title: Bacterial genomes: habitat specificity and uncharted organisms.
abstract: The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.
authors.affiliation: Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil.
authors.forename: Francisco
authors.initials: F
authors.lastname: Dini-Andreote
authors.forename: Fernando Dini
authors.initials: FD
authors.lastname: Andreote
authors.forename: Welington Luiz
authors.initials: WL
authors.lastname: Araújo
authors.forename: Jack T
authors.initials: JT
authors.lastname: Trevors
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D017753:Ecosystem; D004783:Environmental Microbiology; D016680:Genome, Bacterial; D006801:Humans; D010802:Phylogeny