Content of review 1, reviewed on May 21, 2015

This data note contains results from metagenomics and metatranscriptomics experiments from one sample from one biogas reactor in Germany.

The data is interesting, but would be even more appealing if it were a time series. Otherwise, it is rather difficult to assess trends in the bioreactor.

Major Compulsory Revisions

None

Minor Essential Revisions

For the 2 figures, the authors have to add a legend with the colors directly in the figure for better readability.

The discussion needs to be merged with the Data description.

Abstract, background:

-metagenome sequencing +shotgun metagenome sequencing

Background

It should be mentionned in the background whether that are similar datasets for metatranscriptome. It should be said that the Martha Zakrzewski et al. paper used 454 amplicon sequencing.

The text surrounding reference 3 and 4 (previous work) should be expanded.

Digester management

Is there a publication describing the reactor ? If not, a general citation on biogas reactor should be provided to the reader because GigaScience publishes papers not always on next-generation sequencing and/or bioreactors.

Library construction

A reference should be provided for the Gubler-Hoffman protocol.

Metagenome assembly

The dataset should also be assembled with MEGAHIT (appeared in 2015 in Bioinformatics) for comparison. Ray Meta is 3 years old.

The copyright on Figure 1 is not compatible with the Creative Common license of GigaScience.

The caption for figure 1 should tell which are the starting compound used to produce the methane.

Discretionary Revisions

The title should be shortened. For example:

Metagenome and metatranscriptome of a biogas-producing community in a biogas plant

The difference between amplicon sequencing and shotgun sequencing should be used a a main selling point. The paper from 2012 was an amplicon sequencing paper. This paper is about shotgun sequencing.

Level of interest An article of importance in its field Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests.

Authors' response to reviewers: (http://www.gigasciencejournal.com/imedia/3232474601750548_comment.pdf)

Source

    © 2015 the Reviewer (CC BY 4.0 - source).

References

    Andreas, B., Irena, M., Peter, B., Felix, E., Anika, W., Andreas, A., Alfred, P., Andreas, S., Alexander, S. 2015. Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. GigaScience.