Representing bacteria with unique genomic signatures

Abstract

Classifying or identifying bacteria in metagenomic samples is an important problem in the analysis of metagenomic data. This task can be computationally expensive since microbial communities usually consist of hundreds to thousands of environmental microbial species. We proposed a new method for representing bacteria in a microbial community using genomic signatures of those bacteria. With respect to the microbial community, the genomic signatures of each bacterium are unique to that bacterium; they do not exist in other bacteria in the community. Further, since the genomic signatures of a bacterium are much smaller than its genome size, the approach allows for a compressed representation of the microbial community. This approach uses a modified Bloom filter to store short k-mers with hash values that are unique to each bacterium. We show that most bacteria in many microbiomes can be represented uniquely using the proposed genomic signatures. This approach paves the way toward new methods for classifying bacteria in metagenomic samples.