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Species of  Xenorhabdus  and  Photorhabdus  bacteria form mutualistic associations with  Steinernema  and  Heterorhabditis  nematodes, respectively and serve as model systems for studying microbe-animal symbioses. Here, we profiled gene expression of  Xenorhabdus koppenhoeferi  during their symbiotic persistence in the newly formed infective juveniles of the host nematode  Steinernema scarabaei  through the selective capture of transcribed sequences (SCOTS). The obtained gene expression profile was then compared with other nematode-bacteria partnerships represented by  Steinernema carpocapsae—Xenorhabdus nematophila  and  Heterorhabditis bacteriophora—Photorhabdus temperata . A total of 29 distinct genes were identified to be up-regulated and 53 were down-regulated in  X .  koppenhoeferi  while in  S .  scarabaei  infective juveniles. Of the identified genes, 8 of the up-regulated and 14 of the down-regulated genes were similarly expressed in  X .  nematophila  during persistence in its host nematode  S .  carpocapsae . However, only one from each of these up- and down-regulated genes was common to the mutualistic partnership between the bacterium  P .  temperata  and the nematode  H .  bacteriophora . Interactive network analysis of the shared genes between  X .  koppenhoeferi  and  X .  nematophila  demonstrated that the up-regulated genes were mainly involved in bacterial survival and the down-regulated genes were more related to bacterial virulence and active growth. Disruption of two selected genes  pta  (coding phosphotransacetylase) and  acnB  (coding aconitate hydratase) in  X .  nematophila  with shared expression signature with  X .  koppenhoeferi  confirmed that these genes are important for bacterial persistence in the nematode host. The results of our comparative analyses show that the two  Xenorhabdus  species share a little more than a quarter of the transcriptional mechanisms during persistence in their nematode hosts but these features are quite different from those used by  P .  temperata  bacteria in their nematode host  H .  bacteriophora .

Comparative Analysis of Xenorhabdus koppenhoeferi Gene Expression during Symbiotic Persistence in the Host Nematode