Microbiome research offers promising insights into the impact of microorganisms on biological systems. Metaproteomics, the study of microbial proteins at the community level, integrates genomic, transcriptomic, and proteomic data to determine the taxonomic and functional state of a microbiome. However, standard metaproteomics software is subject to several limitations, commonly supporting only spectral counts, emphasizing exploratory analysis rather than hypothesis testing and rarely offering the ability to analyze the interaction of function and taxonomy - that is, which taxa are responsible for different processes. Here we present metaQuantome, a novel, multifaceted software suite that analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information, emphasizing label-free intensity-based methods. For experiments with multiple experimental conditions, metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. We benchmark meta- Quantome analysis against standard methods, using two previously published datasets: (1) an artificially assembled microbial community dataset (taxonomy benchmarking) and (2) a dataset with a range of recombinant human proteins spiked into an Escherichia coli background (functional benchmarking). Furthermore, we demonstrate the use of metaQuantome on a previously published human oral microbiome dataset. In both the taxonomic and functional benchmarking analyses, metaQuantome quantified taxonomic and functional terms more accurately than standard summarization- based methods. We use the oral microbiome dataset to demonstrate metaQuantome's ability to produce publication- quality figures and elucidate biological processes of the oral microbiome. metaQuantome enables advanced investigation of metaproteomic datasets, which should be broadly applicable to microbiome-related research. In the interest of accessible, flexible, and reproducible analysis, metaQuantome is open source and available on the command line and in Galaxy.
Bibliographical noteFunding Information:
* We acknowledge funding for this work from the grant National Cancer Institute - Informatics Technology for Cancer Research (NCI-ITCR) grant 1U24CA199347 and National Science Foundation (U.S.) grant 1458524 to T.G. We would also like to acknowledge the Extreme Science and Engineering Discovery Environment (XSEDE) research allocation BIO170096 to P.D.J. and use of the Jetstream cloud-based computing resource for scientific computing (https:// jetstream-cloud.org/) maintained at Indiana University. We also acknowledge the support from the Minnesota Supercomputing Institute for maintenance and update of the Galaxy instances. §§ To whom correspondence should be addressed: 7-136 MCB, 420 Washington Ave SE, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455; Phone: 612-816-4232; E-mail: email@example.com.
© 2019 Easterly et al.