RESEARCH ARTICLE Functional Basis of Microorganism Classification Chengsheng Zhu1*, Tom O. Delmont2, Timothy M. Vogel2, Yana Bromberg1,3* 1 Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America, 2 Environmental Microbial Genomics, Laboratoire Ampere, École Centrale de Lyon, Université de Lyon, Ecully, France, 3 Institute for Advanced Study, Technische Universität München, Garching, Germany *
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[email protected] (YB) Abstract Correctly identifying nearest “neighbors” of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classifi- cation based on similarity of physiological and genetic organism traits (polyphasic similarity) OPEN ACCESS is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from Citation: Zhu C, Delmont TO, Vogel TM, Bromberg Y phylogenetic markers, facilitates classification but does not guarantee functional identity (2015) Functional Basis of Microorganism Classification. PLoS Comput Biol 11(8): e1004472. between members of the same taxon or lack of similarity between different taxa. Using over doi:10.1371/journal.pcbi.1004472 thirteen hundred sequenced bacterial genomes, we built a novel function-based microor- Editor: Christine A. Orengo, University College ganism classification scheme, functional-repertoire similarity-based organism network London, UNITED KINGDOM (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively Received: March 27, 2015 defined organism relationships across the known prokaryotic space. It correlates signifi- cantly with the current taxonomy, but the observed discrepancies reveal both (1) the incon- Accepted: July 21, 2015 sistency of functional diversity levels among different taxa and (2) an (unsurprising) bias Published: August 28, 2015 towards prioritizing, for classification purposes, relatively minor traits of particular interest to Copyright: © 2015 Zhu et al.