Overview A Flood of Microbial Genomes–Do We Need More? Niyaz Ahmed* Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India Complete genome sequences of impor- tant bacterial pathogens and industrial organisms hold significant consequences and opportunities for human health, industry and the environment. Addressing biological and clinical problems through genome sequence based approaches offers many commercial opportunities. The af- termath of whole genome sequencing has revealed new insights into evolution of bacterial lifestyles including strategies for adaptation to new niches and overcoming competitors. Whole genome sequences representing more than 1500 prokaryotic organisms combined with the dozens (to hundreds) of strain re-sequencing projects are posing mind boggling problems on the optimal utilization of the resultant ‘omic’ datasets. Consequently, microbiologists are confronted with the challenge to translate these data into better human and animal healthcare solutions and pursue basic research approaches to inter- pret the data in ecological and evolution- ary perspectives. New informatic ap- proaches towards optimal utilization, holistic integration and meaningful inter- pretation of the genome sequence data are extremely necessary. Introduction Whole genome sequence analysis of prokaryotes is fundamentally important in understanding human infections, devel- opment of diagnostics and vaccines, bio- defense studies, antimicrobial target iden- tification and drug design. Rapid advances in sequencing technology have provided the capability to quickly and cheaply produce several hundreds of prokaryotic genomes each year. The next generation sequencing plat- forms (454 from Roche, Solexa of Illu- mina, and SoLiD from ABI) hold promise to further reduce time and cost of whole genome sequencing. Multiple species of bacteria and hundreds of strains thereof are being sequenced every year, thanks to cutting edge approaches such as re- sequencing wherein genome sequence of a reference organism is used as a scaffold to direct analysis of several different strains [1]. Using this method, multiple whole- genome bacterial sequencing projects can now be completed in less than two weeks instead of months. The total number of completed genomes (including reference and strain re-sequencing projects) is con- sistently doubling every 16 months [2] by adding about 20 new genomes every month [3]. By the end of March 2009, a total of 1775 prokaryotic genome sequenc- es and draft assemblies were available in the NCBI genome database. At this pace of sequencing output, study of a single bacterial genome has become almost pedestrian while the comparisons of mul- tiple strains of a single species is within the relatively easy reach. Comparison of genomic sequences has revealed mechanism of changes in bacte- rial lifestyles. We have learned how species have evolved strategies to survive and compete as part of adaptation to their preferred hosts, habitats or niches. Geno- mic comparison of multiple species and strains has facilitated insights into adaptive mechanisms leading to host or tissue tropism. Such inferences however need to be tested functionally and thus the need for integration of genome data with cues obtainable from downstream ‘omic’ ex- periments that have sampled a variety of conditions or treatments. New informatic approaches are emerging which are capa- ble of integrating genomic and functional datasets and also making use of data available through published resources. The emergence of e-Science, Semantic Web, and Science 2.0 approaches hold a lot of promise for holistic data integration and meaningful interpretation of commu- nity genomics and microarray experiments in an interactive and collaborative fashion. The present overview discusses some of these issues and ideas in relation to the ‘PLoS ONE prokaryotic genomes collec- tion’. Genomic insights - lifestyles, adaptations and pathogenic mechanisms Comparative genomics of whole ge- nome sequences of many different patho- genic and commensal forms of microor- ganisms have improved our perception of the mechanisms of pathogenesis and the transition between pathogenic and non- pathogenic varieties within the same species. It is becoming increasingly evident that distinct genomic differences found in different microbes have a definite impact on pathogenic potential, adaptation to parasitic lifestyles and host/tissue tropism. Some examples in this context are dis- cussed. In the case where different species of the same genus represent diverse lifestyles it is imperative to have sampled genome sequences from varieties of all forms. For example, the availability of three complete genome sequences from Acinetobacter (i.e. AYE, SDF and A. baylyi ADP1) has enabled comparison in a more general context to tease apart likely genetic changes that enabled adaptation of Acine- tobacter species to specific environments [4]. While the three organisms share a large chunk of genes, major differences exist in terms of their flexible genome component such as prophages and inser- tional sequences [4]. Another interesting lifestyle has been deciphered from the genome sequence of Citation: Ahmed N (2009) A Flood of Microbial Genomes–Do We Need More? PLoS ONE 4(6): e5831. doi:10.1371/journal.pone.0005831 Editor: Jason E. Stajich, University of California, Berkeley, United States of America Received April 16, 2009; Accepted May 1, 2009; Published June 9, 2009 Copyright: 2009 Ahmed. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Research in Ahmed laboratory is funded by grants from the Department of Biotechnology of the Indian Government and support from the University of Hyderabad under OBC/XI-Plan and UoH-DBT CREBB funds. The School of Life Sciences at the University of Hyderabad has been recognized as ‘Centre of Advanced Studies’ and supported under SAP program (UGC-SAP-CAS-I) of the University Grants Commission (India). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: ahmed.nizi@gmail.com PLoS ONE | www.plosone.org 1 June 2009 | Volume 4 | Issue 6 | e5831