title: Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library.
abstract: BACKGROUND
  Bacteroides fragilis is a Gram-negative anaerobe that is normally a human gut commensal; it comprises a small percentage of the gut Bacteroides but is the most frequently isolated Bacteroides from human infections. Identification of the essential genes necessary for the survival of B. fragilis provides novel information which can be exploited for the treatment of bacterial infections.
  
  
  RESULTS
  Massive parallel sequencing of saturated transposon mutant libraries (two mutant pools of approximately 50,000 mutants each) was used to determine the essential genes for the growth of B. fragilis 638R on nutrient rich medium. Among the 4326 protein coding genes, 550 genes (12.7%) were found to be essential for the survival of B. fragilis 638R. Of the 550 essential genes, only 367 genes were assigned to a Cluster of Orthologous Genes, and about 290 genes had Kyoto Encyclopedia of Genes and Genomes orthologous members. Interestingly, genes with hypothetical functions accounted for 41.3% of essential genes (227 genes), indicating that the functions of a significant percentage of the genes used by B. fragilis 638R are still unknown. Global transcriptome analysis using RNA-Seq indicated that most of the essential genes (92%) are, in fact, transcribed in B. fragilis 638R including most of those coding for hypothetical proteins. Three hundred fifty of the 550 essential genes of B. fragilis 638R are present in Database of Essential Genes. 10.02 and 31% of those are genes included as essential genes for nine species (including Gram-positive pathogenic bacteria).
  
  
  CONCLUSIONS
  The essential gene data described in this investigation provides a valuable resource to study gene function and pathways involved in B. fragilis survival. Thorough examination of the B. fragilis-specific essential genes and genes that are shared between divergent organisms opens new research avenues that will lead to enhanced understanding of survival strategies used by bacteria in different microniches and under different stress situations.
authors.affiliation: GLAVAHCS, Bldg, 115 Room 312 11301 Wilshire Blvd, Los Angeles, CA 90073, USA. veereshagy@gmail.com.
authors.forename: Yaligara
authors.initials: Y
authors.lastname: Veeranagouda
authors.forename: Fasahath
authors.initials: F
authors.lastname: Husain
authors.forename: Elizabeth L
authors.initials: EL
authors.lastname: Tenorio
authors.forename: Hannah M
authors.initials: HM
authors.lastname: Wexler
mesh_terms: D001441:Bacteroides fragilis / Q000235:genetics* / Q000502:physiology*; D003470:Culture Media / Q000737:chemistry; D004251:DNA Transposable Elements; D015723:Gene Library; D005798:Genes, Bacterial; D020043:Genes, Essential; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation
chemical_list: D003470:Culture Media; D004251:DNA Transposable Elements