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The authors have carefully addressed all the concerns raised by the 3 reviewers and myself. The manuscript should be accepted in its present form.
This is a very good work, all reviewers agree that it should be accepted, one of them loves it, another accepted with minor revisions, the last one is not pleased with the writing style and presentation (that should be addressed). However, since none of them, or the editor, has any problem with the science, I think the authors should follow all the possible recommendations in order to have a better manuscript. I look forward to seeing your revised version.
Please make public the data sets and include the accession numbers.
This paper shows an excellent experimental design and analysis. It has been a pleasure to have the opportunity to read it. I have a few minor comments.
It would be important to reproduce the results to be more explicit about how the statistical analysis was done, particularly PERMANOVA and NMDS. Both analyzes are complex and essential to understand the work. Please consider sharing your scripts.
Table 1 and 3. Clearly indicate the difference between "occupied" and "3 people".
Legend of figure 2C. It says “predict” which is inconsistent with what is mentioned in the discussion (lines 210-222). Change it for a less categorical phrase.
The paper is clearly written and includes sufficient information in the introduction and in all other sections.
I found the text somehow arcane, being myself not an expert in bioinformatics. Nonetheless I believe the text is generally consistent and mostly not repetitive.
The work described is clearly original, relevant and meaningful, representing the novel ways where current DNA sequencing technology can be used. In this case to investigate the microbial environment in closed spaces, as related to human occupancy.
I can not offer a strong review on the soundness of the detailed protocols. In general terms they appear controlled and properly executed.
The conclusions are appropriate and justified in my view.
The manuscript reports a very interesting enquire on the nature of the microbial cloud emmited by humans, including its differentiating capacity. It consists on initial observations that appear sound and should serve as the basis for future research.
This is a fascinating study done to characterize the sometimes person-specific microorganisms shed from the human body. Unfortunately, the manuscript was not well written and consequently it was difficult to understand.
As the authors explain the influence of humans on the built environment has been studied by others and a fair amount is known. So I found the goal stated in the Introduction — to understand the human contribution to bioaerosols within built environments (lines 46-49) — to be vague and wanting. Similarly, after reading the first paragraph of the Discussion I was unsure which findings in the present study were truly novel. The authors should try harder to articulate the specific questions addressed and to describe the knowledge gap filled by the present study.
The means used to collect samples (sanitized experimental climate chambers) allowed sampling of intake and exhaust air as well as settled particles and seem perfectly suited for the task. The experiments done were reasonable and the data were suitably analyzed.
It is a bit curious that the skin of subjects themselves was not sampled. It might answer the question of whether the organisms found in shed material reflect those found on the skin itself. It is presumed that many of the organisms in microbial cloud are derived from the skin, but this simple analysis would have provided insight to the source of organisms.
The manuscript is not well written and the Tables and Figures are not carefully prepared. Here are some examples:
⁃ There are various problems with syntax that should be addressed. Some examples are pointed out in MINOR COMMENTS below. The manuscript should be carefully edited to increase the precision of these problem sentences.
⁃ Figure 1. The figure legend should better explain the figure. For example, are ordination plots shown in this figure?
⁃ Table 1 and 2 desperately need greater transparency and footnotes to explain abbreviations, “n”, “R^2”, and so forth.
⁃ Table 3. Heading of column 1 is jargon and incomplete. Were these actually isolates? Is it correct to refer to isolated and named bacterial species as OTUs? (I don’t think so.) Similarly, does it make sense to refer to a “Staphylococcus OTU”? (I think an OTU is a gene sequence is that has similarity to a known and named genus or species.) Also see line 113 and other instances in the text.
- Figure 2. The information in this figure is dense and not readily understood. The authors could help by explaining the graphics better in the figure legend. For example, what do the different colors represent? What are the samples being clustered in panel A — for example what is “s05” and why does it show up four times? What do the circles, triangles and squares in panel C represent?
⁃ Simplify the text — some sentences are far too complex. For example, see lines 121-125, 130-133, 170-173, and 195-198.
OTHER MINOR COMMENTS:
a) Lines 19-21. The sentence is a bit clumsy. Also, what is “active human emission”?
b) Lines 21-22. References misplaced in sentence. Also, somewhere in the manuscript the authors should explain how the present work builds upon and/or differs from these previous studies? Is the present work novel and, if so, how?
c) Line 38. “Detectable human bacterial signal”. Syntax problem.
d) Line 58-59. “Interpersonal nature”? A bit mysterious.
e) Line 68. “occupied and unoccupied samples”? Syntax problem.
f) Line 70-71. “when considering individual sampling periods” and “all three individuals could be detected”. Syntax problems.
g) Figure 1. “simultaneous unoccupied air”. Syntax problem.
h) Figure 2 legend. “Depended on the proportion of human-associated bacteria shed”. Syntax problem.
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