BackgroundRapidly characterizing the operational interrelationships among all genes in a given organism is a critical bottleneck to significantly advancing our understanding of thousands of newly sequenced microbial and eukaryotic species. While evolving technologies for global profiling of transcripts, proteins, and metabolites are making it possible to comprehensively survey cellular physiology in newly sequenced organisms, these experimental techniques have not kept pace with sequencing efforts. Compounding these technological challenges is the fact that individual experiments typically only stimulate relatively small-scale cellular responses, thus requiring numerous expensive experiments to survey the operational relationships among nearly all genetic elements. Therefore, a relatively quick and inexpensive strategy for observing changes in large fractions of the genetic elements is highly desirable.ResultsWe have discovered in the model organism Halobacterium salinarum NRC-1 that batch culturing in complex medium stimulates meaningful changes in the expression of approximately two thirds of all genes. While the majority of these changes occur during transition from rapid exponential growth to the stationary phase, several transient physiological states were detected beyond what has been previously observed. In sum, integrated analysis of transcript and metabolite changes has helped uncover growth phase-associated physiologies, operational interrelationships among two thirds of all genes, specialized functions for gene family members, waves of transcription factor activities, and growth phase associated cell morphology control.ConclusionsSimple laboratory culturing in complex medium can be enormously informative regarding the activities of and interrelationships among a large fraction of all genes in an organism. This also yields important baseline physiological context for designing specific perturbation experiments at different phases of growth. The integration of such growth and perturbation studies with measurements of associated environmental factor changes is a practical and economical route for the elucidation of comprehensive systems-level models of biological systems.

Bacillus anthracis is the causative agent of anthrax, and it is classified as "category A" biological weapon. There were six available complete genomes (A0248, Ames, Ames Ancestor, CDC684, H0491 and Sterne). Here, one Gambian and two Senegalese strains (Gmb1, Sen2Col2 and Sen3) were added. In this work, the pan-genome of B. anthracis was studied based on nine strains and using bioinformatics tools as Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Thereafter, B. anthracis pan-genome having 2893 core genes and 85 accessory genes was estimated. With Mauve method, the pan-genome of B. anthracis was verified and it was found to be very narrow and clonal. To have confidence in this study, different tools were used to compare and validate the results. All of the tools yielded the same results; the addition of the Senegalese and Gambian strains did not change the nature of the B. anthracis pan-genome (2893 core genes and 85 accessory genes), which had a core/pan-genome ratio of 99%. The closed nature of the pan-genome of B. anthracis (the core genome) represents 99% of the pan-genome size. The hypothesis that B. anthracis had a closed pan-genome was hereby validated.