Functional Basis of Microorganism Classification

PLoS Computational Biology
Chengsheng ZhuYana Bromberg

Abstract

Correctly identifying nearest "neighbors" of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classif...Continue Reading

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Citations

Jun 29, 2018·Bioinformatics·Yannick MahlichYana Bromberg
Nov 2, 2019·Biology Direct·Chengsheng ZhuYana Bromberg
Feb 10, 2018·PeerJ·Tom O Delmont, A Murat Eren
May 1, 2021·Frontiers in Microbiology·Reid G GriggsNicholas A Bokulich
May 8, 2021·FEMS Microbiology Ecology·Damien R FinnTimothy M Vogel

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Software Mentioned

PHYLIP
RAST
Patristic
BLAST
hmmscan
ForceAtlas2
myRAST )
Fusion
EggNOG
HSSP

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