Metagenomics / Q000592:standards*; D064307:Microbiota / Q000235:genetics*; D015233:Models, Statistical