A new comparative-genomics approach for defining phenotype-specific indicators reveals specific genetic markers in predatory bacteria

Zohar Pasternak, Tom Ben Sasson, Yossi Cohen, Elad Segev, Edouard Jurkevitch

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Predatory bacteria seek and consume other live bacteria. Although belonging to taxonomically diverse groups, relatively few bacterial predator species are known. Consequently, it is difficult to assess the impact of predation within the bacterial realm. As no genetic signatures distinguishing them from non-predatory bacteria are known, genomic resources cannot be exploited to uncover novel predators. In order to identify genes specific to predatory bacteria, we developed a bioinformatic tool called DiffGene. This tool automatically identifies marker genes that are specific to phenotypic or taxonomic groups, by mapping the complete gene content of all available fully-sequenced genomes for the presence/absence of each gene in each genome. A putative 'predator region' of ∼60 amino acids in the tryptophan 2,3-dioxygenase (TDO) protein was found to probably be a predator-specific marker. This region is found in all known obligate predator and a few facultative predator genomes, and is absent from most facultative predators and all non-predatory bacteria. We designed PCR primers that uniquely amplify a ∼180bp-long sequence within the predators' TDO gene, and validated them in monocultures as well as in metagenetic analysis of environmental wastewater samples. This marker, in addition to its usage in predator identification and phylogenetics, may finally permit reliable enumeration and cataloguing of predatory bacteria from environmental samples, as well as uncovering novel predators.

Original languageAmerican English
Article numbere0142933
JournalPLoS ONE
Issue number11
StatePublished - 1 Nov 2015

Bibliographical note

Funding Information:
This work was supported by the Israel Science Foundation (grant 1583/12) and the Deutsche Forschungsgemeinschaft (DFG) ( grant CH 731/2-1).

Publisher Copyright:
© 2015 Pasternaket al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


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