and metabolomes of organisms in a dynam- ic and interactive fashion. Academic institutions and publicly funded research consortia are generating large sets of ‘omic’ data that are capable of serving collaborative groups across differ- ent disciplines. With the cutting-edge approaches as discussed above, it will be possible to facilitate these groups to bring in and compare their sets of data with other experimental results and pathways available in the public domain. Web tools based on these concepts (for example, nextBio; http://www.nextbio.com) rou- tinely extract, integrate and compare information and observations contained in publications while juxtaposing colossal amounts of disparate, biological or clinical and ‘omic’ data from public and propri- etary sources, regardless of data type and origin. Other tools such as Ondex [30] display biological data as a set of linked graphs with the nodes representing a data object and the edges representing a relationship between the two nodes (http://ondex.sourceforge.net/). PLoS ONE Prokaryotic Genomes Collection The possibilities and proposals towards computational processing of genome data as discussed appear mind boggling at this stage, but ultimately scientists will be empowered to swiftly interpret their own experimental results within the context of References 1. Green P (2007) 2x genomes—does depth matter? Genome Res 17: 1547–1549. 2. Craddock T, Harwood CR, Hallinan J, Wipat A (2008) e-Science: relieving bottlenecks in large- scale genome analyses. Nat Rev Microbiol 6: 948–954. 3. Suen G, Goldman BS, Welch RD (2007) Predicting prokaryotic ecological niches using genome sequence analysis. PLoS ONE 2: e743. 4. Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, et al. (2008) Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS ONE 3: e1805. 5. Bellgard MI, Wanchanthuek P, La T, Ryan K, Moolhuijzen P, et al. (2009) Genome sequence of the pathogenic intestinal spirochete Brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine. PLoS ONE 4: e4641. 6. Ahmed N, Saini V, Raghuvanshi S, Khurana JP, Tyagi AK, et al. (2007) Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution. PLoS ONE 2: e968. 7. Ahmed N, Dobrindt U, Hacker J, Hasnain SE (2008) Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nature Rev Microbiol 6: 387–394. 8. Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, et al. (2004) Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 101: 13826–13831. 9. Crasta OR, Folkerts O, Fei Z, Mane SP, Evans C, et al. (2008) Genome sequence of Brucella abortus other published research findings in a more interactive and collaborative way. These advances underscore the need for important biological information such as genome sequences and microarray data sets to be made freely available and the literature describing the data interpreta- tion to be available through Open Access platforms such as PLoS ONE. Since PLoS ONE publishes research through extensi- ble markup language (XML), it is possible to quickly exchange experimental results and their interpretations across different platforms. This in turn simplifies utiliza- tion and processing of genomic informa- tion contained in research publications so that details such as decipherment of novel pathways or evolutionary relationships etc. could be discussed globally and interpret- ed through community genomics environ- ments. To this end, ‘PLoS ONE prokaryotic genomes collection’ represents a novel initiative to compile a permanent archive of all important articles describing whole genome sequence based biology of pro- karyotic organisms. This collection of articles will facilitate understanding of the biology and lifestyle of the underlying organisms not only through main contents of articles but also via information from external sources that discuss and link to the results, such as citations from PubMed Central, Google Scholar and Scopus; evaluations and ratings at Faculty of vaccine strain S19 compared to virulent strains yields candidate virulence genes. PLoS ONE 3: e2193. 10. Tsolis RM, Seshadri R, Santos RL, Sangari FJ, Garc´ıa Lobo JM (2009) Genome degradation in Brucella ovis corresponds with narrowing of its host range and tissue tropism. PLoS ONE (In press). 11. Beres SB, Musser JM (2007) Contribution of exogenous genetic elements to the group A Streptococcus metagenome. PLoS ONE 2: e800. 12. Hugenholtz P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3(2): reviews0003.1–0003.8. 13. Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome. Trends Genet 25: 107–110. 14. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, et al. (2005) Genome analysis of multiple pathogenic isolates of Strepto- coccus agalactiae: implications for the microbial ‘‘pan-genome’’. Proc Natl Acad Sci USA 102: 13950–13955. 15. Ge Z, Taylor DE (1999) Contributions of genome sequencing to understanding the biology of Helicobacter pylori. Annu Rev Microbiol 53: 353–387. 16. Rizwan M, Alvi A, Ahmed N (2008) Novel protein antigen (JHP940) from the genomic plasticity region of Helicobacter pylori induces tumor necrosis factor alpha and interleukin-8 secretion by human macrophages. J Bacteriol 190: 1146–1151. 17. Yamaoka Y (2008) Roles of the plasticity regions of Helicobacter pylori in gastroduodenal pathogen- esis. J Med Microbiol 57: 545–53. Prokaryotic Genomes Multiply 1000; bookmarks from social networking sites such as CiteULike and Connotea; and blog posts from experts and readers in the field. Just like other PLoS content, it will be possible to make utilization of individual articles interactive for the users (human or machine) to harness elements of research (annotation tables, phylogenet- ic trees, evolutionary hierarchies, gene expression data, graphs, texts etc.) and associated content in the form of relevant discussions (and raw data posted in response to a discussion). This content can be processed in a variety of compu- tational formats such as graphs or net- works that can be inspected visually, cured manually or mined computationally. Link- ing therefore the secondary contents and Science 2.0 based enhancements to pub- lished information and their subsequent harnessing through different knowledge- platforms is likely to underpin formation of new ideas and insights in a more holistic and interdisciplinary manner. Such novel theses in the form of alternative or even more provocative interpretations could ultimately be linked back to the original genome sequences thus completing a cycle of information sharing through Open Access. Acknowledgment I am thankful to Professor Seyed E. Hasnain for his guidance and support. 18. Prouzet-Maule´on V, Hussain MA, Lamouliatte H, Kauser F, Me´graud F, et al. (2005) Pathogen evolution in vivo: genome dynamics of two isolates obtained 9 years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain. J Clin Microbiol 43: 4237–4241. 19. Israel DA, Salama N, Krishna U, Rieger M, Atherton JC, et al. (2001) Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc Natl Acad Sci USA 98: 14625–14630. 20. Alvi A, Devi SM, Ahmed I, Hussain MA, Rizwan M, et al. (2007) Microevolution of Helicobacter pylori type IV secretion systems in an ulcer disease patient over a ten-year period. J Clin Microbiol 45: 4039–4043. 21. Maiden MC (2006) Multilocus sequence typing of bacteria. Annu Rev Microbiol 60: 561–588. 22. Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, et al. (2008) Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis. PLoS ONE 3: e1607. 23. Victoria B, Ahmed A, Zuerner RL, Ahmed N, Bulach DM, et al. (2008) Conservation of the S10- spc-a locus within otherwise highly plastic ge- nomes provides phylogenetic insight into the genus Leptospira. PLoS ONE 3(7): e2752. 24. Ahmed N, Devi SM, Valverde Mde L, Vijayachari P, Machang’u RS, et al. (2006) Multilocus sequence typing method for identifi- cation and genotypic classification of pathogenic PLoS ONE | www.plosone.org 4 June 2009 | Volume 4 | Issue 6 | e5831