title: Microbial co-habitation and lateral gene transfer: what transposases can tell us.
abstract: BACKGROUND
  Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with?
  
  
  RESULTS
  All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections.
  
  
  CONCLUSIONS
  We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.
authors.affiliation: Department of Energy Joint Genome Institute, Genome Biology Program, Mitchell Drive, Walnut Creek, CA 94598, USA. SHooper@lbl.gov
authors.forename: Sean D
authors.initials: SD
authors.lastname: Hooper
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
mesh_terms: D001409:Bacillus cereus / Q000235:genetics / Q000254:growth & development; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D001426:Bacterial Proteins / Q000235:genetics; D030541:Databases, Genetic; D017753:Ecosystem; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development; D005618:Fresh Water / Q000382:microbiology; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics / Q000254:growth & development; D019779:Salmonella enterica / Q000235:genetics / Q000254:growth & development; D012623:Seawater / Q000382:microbiology; D012988:Soil Microbiology; D019895:Transposases / Q000235:genetics; D014871:Water Microbiology
chemical_list: D001426:Bacterial Proteins; D019895:Transposases