Referee 2's review:

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N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication, the manuscript has been revised in light of these comments and to address other editorial requirements.
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The manuscript by Jaing et al describing "A functional gene array for detection of bacterial virulence elements" is well written, interesting and timely. The functional gene array can be used to identify microbes and also identify key potential capabilities such as antibiotic resistance or virulence gene detection. Knowledge of such capabilities form environmental samples of unknown origin can be of great assistance in the context of a biothreat.

To validate the concept, target virulence gene sequences from 4 bacterial strains were identified using HMMs. Target probes were selected based on having a perfect match to one genome and no more than a 16 nt match to any of the other genomes. Plots of Log2 intensities vs G complement with either Escherichia coli CFT073 or Enterobacterthe faecalis show consistent notably higher signal intensities for the target strain compared to the others (Fig 4). The reported false positive rate of 0.29% supports the robustness of the approach.

The utility of detecting orthologs with non-identical sequences using probes from one organism was studied by observing probe intensities for gene families with and without orthologs, (Fig 5, 6). These studies show that orthologs from one species can be detected using probes designed for gene family members from different species of the same genus or even different genera. The authors also used a variety of mismatch criteria to study probe sensitivity and show that for long probes, mismatches nearer the 5' end of the probe were less tolerable than mismatches nearer the 3' end.

To determine the lower detection limit of genomic DNA from an environmental sample, aerosol-collected samples (complex) were spiked with varying amounts of known DNA. Concentrations as low as 0.3 fg (amplified) were found to be detectable.

Overall this is a strong techniques paper using a functional gene array approach for detecting microbial gene family orthologs from complex samples of DNA. The potential applications are many and importantly for detection of antibiotic resistance genes from unknown microorganisms.