Bacillus Genomics & Evolution

The genus Bacillus consists of a variety of species, including industrial applied saprophytes and fatal pathogens. Despite the adaptation to completely different habitats a substantial number of the genomes are conserved [Figure 1].

bacillus genomes

Figure 1: Biblast and sRNAfinder analysis of five selected Bacillus genomes.

The genomic circles demonstrate conserved chromosomal proteins and small RNAs on a (a) B. licheniformis DSM13 and (b) B. anthracis Ames Ancestor centered view. The outer rings depict the proteins of the query organisms, color coded for the direction of transcription. The second ring shows query organisms specific regions, which represent prophages and IS-elements. Prophages are explicitly marked. The four inner rings show the genomes of the hit organisms. Conserved proteins are depicted in red, small RNAs in blue and missing genes in grey. The inner rings show the GC-skew. The genomes used in the BiBaG comparisons are B. licheniformis DSM13, B. subtilis 168, B. amyloliquefaciens FZB42, B. cereus E33L and B. anthracis Ames Ancestor. In the sRNAfinder analysis of B. licheniformis DSM13 the chromosomes of B. subtilis 168, B. amyloliquefaciens FZB42 and B. anthracis Ames Ancestor have been used as references.

Based on the complete genome sequences of B. licheniformis [1], B. amyloliquefaciens [2] and B. cereus biovar anthracis [3] all sequenced by the Göttingen Genomics Laboratory - we focus our work on central topics of Bacillus evolution. Based on functional and comparative genomics we address the questions:

What are the molecular events (SNPs, INDELs, recombination, phage integration, ... ) which shape a genome?
What is the speed of evolution and how fast do strains adapt to new habitats?
What is the impact of genome evolution on the biological activities of an organism?
What distinguishes a pathogen from a commensal and a probiotic organism? In short: how do life styles evolve?

The topics are approached by genome sequencing, RNA-seq based transcriptomics, epigenome sequencing, molecular phylogeny and sequence based bioinformatics. Currently we are working on the finishing of four genomes of Bacillus thuringiensis to generate high quality reference genomes for host-parasite coevolution experiments funded by the DFG priority program SPP1399 (http://ieb.uni-muenster.de/spp) [4].

References

[1] Veith B, Herzberg C, Steckel S, Feesche J, Maurer KH, Ehrenreich P, Bäumer S, Henne A, Liesegang H, Merkl R, Ehrenreich A, Gottschalk G. (2004) The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential. J Mol Microbiol Biotechnol. 7(4):204-11 (abstract).
[2] Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R. (2007) Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol. 25(9):1007-14 (abstract).
[3] Klee SR, Brzuszkiewicz EB, Nattermann H, Brüggemann H, Dupke S, Wollherr A, Franz T, Pauli G, Appel B, Liebl W, Couacy-Hymann E, Boesch C, Meyer FD, Leendertz FH, Ellerbrok H, Gottschalk G, Grunow R, Liesegang H (2010) The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids. PLoS One. 5(7):e10986 (abstract).
[4] Sheppard AE, Poehlein A, Rosenstiel P, Liesegang H, Schulenburg H (2013) Complete genome sequence of Bacillus thuringiensis strain 407 Cry-. Genome Announcements 1(1):e00158-12 (abstract).