On 2017 Jan 18, Jack Gilbert commented:

We have been following some of the comments about this paper and accept that the wording of parts of our paper could be interpreted in ways we did not intend and that do not reflect the work performed.  We want to make it clear that for this paper we made predictions about nitrate, etc based on analysis of rRNA amplicon sequences and matching them to known genomes.  We did not directly measure these genes involved in nitrate metabolism (nitrate reductase, nitrite reductase, etc.), or know for certain that the strains present in the samples have such functions (although they are widely distributed in the matching phylogenetic groups).  Some of the wording (e.g., of the title in the abstract) did not come across as we intended, and could be interpreted as implying that we made direct measurements.  We want to note that we believe the predictions we made are useful, but acknowledge that they have limitations. We also want to stress that to test these hypotheses and advance clinical practice, we would need to perform extensive validation through intervention studies in carefully controlled clinical populations, which is obviously considered beyond the scope of the Observation format. However, we are currently performing ongoing studies that we believe will advance this research including some work based on public comments made about the lack of validation of the specific claims of the paper.

On 2017 Jan 18, Jack Gilbert commented:

We have been following some of the comments about this paper and accept that the wording of parts of our paper could be interpreted in ways we did not intend and that do not reflect the work performed.  We want to make it clear that for this paper we made predictions about nitrate, etc based on analysis of rRNA amplicon sequences and matching them to known genomes.  We did not directly measure these genes involved in nitrate metabolism (nitrate reductase, nitrite reductase, etc.), or know for certain that the strains present in the samples have such functions (although they are widely distributed in the matching phylogenetic groups).  Some of the wording (e.g., of the title in the abstract) did not come across as we intended, and could be interpreted as implying that we made direct measurements.  We want to note that we believe the predictions we made are useful, but acknowledge that they have limitations. We also want to stress that to test these hypotheses and advance clinical practice, we would need to perform extensive validation through intervention studies in carefully controlled clinical populations, which is obviously considered beyond the scope of the Observation format. However, we are currently performing ongoing studies that we believe will advance this research including some work based on public comments made about the lack of validation of the specific claims of the paper.