To evaluate the sensitivity of high-throughput DNA sequencing for monitoring biowarfare agents in the environment, we analysed soil samples inoculated with different amounts of $Bacillus\ atrophaeus$, a surrogate organism for $Bacillus\ anthracis$. The soil samples considered were a poorly carbonated soil of the silty sand class, and a highly carbonated soil of the silt class. Control soil samples and soil samples inoculated with 10, 10$^3$ , or 10$^5$ cfu were processed for DNA extraction. About 1% of the DNA extracts was analysed through the sequencing of more than 108 reads. Similar amounts of extracts were also studied for $Bacillus\ atrophaeus$ DNA content by real-time PCR. We demonstrate that, for both soils, highthroughput sequencing is at least equally sensitive than real-time PCR to detect $Bacillus\ atrophaeus$ DNA. We conclude that metagenomics allows the detection of less than 10 ppm of DNA from a biowarfare simulant in complex environmental samples.