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Open Access Research article

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

Yaligara Veeranagouda12*, Fasahath Husain1, Elizabeth L Tenorio3 and Hannah M Wexler12

Author Affiliations

1 GLAVAHCS, Bldg. 115 Room 312 11301 Wilshire Blvd, Los Angeles, CA 90073, USA

2 UCLA School of Medicine, Los Angeles, CA, USA

3 Division of Geographic Medicine and Infectious Disease, Tufts Medical Center, Boston, MA 02111, USA

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BMC Genomics 2014, 15:429  doi:10.1186/1471-2164-15-429

Published: 4 June 2014

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.

Keywords:
Bacteroides fragilis; Transposon mutants; Essential genes; Massively parallel sequencing; COG; DEG