The Microbial Genomes Group, led by Lisa Crossman, analyse next generation whole genome sequence information for a large variety of bacteria and small eukaryotes with the aim of annotating and visualising comparative genomics data.

We work closely with other groups at TGAC to improve on assemblies and capitalise on the core bioinformatics facilities.

Current research interests include Molecular Biodiversity, Comparative Genomics and Phylogenetics.

Our projects range from single sequences of high molecular biodiversity to deep resequencing projects with small specific areas of diversity.  Genome sequence analysis can be extended by transcriptome data, which will decisively determine transcription start sites as well as providing an excellent expression resource.

We use comparisons between environmental and clinically isolated organisms to identify important genetic regions for each type of isolate.  Using phylogenetic analysis we aim to cluster groups, creating understanding from their taxonomic positioning and tracking horizontal gene flow.

Key activities include:

• Assembly validation
• Annotation
• Comparative genomics

• Lisa Crossman - Project Leader
• Shabhonam Caim - Scientific Programmer

• Healthy and Safe Food and Clinical Epidemiology e.g. deep resequencing Campylobacter spp.
• Biodiversity and Bioenergy - Culture collection sequencing (e.g. National Yeast Culture Collection)
• Biodiversity and evolution – single cell sequencing

• Large scale expansion of mobile elements in specific hotspot regions of the German Outbreak Escherichia coli O104:H4.  Crossman LC. 2011. Nature Precedings: http://hdl.handle.et/10101/npre.2011.6466.1
• Draft Genome Sequence of Streptomyces strain S4, a symbiont of the leaf-cutting ant Acromyrmex octospinosus. Seipke R, Crossman L et al. J. Bacteriol. 2011.  193(16) 4270-1.
• Genome Sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608. Heavens D, Tailford LE, Crossman L. et al. J. Bacteriol. 2011 193(15): 4015-6.
• Complete Genome Sequence of the proteolytic Clostridium botulinum type A5 (B3') strain H04402 065.Carter AT, Pearson BM, Crossman LC et al.  J. Bacteriol. 2011.  193(9):2351-2.
• A commensal gone bad: complete genome sequence of the prototypical Escherichia coli strain H10407.Crossman LC et al. J. Bacteriol. 2010.  192(21):5822-31.
• Comparative genomics of the emerging human pathogen Photorahabdus asymbiotica with the insect pathogen Photorhabdus luminescens. BMC Genomics. 2009. 7, 10:302.
• The versatility and adaptation of bacteria from the genus Stenotrophomonas. Ryan RP, Monchy S., Cardinale M, Taghavi S, Crossman L et al. 2009.  Nat Rev Microbiol 7(7):514-25.
• The Genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. Holden MT, Seth-Smith HM, Crossman LC et al. J. Bacteriol. 2009 191(1):261-77.
• A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. Crossman LC et al. PLoS One. 2008. 2,3(7):e2567.
• The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Crossman LC et al. Genome Biol. 2008 17,9(4):R74
• Sequence-based analysis of pQBR103; a representative of a unique, transfer proficient mega plasmid resident in the microbial community of sugar beet. Tett A, Spiers AJ, Crossman LC et al. ISME J. 2007. 1(4):331-40.
• Sink or Swim. Crossman LC.  Nat Rev Microbiol. 2007. 5(11):834-5.
• Genome Sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Sebiahia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR, Crossman LC et al.  Genome Research, 2007. 17(7):1082-92.
• It's hip to be square! Crossman LC & Walker A. Nat. Rev. Microbiol. 2007 5(6):400-1.
• This place is big enough for both of us. Walker A. & Crossman LC. Nat. Rev. Microbiol. 2007 5(2):90-2.
• The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. Thomson NR, Howard S., Wren BW, Holden MT, Crossman LC et al. PLoS Genet. 2006 15,2(12):e206.
• The genome of Rhizobium leguminosarum has recognizable core and accessory components. Young JP, Crossman LC et al.  Genome Biol. 2006: 7(4):R34.
• Cell-cell signalling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover. Ryan RP, Fouhy JF, Crossman LC et al.  PNAS 2006. 103(17) 6712-7
• Livelihood hazards. Sebaihia M, Thomson NR, Crossman LC, Parkhill J. Nat Rev. Microbiol. 2005.  3(4):278-9.
• Extensive DNA inversion in the B. fragilis genome control variable gene expression. Cerdeño-Tárraga AM, Patrick S, Crossman LC et al.  2005. Science. 4, 307(5714):1463-5.
• Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Holden MW, Titbull RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T, Crossman LC et al. PNAS 2004.  28, 101(39):14240-5.
• Biofilm dispersal in Xanthomonas campestris is controlled by cell-cell signalling and is required for full virulence in plants. Dow JM, Crossman LC et al.  2003.  PNAS. 16, 100(19):10995-1000.