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The objective of this study was to determine the bacterial pathogen and gene content of the Etroplus suratensis (pathogenic shrimp). PCR-based subtractive hybridization method detected with the help of Escherichia coli on shrimp liver and granulose cells for efficiently detecting the DNAs and applies in to liver pathogen. Seventeen DNAs specific to a mono-key colonizing strain (J140) were obtained by subtractive hybridization against an unrelated strain whose genome has been fully sequenced (ABO18799). Among the seventeen different clones 14 were unique and other three numbers were each represented at twice. Nine of the clones DNAs were found by sequencing to be absent or very divergent from those in the same direction on disappeared blank region of this liver and granulosa cells. Nine others had no database match with proteins of assigned function. PCR tests of 13 unrelated E.coli strains by using primer specific for 12 subtracted clones and complementary southern hybridizations indicated that these DNAs are highly polymorphic in the E. coli population with each strain yielding a different pattern of gene-specific PCR amplification. When described about this Polymorphic immune response gene, it helps to identify the previously unknown virulent genes in the pathogens and it provides a new insight of microbial genetic diversity and evolution.