ArticleBMC genomics2014
Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- High-throughput analyses ofGut microbes · 2026Article
- Distinct prophage infections in colorectal cancer-associated Bacteroides fragilis.Communications medicine · 2026Article
- Article
- Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R.PLoS computational biology · 2023Article
- Identification of discriminant features from stationary pattern of nucleotide bases and their application to essential gene classification.Frontiers in genetics · 2023Article
- Non-essential ribosomal proteins in bacteria and archaea identified using COGs.Journal of bacteriology · 2021Article
- DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools.Nucleic acids research · 2021Article
- A Computational Framework Based on Ensemble Deep Neural Networks for Essential Genes Identification.International journal of molecular sciences · 2020Article
- Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- ePath: an online database towards comprehensive essential gene annotation for prokaryotes.Scientific reports · 2019Article
- Comparative Analyses of Fecal Microbiota in European Mouflon (Frontiers in microbiology · 2019Article
- The essential genome of the crenarchaeal model Sulfolobus islandicus.Nature communications · 2018Article
- Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes.PLoS computational biology · 2018Article
- A Two-Component System Regulates Bacteroides fragilis Toxin to Maintain Intestinal Homeostasis and Prevent Lethal Disease.Cell host & microbe · 2017Article
- The essential genomic landscape of the commensal Bifidobacterium breve UCC2003.Scientific reports · 2017Article
- The Suf Iron-Sulfur Cluster Biosynthetic System Is Essential in Staphylococcus aureus, and Decreased Suf Function Results in Global Metabolic Defects and Reduced Survival in Human Neutrophils.Infection and immunity · 2017Article
- Illumina Sequencing Approach to Characterize Thiamine Metabolism Related Bacteria and the Impacts of Thiamine Supplementation on Ruminal Microbiota in Dairy Cows Fed High-Grain Diets.Frontiers in microbiology · 2017Article
- Exploratory Investigation ofFrontiers in microbiology · 2016Article
- Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea.The FEBS journal · 2015Article
- Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M.Drug design, development and therapy · 2015Article
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4 authors.
Funding
Abstract
backgroundBacteroides 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.
resultsMassive 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).
conclusionsThe 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.
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