BMC Genomics 2006, 7:154 http://www.biomedcentral.com/1471-2164/7/154 end of the vector and 58% of these resulting sequences overlapped significantly with the associated 3' sequence to generate 8,067 contigs with an average sequence length of 1,065 bp. All sequences were annotated with BLASTX (E- value < -03) and Gene Ontology (GO). Conclusion: Both the number of ESTs generated from each library and GO categorizations are reflective of the activity state of the light organ during these early stages of symbiosis. Future analyses of the sequences identified in these libraries promise to provide valuable information not only about pathways involved in colonization and early development of the squid light organ, but also about pathways conserved in response to bacterial colonization across the animal kingdom. Background The study of the interactions of animals with their benefi- cial or mutualistic bacterial partners is a frontier field with a vast array of largely unanswered questions. A major sub- set of such associations, e.g., those of mammals, com- prises the horizontally transmitted partnerships, i.e., associations in which the host and symbiont population or community re-establishes the relationship with each new host generation [1]. For this specific array of partner- ships, some principal questions include: how are the bac- terial partners harvested from the environment? In associations with consortia of bacteria, who are the natu- rally coevolved symbionts, or residents, and who are the 'tourists'? What factors mediate partner recognition and specificity? How do the partners impact one anothers' developmental programs? How is stability of the associa- tion achieved so that the bacterial partners are not elimi- nated nor are they allowed to overgrow host tissues? What are the principal similarities and differences in the mech- anisms underlying beneficial and pathogenic interac- tions? Biologists know little about beneficial animal-bacterial relationships principally because of technological imped- iments, many of which have been alleviated by advances in molecular biology and biotechnology. These techno- logical breakthroughs have poised the community of biol- ogists to address the above-mentioned questions. Specifically, large-scale sequencing efforts are allowing biologists to define the communities associated with par- ticular animal species (e.g., [2-6]), and development of such methods as microarray analyses are enabling biolo- gists to determine host and symbiont responses under natural and experimental conditions [6,7]. In addition to these technological advances, the develop- ment of powerful models for the study of animal-bacterial interactions has been essential. As in developmental biol- ogy, the study of a wide variety of models will shed light on evolutionarily conserved mechanisms as well as the basis of diversity. To this end, two principal, complemen- tary model types are under investigation: those using germ-free or gnotobiotic animals and binary associations. Most notably for the former, Gordon and coworkers have been experimentally manipulating germ-free, gnotobiotic and 'conventionalized' (provided with their normal microbiota) zebrafish and mice to characterize interac- tions with their microbial partners [6,8]. These studies have revealed that the diverse community of microbiota in the vertebrate gut has profound effects on the gene expression, anatomy and physiology of the host animals (see e.g., [9,10]). Binary associations, i.e., those composed on one host species and a population of one microbial species, occur most often in invertebrate animals and offer relatively simple experimental systems for the study of animal-microbe relationships [11-13]. The association between the Hawaiian sepiolid squid Euprymna scolopes and its luminous bacterial partner Vibrio fischeri is a binary model system that has been under investigation for the last fifteen years (for review see [13]). The relationship, in which the symbiont lives extracellu- larly in crypts of the light organ, begins in the hours after the juvenile host hatches from the egg. During embryo- genesis, the host develops a nascent light organ that pro- motes specific colonization by V. fischeri (Fig. 1). Once light organ tissues have been colonized, development of the partners is induced (Fig. 2). The bacterial symbiont triggers an elaborate developmental program in the host animal that leads to the transformation of the organ from an anatomy, physiology and biochemistry that promotes infection to one that fosters the functioning of the mature, bioluminescent organ. Likewise, the bacterial partner transforms its biology from that characteristic of its niche in the bacterioplankton to that of its niche as a luminous bacterial symbiont. In developing the squid-vibrio model, researchers in the field have sought not only to describe the nature of the system, from both the host and symbiont sides of the association, but also to apply new tools, as they became available, for its study. Specifically, early efforts resulted in the development of genetics in the bacterial symbiont [14] and, more recently, the annotated sequence of the V. fischeri genome has become available [15]. The collabora- tive work presented here describes the first efforts to gen- erate bioinformatics tools for the host side of the squid- vibrio association. Our goal was to define a representative set of host genes expressed in the juvenile light organ dur- ing the early developmental stages. To this end, we gener- Page 2 of 10 (page number not for citation purposes)