integron_gene_fetch

integron_gene_fetch extracts integron gene cassettes from metagenomic sequencing reads and targeted assemblies to detect mobile integron genes and characterize integron-associated gene pools.

Key Features:

• Targeted Assembly Approach: Targets recombination sites associated with chromosomal integrons to assemble gene cassettes, effective for organisms such as Treponema that contain multiple recombination site repeats.
• De Novo Assembly: Performs constrained de novo assembly using de Bruijn graph information to assemble integron gene cassettes often missed in whole-metagenome assemblies and not mappable to known reference genomes.
• Efficient Detection of Mobile Genes: Identifies integron genes by tracing potential paths between contigs containing recombination sites, enriching the gene pool associated with chromosomal integrons.
• Recombination Site Guidance: Uses a pre-determined set of recombination site sequences to guide assembly and path tracing.

Scientific Applications:

• Human oral microbiome surveying (HMP): Surveyed oral spirochetes in the NIH Human Microbiome Project and identified integron-containing Treponema species in approximately 80% of subjects.
• Treponema integron gene discovery: Expanded the Treponema chromosomal integron gene pool, reporting 826 genes with 598 nonredundant at 97% identity.
• Novel gene cassette discovery and community comparison: Revealed high dynamism of integron gene cassette arrays in the human microbiome, showing different microbial communities share few common integron genes and many identified genes have unknown functions.

Methodology:

Assembles sequencing datasets using a constrained de novo approach leveraging de Bruijn graph information, and traces potential paths between contigs that contain recombination sites guided by a pre-determined set of recombination site sequences.