Decision letter | The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

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The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

Decision letter

Affiliation details

Cornell University, United States; University of California, Berkeley, United States; King’s College London, United Kingdom
Roberto Kolter, Reviewing editor, Harvard Medical School, United States

eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see review process). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.

[Editors’ note: a previous version of this study was rejected after peer review, but the authors submitted for reconsideration. The two decision letters after peer review are shown below.]

Many thanks for submitting your work on the genome reconstruction and subsequent analyses of the several members of the previously only poor characterized ‘deep branching Cyanobacteria’ (The human gut and subsurface sediment harbor non-photosynthetic Cyanobacteria). In addition to myself (Roberto Kolter), two other individuals read and offered comments on the manuscript. Overall we found the analyses quite intriguing and have discussed our opinions extensively since providing our initial reviews. My sense is that we have come to a good consensus about the manuscript. We all see some important work here but have some serious concerns that can be summarized as follows:

1) There is a major concern that there needs to be better support for the claim that these genomes, as constructed from metagenomic data, do indeed occur in nature (i.e., that they are ‘real’). We see two possibilities here. It may be that you can indeed develop an argument that from the bioinformatic analyses you have absolute confidence that the assembled sequences are true representations of extant genomes in nature. Alternatively, there are experimental ways to determine this. In the spirit of eLife, we do not wish to recommend “make work” types of experiments. The former solution should not necessitate bench work; the latter does and could take a lot of time. We recognize that. But you might already have some of those data.

2) A second major concern has to do with the designation of these organisms as Cyanobacteria to begin with. In fact, if anything, we would argue that your results make a very compelling argument that these bacteria need to be considered in a class (phylum?) all by themselves. In this regard, the paper would have to be revised greatly because it currently rests on the assertion that these are “truly non-photosynthetic Cyanobacteria”. This concern is a bit larger than it seems. After all, the main interest in this manuscript was the characterization of non-photosynthetic cyanos. But after reading the results, it is clear that the initial designation of these as Cyanobacteria was probably premature and off the mark. Nonetheless, we feel that this correction should be communicated.

Regarding the overall writing of manuscript (particularly as it pertains to the usage of inappropriate usage of the term ‘Cyanobacteria’) we had split reactions. One reviewer found the paper well written, I must confess that I did not. I marked the PDF extensively with suggested edits.

Considering these major concerns, and the possibility that additional experiments might be needed, I am recommending that the submission be rejected. That will free you and your colleagues to submit the work (perhaps editing it as a results of our comments) elsewhere. However, I want you to consider this a “soft reject” that leaves open the opportunity for a resubmission. If you can make a compelling case that this new phylum is intrinsically important and interesting and can provide a stronger case that the genomes are real, we would be glad to reconsider it. I, for one, would love to see how knowledge of the genomes might guide you and your colleagues to cultivate members of this group. Not that I would hold you to it, but some discussion of why they have not been cultivated based on genome knowledge would be welcome.

[Editors’ note: what now follows is the decision letter after the authors submitted for further consideration.]

Thank you for sending your resubmission to eLife, which is now entitled “The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new phylum sibling to Cyanobacteria”. This new version of your article has been favorably evaluated by a Senior editor, myself as a member of the Board of Reviewing Editors, and two expert reviewers (one of them, Jon Zehr agreed to reveal his identity).

After our initial individual evaluation of the manuscript we discussed our comments and reached a consensus that by and large you and your co-authors have addressed our prior main concerns which were: (a) that this division was called “deep branching Cyanobacteria” when all evidence pointed to the bacteria not being cyanos and (b) that there was not enough description of how the genomes had been assembled. In addition, we feel that the revised manuscript is much improved in terms of its written style. Nonetheless, all of us felt that the manuscript could still use some revising before it can be accepted for publication. In short, the key changes still needed include:

1) Given the lack of cultured representatives, this should be still referred to as “candidate phylum”.

2) The discussion of the light sensing genes should be modified and streamlined because the direct evidence that the homologs are indeed involved in light sensing is somewhat weak.

3) The discussion of the evolution of nitrogenase may need to be re-pitched as there is no well-accepted view on the original evolution of nitrogenase. We feel some of your arguments could be used in favor of its being present in the last common ancestor of Cyanobacteria.