Beutenbergia cavernae (Groth et al. 1999) is the type species of the genus and is of phylogenetic interest because of its isolated location in the actinobacterial suborder Micrococcineae. B. cavernae HKI 0122T is a Gram-positive, non-motile, non-spore-forming bacterium isolated from a cave in Guangxi (China). B. cavernae grows best under aerobic conditions and shows a rod-coccus growth cycle. Its cell wall peptidoglycan contains the diagnostic L-lysine - L-glutamate interpeptide bridge. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the poorly populated micrococcineal family Beutenbergiaceae, and this 4,669,183 bp long single replicon genome with its 4225 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Thermobifida fusca is a moderately thermophilic soil bacterium that belongs to Actinobacteria. 3 It is a major degrader of plant cell walls and has been used as a model organism for the study of 4 secreted, thermostable cellulases. The complete genome sequence showed that T. fusca has a 5 single circular chromosome of 3642249 bp predicted to encode 3117 proteins and 65 RNA6 species with a coding density of 85 percent. Genome analysis revealed the existence of 29 putative 7 glycoside hydrolases in addition to the previously identified cellulases and xylanases. The 8 glycosyl hydrolases include enzymes predicted to exhibit mainly dextran/starch and xylan 9 degrading functions. T. fusca possesses two protein secretion systems: the sec general secretion 10 system and the twin-arginine translocation system. Several of the secreted cellulases have 11 sequence signatures indicating their secretion may be mediated by the twin-arginine12 translocation system. T. fusca has extensive transport systems for import of carbohydrates 13 coupled to transcriptional regulators controlling the expression of the transporters and14 glycosylhydrolases. In addition to providing an overview of the physiology of a soil 15 actinomycete, this study presents insights on the transcriptional regulation and secretion of16 cellulases which may facilitate the industrial exploitation of these systems.

The cereus group represents sporulating soil bacteria containing pathogenic strains which may cause diarrheic or emetic food poisoning outbreaks. Multiple locus sequence typing revealed a presence in natural samples of these bacteria of about thirty clonal complexes. Application of genomic methods to this group was however biased due to the major interest for representatives closely related to B. anthracis. Albeit the most important food-borne pathogens were not yet defined, existing data indicate that they are scattered all over the phylogenetic tree. The preliminary analysis of the sequences of three genomes discussed in this paper narrows down the gaps in our knowledge of the cereus group. The strain NVH391-98 is a rare but particularly severe food-borne pathogen. Sequencing revealed that the strain must be a representative of a novel bacterial species, for which the name Bacillus cytotoxis is proposed. This strain has a reduced genome size compared to other cereus group strains. Genome analysis revealed absence of sigma B factor and the presence of genes encoding diarrheic Nhe toxin, not detected earlier. The strain B. cereus F837/76 represents a clonal complex close to that of B. anthracis. Including F837/76, three such B. cereus strains had been sequenced. Alignment of genomes suggests that B. anthracis is their common ancestor. Since such strains often emerge from clinical cases, they merit a special attention. The third strain, KBAB4, is a typical psychrotrophe characteristic to unbiased soil communities. Phylogenic studies show that in nature it is the most active group in terms of gene exchange. Genomic sequence revealed high presence of extra-chromosomal genetic material (about 530 kb) that may account for this phenomenon. Genes coding Nhe-like toxin were found on a big plasmid in this strain. This may indicate a potential mechanism of toxicity spread from the psychrotrophic strain community. The results of this genomic work and ecological compartments of different strains incite to consider a necessity of creating prophylactic vaccines against bacteria closely related to NVH391-98 and F837/76. Presumably developing of such vaccines can be based on the properties of non-pathogenic strains such as KBAB4 or ATCC14579 reported here or earlier. By comparing the protein coding genes of strains being sequenced in this project to others we estimate the shared proteome in the cereus group to be 3,000?b200 genes and the total proteome to be 20-25,000 genes.