Discuss Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination

Feedback from Levi Waldron

1. in the Group 0 and 1 names, try to pick names that will be informative to someone seeing only that name without having read the paper, without using abbreviations or table references. Here the use of "S1 Table (control group)" shouldn't refer to the table # and ideally would say something about what kind of controls they are (healthy unvaccinated controls?) "T1, T2, T3, T4,(experimental group)" doesn't tell me anything unless I read the paper, and we're trying to make these data analyzable while rarely having to read the papers in detail. Use Group 1 definition to make clear what distinguishes Group 1 from Group 0.
2. The "Condition" should refer to what condition is being studied by the contrast made in this experiment. If the contrast is response to an HIV vaccine, then the condition is "response to vaccine" and not "HIV infection". Even if the contrast were response to a vaccine among HIV infected individuals, HIV infection is not a condition of study if the controls have the same condition. Choosing the correct Condition is critical to being able to group together experiments that are making the same or similar contrasts to produce their signatures.
3. Since there is only one microbiome sample from each participant, this is not a time series / longitudinal observational study. It appears to be cross-sectional observational, not case-control study (everyone was vaccinated, and the contrast is of immunological response to the vaccine) ("Samples from the earliest available sample (day 0 for 3 participants, month 6.5 for 11 participants and month 12 for 7 participants; S1 Table) were amplified with barcoded primers that targeted the hypervariable sequence containing V3-V4 region of the 16S rRNA gene and sequenced on a Roche 454")
4. It's not clear how signatures were extracted from Figures 4A-D; this would be good to explain in the "Description" of these signatures.
5. Different rank of taxa should be combined into a single signature rather than creating different signature for each rank as this paper did. In fact it looks like a separate Experiment 2 was created here for the same contrast, just to report taxa of different rank. Remember: an experiment is defined by the contrast between two groups, and signatures are the taxa that are either increased (one signature) or decreased (one signature) in Group 1 compared to Group 0 of that experiment.