A couple minor edits.

revfiles/ReviewerComments.md

@@ -1,8 +1,8 @@
 We would like to thank the editor and reviewers for taking the time to provide their thoughtful and valuable feedback. These constructive comments greatly improved our manuscript.
 
-There were two primary concerns in the reviewer feedback. The **first** was around the wording and descriptions, which we addressed in our overall tone, clarity in the methods sections, and interpretation/discussion of the results. The **second** primary concern was related to our data in controlling for contamination (negative controls, validation of phage sequence sources, etc). We provided further explanation and data around the negative (background) controls that we used, as well as more clearly validated that we are measuring a real signal. This included the addition of filtering steps and re-running all of our analyses with more conservatively filtered data. Here we present a revised manuscript with modified text and figures.
+There were two primary concerns in the reviewer feedback. The **first** was around the wording and descriptions, which we addressed in our overall tone, clarity in the methods sections, and interpretation/discussion of the results. The **second** primary concern was related to our data in controlling for contamination (negative controls, validation of phage sequence sources, etc), especially considering the possibility of detected phages actually being prophage elements from bacterial genomes. We provided further explanation and data around the negative (background) controls that we used, as well as more clearly validated that we are measuring a real phage signal. This included the addition of filtering steps and re-running all of our analyses with more conservatively filtered data (this means almost all figures were re-run). Here we present a revised manuscript with modified text and figures.
 
-Below we provide a point-by-point response to the reviewer comments. Our changes in the manuscript are marked in red and blue text.
+Below we provide a point-by-point response to the reviewer comments. Our changes in the annotated manuscript are marked in red and blue text, and line numbers also refer to the "marked up" manuscript.
 
 
 
@@ -16,7 +16,7 @@ Overall the authors have generated a very interesting and likely very important
 
 - Much of the premise is about how viruses can cause cancer, but there is no evidence from the literature (that I am aware of) or evidence provided in this manuscript to indicate that bacteriophage can directly induce cancer. Instead, the premise is that bacteriophage are modulating bacteria which may result in changes associated with or potentially causing cancerous state. Statements like this: Due to their mutagenic abilities and propensity for functional manipulation, human viruses are strongly associated with, and in many cases cause, cancer" confuse the interpretation of the results and the manuscript would be more clear if the concept of viruses directly causing cancer were isolated and conceptually distinct from the phage-bacteria components. This is particularly confusing as the study only analyzed the DNA virome and could be missing a huge number of viruses that may be directly involved in cancer formation or acceleration.
 
-> *We agree that this needs to be clearer. When we used the term "human viruses" we were referring to viruses that only infect humans, and not bacteriophages. This is confusing because the human virome consists of both of these types of viruses, and ultimately this paper focuses on the bacteriophage component because that is the direction the data took us. We re-worded this section of the text to better differentiate those viruses that we would expect to indirectly and directly impact cancer development.* **LINES 19, 33, 41-54, 225-227**
+> *We agree that this needs to be clearer. When we used the term "human viruses" we were referring to viruses that only infect humans, and not bacteriophages. This is confusing because the human virome consists of both of these types of viruses, and ultimately this paper focuses on the bacteriophage component because that is the direction the data took us. We re-worded this section of the text to better differentiate those viruses that we would expect to indirectly and directly impact cancer development.* **LINES 19, 33, 41-54, 226-227**
 
 - What defines a "healthy human colon"? It is normal practice that "healthy control" samples obtained for studies like this are actually from patients who enter into the clinic for a different disorder. It is unclear how colons would be taken from 'healthy' individuals as this is not normal. The authors need to describe the criteria defining 'healthy'. The section "Study Design and Patient Sampling". Should include detailed information about controls.
 

revfiles/internalComments.rmd

@@ -6,7 +6,7 @@ https://docs.google.com/document/d/1hW_4z9Uj_mOIxonJWkYWxQ7T9lf4Boj8IXG2JVI--wU/
 
 Sorry I don't see the discordance between the figures. Maybe we are looking at different versions? Regardless it should be fixed now.
 
-Rewording was also great.
+Rewording was also great, thanks.
 
 ## COMMENT 2
 
@@ -46,7 +46,7 @@ This is great. Changed it.
 
 ## COMMENT 10
 
-Thanks for the feedback. I'll also try to make it sound less dodgy.
+Thanks for the feedback. I also tried to make it sound less dodgy.
 
 ## COMMENT 11
 
@@ -56,7 +56,7 @@ Changed it.
 
 This is great and incorporated the changes.
 
-I agree that it should be self evident but this is something that some of my colleagues, who are not familiar with phages, appreciated hearing.
+I agree that it should be self evident but this is something that some of my colleagues, who are not familiar with phages (e.g. clinicians), have appreciated hearing.
 
 These are also great points about how phages will interact with their bacterial hosts, and their lysogenic replication cycles. These will be important as we work to understand the system.
 

submission/Figure03.eps

@@ -1 +1 @@
-../figures/phage-bacteria-cor.eps
+../figures/lysogenic-relabund.eps

submission/Figure04.eps

@@ -1 +1 @@
-../figures/lysogenic-relabund.eps
+../figures/phage-bacteria-cor.eps