We have been working on a revised taxonomy of rumen methanogens that will allow us to better identify the dominant methanogen species in NZ ruminants. To do that, we need to have reference sequences in the taxonomy database that we use.

There is a flow of processes here that I am trying to simplify by asking for permission to submit these 16S rRNA gene sequences to GenBank. Please note these are not genomes or gene of mitigation technology targets.

The logic is as follows:

We have methanogen community profiles of 16S rRNA gene sequences from 252 NZ rumen samples. I would like to identify the dominant methanogen species, to focus the vaccine and inhibitor work onto these.

To identify the dominant methanogen species, we would like to use all the data that are available. Obviously, cultures that we have in our collection are very useful reference sequences. These are the sequences that I have asked permission to deposit in GenBank.

The reason for depositing them in GenBank is that we would like to publish the archaeal taxonomy that we have refined. However, we cannot publish the taxonomy without releasing any unpublished reference 16S rRNA gene sequences. At the moment, the taxonomy has almost 2400 sequences from many different studies around the world, all of which are deposited in GenBank except for the 20 that I have asked to deposit.

We don’t want to start the analysis of the 16S rRNA gene sequence data from the 252 rumen samples until the sequences in the taxonomy to which we will compare the rumen samples are finalised. Otherwise, we might do all these analyses, and then not have permission to deposit the reference sequences, and would have to redo the analyses.

Once we have permission to deposit the 20 reference sequences in GenBank (or a subset of these), we can finalise the taxonomy database, and finish the analysis of the 16S rRNA gene sequences from the 252 rumen samples.

None of the twenty 16S rRNA gene sequences that I have asked to deposit in GenBank are from species for which there are no sequences available already. In some cases, we might have the only known cultures available, and all other sequences from that species are from molecular biology studies only. Inclusion of the 16S rRNA sequences from our cultures in the database will allow us to identify if these isolates that we have in our collection represent dominant NZ methanogen species.

Obviously we could do the analyses twice. Once with the 20 reference sequences in for our own information, and once without them for publication. However, that would double the work (which is bearable) and would lessen the value of publications (which is less bearable). We would like to (1) use the data to guide the chemogenomics and vaccine programmes and (2) publish the taxonomy and the identity of dominant NZ rumen methanogens in one paper (once the analyses are complete). Aim 1 can be done immediately, without depositing the sequence data in GenBank. My thoughts were that if we had permission to deposit the 20 reference sequences, then we could do the analyses with aim 2 in mind at the same time. 