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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.    Electronic supplementary material  The online version of this article (doi: 10.1186/1471-2164-15-429) contains supplementary material, which is available to authorized users.

Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library