arsenaticum. Within this genome, 145 non-coding RNA genes are described. These include a single operon encoding 16S and 23S ribosomal RNA, the associated 5S rRNA, the 7S signal recognition particle(SRP), and the RNase P RNA. Ganetespib cost There are 47 annotated tRNA genes, plus a single tRNA pseudogene. Also included are 83 predicted C/D box sRNA genes and nine additional H/ACA-like sRNA, each of which has been transcriptionally validated [31]. The non-coding RNA content of the P. oguniense genome has become the most extensively annotated among crenarchaeal genomes to date. The use of a not-quite-clonal cell population for DNA isolation, coupled with ultra-deep sequencing has provided a view of three major inversions that are each present in over 17% of the sample population.

The boundaries of one of these inversions are defined by an inverted repeat encoding a duplication of glutamate dehydrogenase (GluDH). Notably, this duplication appears to be present in each of the currently sequenced Pyrobaculum members, suggesting that those genomes may also host similar inversions. A second inversion has at its termini another inverted duplication, encoding a gene associated with one of the paREP members and a CRISPR-associated gene. It remains unclear if these common structural variants impart a physiological advantage, and if so, how the variation provides utility to its host. Based on our expanded genome diversity observations, we suggest that avoiding the use of a strictly clonal population for sequencing purposes can provide a significant benefit to understanding both the biology of the host and a clearer understanding of the genome dynamics of the species.

Acknowledgements Sequencing was provided by the UCSC Genome Sequencing Center. We would like to thank Nathan Boyd, Eveline Hesson and Nader Pourmand for their expertise and advice in this work. This work was supported by National Science Foundation Grant DBI-0641061 (T.L. and D.B.) and the Graduate Research and Education in Adaptive Bio-Technology (GREAT) Training Program sponsored by the University of California Biotechnology Research and Education Program (D.B.).
Alistipes senegalensis strain JC50T (= CSUR P156= DSM 25460) is the type strain of A. senegalensis sp. nov. This bacterium was isolated from the stool of a healthy Senegalese patient as part of a ��culturomics�� study aiming at cultivating all species in human feces, individually.

Bacterial species definition is a matter of debate. This is notably due to the high cost, poor reproducibility and inter-laboratory comparability Batimastat of the ��gold standard�� of DNA-DNA hybridization and G+C content determination [1]. In contrast, the development of PCR and sequencing methods, both of which are now widely available and cost-effective, has profoundly changed the way of classifying prokaryotes.