Comments on abstract, title, references

The aim of the research paper -a comprehensive analysis of the tumour microbiome- which the authors provide clearly. The abstract provides a well succinct explanation of the researches finds; the author's usage of the words "comprehensive analysis'' can be considered a good coverage for the analysis done, but the reviewer suggests that some examples of the tools can be given in parenthesis thus improving the value of the indexed abstract. The title of the study is informative of the paper presented and relevant to the findings highlighted in the paper.

Comments on introduction/background

The introduction of the paper provides a good and short background about the current knowledge regarding the tumour microbiome. However, the reviewer suggests the authors use the following study as a reference: Riquelme E, Zhang Y, Zhang L, Montiel M, Zoltan M, Dong W, Quesada P, Sahin I, Chandra V, San Lucas A, Scheet P. Tumor microbiome diversity and composition influence pancreatic cancer outcomes. Cell. 2019 Aug 8;178(4):795-806. It is the reviewer's informed opinion that the study mentioned qualifies as a factual reference when addressing the ''tumour microbiome''. The study research questions are clearly outlined and the authors have a clear path outlined of the missing knowledge present in the field of the tumour microbiome and how the current paper addresses them.

Comments on methodology

The methodology presented in the paper is very well structured and the fact that the authors elaborated a 6 tier filter system for the elimination of contaminants, that would have corrupted the data, can be considered a very important strength of the article. The study methods are valid and reliable and there is sufficient information, especially in the supplement materials, for the replication of the study.

Comments on data and results

The research data and results are presented in the subsections of the paper. These subsections are titled with the main finding of the research, this is a good choice by the authors as it provides a very structured form to the paper, and "unclouds" the findings.

Comments on discussion and conclusions

As stated before in comments on data and results, the paper is not structured in the normal fashion of the IMRaD format. As this is the case the results and discussions/finding are compressed in subsections of the paper. The format of the presentation of the paper chosen by the author provides more clear viewing of the research, as per the informed opinion of the reviewer. As mentioned before the reviewer recommends the inclusion of the paper: Riquelme E, Zhang Y, Zhang L, Montiel M, Zoltan M, Dong W, Quesada P, Sahin I, Chandra V, San Lucas A, Scheet P. Tumor microbiome diversity and composition influence pancreatic cancer outcomes. Cell. 2019 Aug 8;178(4):795-806. both as a reference for the introduction as well as a very important result and discussion point, especially because the paper deals with the microbiota of pancreatic cancer, an important research finding in the authors' paper as well. To further elaborate on this point in the above-mentioned reference the finding of intra-tumoral microbiome signature (Pseudoxanthomonas-Streptomyces-Saccharopolyspora-Bacillus clausii) is in partial opposition with the present findings, this point should be expanded by the authors.

Overall the study answers its aims, has several solid strengths and greatly expands the current knowledge regarding the tumour microbiome.