Potential role of Gut Bacteria in the development of hepatocellular carcinoma
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Liver cancer is the fourth most deadly cancer and early detection and timely treatment apparently play a crucial role in it. Intestinal bacteria affect the development of liver cancer through various pathways. In this study, the gut bacteria of liver cancer patients are analyzed in detail by using metagenomic sequencing technology, and some of the bacterial species and metabolic pathways that may affect the development of liver cancer have been identified. Additionally, we identified bacterial factors that may impact key clinical indicators of the tumor. The findings of this study provide a scientific foundation for understanding the mechanisms underlying liver cancer development. This study freshed insights into clinical treatment strategies for liver cancer.
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Dear Dr. Bingqing Yan, Your revised manuscript has been reviewed by one of the original reviewers. The reviewer again raised important points regarding the intelligibility of your figures which should be interpreted without reference to the text (figures lacking legends are not acceptable) and the lack of critical analysis in the discussion. It is crucial that you discuss what this piece of research adds to the field and how it is interpreted in a larger context. Moreover, the English needs amendment throughout the text. Please complete your revisions and resubmit within 2 weeks. When doing so, you must include a point-by-point response to the reviewer's comments and a tracked version of the manuscript in addition to a clean version without tracked changes. Please note that we do not normally consider sending papers out for a third …
Dear Dr. Bingqing Yan, Your revised manuscript has been reviewed by one of the original reviewers. The reviewer again raised important points regarding the intelligibility of your figures which should be interpreted without reference to the text (figures lacking legends are not acceptable) and the lack of critical analysis in the discussion. It is crucial that you discuss what this piece of research adds to the field and how it is interpreted in a larger context. Moreover, the English needs amendment throughout the text. Please complete your revisions and resubmit within 2 weeks. When doing so, you must include a point-by-point response to the reviewer's comments and a tracked version of the manuscript in addition to a clean version without tracked changes. Please note that we do not normally consider sending papers out for a third round of revision. Therefore, if the issues raised by the reviewer are not resolved during this round of corrections your manuscript will no longer be considered for publication. Best regards, Gustavo
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Comments to Author
This paper compares bacteria present in faecal samples from 15 liver cancer patients with those in 5 control samples. The genome sequencing data appear to be high quality and are analysed using a wide range of computer programmes. Variations between the 20 individual samples are enormous, so the results are predominantly archival. Nevertheless, a few trends are identified that are of sufficient interest to be considered for publication. However, before the paper can be published, three main points plus a few minor language errors require further attention. 1. Figures should be intelligible without reference to the text, Currently some figure have titles, but no legend. The authors should please refer to high impact journals to see the much higher level of detail that would be adequate. Figure 1 …
Comments to Author
This paper compares bacteria present in faecal samples from 15 liver cancer patients with those in 5 control samples. The genome sequencing data appear to be high quality and are analysed using a wide range of computer programmes. Variations between the 20 individual samples are enormous, so the results are predominantly archival. Nevertheless, a few trends are identified that are of sufficient interest to be considered for publication. However, before the paper can be published, three main points plus a few minor language errors require further attention. 1. Figures should be intelligible without reference to the text, Currently some figure have titles, but no legend. The authors should please refer to high impact journals to see the much higher level of detail that would be adequate. Figure 1 needs a clear explanation. Below figure 3, the authors state: Red color indicates high abundance species in liver cancer patients, blue color indicates low abundance species. s: species. The figure itself is labelled red = case; blue = control! A full, intelligible legend is required. There is no legend at all to figure 4 (just a brief title) and the heatmap in figure 7 is totally unexplained. 2. The Discussion lacks critical analysis. How do the data in this paper compare with other similar studies? In short, what is new? 3. Throughout the paper the authors link statements with an and to generate long, unhelpful sentences. Sentences should be kept as short as possible so statements are clear. Examples: (L refers to line numbers) l 12 to 18. Split into 3 sentences. ; 111 to 1. Split into 32 sentences. L 176 to 182. Split into 4(!!) sentences. The following language problems require attention. L 28 Delete - - - ; replace with a comma. L45 Replace is to be with was (past tense) L 52 Replace are with were. L122 the use of the word changes is incorrect. The authors are not reporting changes - but differences. L131; 132. Please use correct bacterial names - delete hyphens between genus and species names. L 167 Authors have not measured "regulation"! Surely they mean abundance - or proportion, but not regulation. L 197 Use of terms "lower diversity" and "more complex" is confusing. Surely more complexity implies more diversity, which is the opposite of what the data show. More thought and explanation are required. L 202 and onwards (for example, lines 206, 207). Authors have not measured "expression"! This implies mRNA levels or rates of transcription. Surely they mean abundance - or proportion, but not expression.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Poor
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Dear author, As reported in my email, the journal requires that the authors submit a tracked version of the manuscript alongside a clean (final) version (please see https://www.microbiologyresearch.org/prepare-an-article#3). Moreover, we did not receive a point-by-point response to the points raised by reviewers 1 and 3 (most importantly), which is relevant for a full assessment of the changes made. I am drawing a Major Revision decision to allow you three weeks to provide both these documents. if you cannot provide these documents your manuscript cannot progress with the final stages of peer review and it will be rejected. Best regards, Gustavo
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Dear authors, The corrected version of your article does not meet the reviewers' comments. Most relevantly: 1. species names are still not presented according to the scientific standard (ie, in italics and without a underscore between genus and species), both in the text and in the figures; 2. the improvements made in the methodological section are not enough, for instance, the authors do not disclose how the samples were preserved until DNA extraction; 3. terms relative to "expression levels" are still used incorrectly; 4. The font in figure 1 needs to be increased, as it is almost impossible to see the text; 5. the discussion has not been sufficiently amended to inform how the current study adds to our undertanding regarding the relationship between cancer and intestinal microbiota (importantly: "flora" is no longer considered …
Dear authors, The corrected version of your article does not meet the reviewers' comments. Most relevantly: 1. species names are still not presented according to the scientific standard (ie, in italics and without a underscore between genus and species), both in the text and in the figures; 2. the improvements made in the methodological section are not enough, for instance, the authors do not disclose how the samples were preserved until DNA extraction; 3. terms relative to "expression levels" are still used incorrectly; 4. The font in figure 1 needs to be increased, as it is almost impossible to see the text; 5. the discussion has not been sufficiently amended to inform how the current study adds to our undertanding regarding the relationship between cancer and intestinal microbiota (importantly: "flora" is no longer considered appropriate when talking about microorganisms, use "microbiota" instead). Also, again, a thorough revising of English language is necessary. Your paper will be taken into consideration again once these issues are addressed. When resubmitting your work, you must include a point-by-point response to reviewers (and not a summary of changes) and a 'marked' corrected version. Best regards, Gustavo Editor Review
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Dear Dr. Bingqing Yan, Your manusript has been reviewed by three independent reviewers and major revision will be necessary before your manuscript can be accepted. The major points raised by the reviewers are related to the description of your methodological approach and to data presentation and significance. Major improvements in the description of the methods, figure display, and in the discussion of the results presented (specially regarding the significance of the present study and what it adds to the current literature) will be necessary. Once the reviewers' comments have been addressed, you may resubmit the revised version of you paper for further consideration. Best regards, Gustavo
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Comments to Author
This paper compares DNA sequence data for microbes present in faeces from 15 patients with liver cancer and 5 healthy controls. The quality of the sequence data appears to be high. The main conclusion is that the microbiota in patients is less diverse than that of the healthy controls. The quality of the English is intelligible, but the text describing the results is far too short to be understood by anyone except specialists in microbiome sequencing. A major revision should be requested before the paper is considered further for publication. This revision should include at least the following points. 1. Figures should be intelligible without reference to the text. All of the figures require much more detailed legends. For example, the y axis of several figures is "percentage": percentage of …
Comments to Author
This paper compares DNA sequence data for microbes present in faeces from 15 patients with liver cancer and 5 healthy controls. The quality of the sequence data appears to be high. The main conclusion is that the microbiota in patients is less diverse than that of the healthy controls. The quality of the English is intelligible, but the text describing the results is far too short to be understood by anyone except specialists in microbiome sequencing. A major revision should be requested before the paper is considered further for publication. This revision should include at least the following points. 1. Figures should be intelligible without reference to the text. All of the figures require much more detailed legends. For example, the y axis of several figures is "percentage": percentage of what? Total retrieved sequences; bacterial populations; or base pairs? Please define. 2. Data analysis depends heavily on the use of specific IT programmes, none of which are described in sufficient detail for anyone other than the specialist to understand. Much more text is required for the non-specialist reader. 3. The Methods section includes a subheading on alpha and beta diversity, but the text fails to explain the basis of the subgroups. Again the authors expect an unrealistic level of knowledge of the IT programmes used for a non-specialist to understand the text. 4. There is an internationally agreed way for writing bacterial names. The name must be in italics without an underscore between the genus and species names. 5. The authors should please decrease the sentence length throughout the paper. An ideal sentence should normally not be more than 10 words, and never more than 20 words. This point applies throughout the paper, but specific examples of sentences that need to be split can be found in lines 12 to 19 (split into 3 sentences); 28-33; 189 - 195; also elsewhere. 6. Lines 60 to 64 require complete rewriting. Perhaps start with The aims of this study were…. 7. There are two major errors in the use of terminology. Both "expression levels" and "changes" are used incorrectly. The paper does not present any mRNA data required to make any comments about whether the genes are actually expressed. Similarly, the data presented represent the microbiota present in a single faecal sample at a fixed time point. No data relating to "changes" over time are presented. Please correct both major errors. Please remember that the data presented reveal only differences in DNA abundance! 8. Define LDPI score. What, for example, do scores above 2.5 or 4 mean? Minor points Line 46 microbiota revealed (past tense). 105. Please rephrase this sentence - ? at and species level? Line 232. Small g, not G
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Poor
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
The manuscript describes presumptive identification. It should be submitted as a brief report. The manuscript has been written very superficially and lacks scientific insights. English language requires tremendous editing.
Please rate the manuscript for methodological rigour
Poor
Please rate the quality of the presentation and structure of the manuscript
Poor
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have …
Comments to Author
The manuscript describes presumptive identification. It should be submitted as a brief report. The manuscript has been written very superficially and lacks scientific insights. English language requires tremendous editing.
Please rate the manuscript for methodological rigour
Poor
Please rate the quality of the presentation and structure of the manuscript
Poor
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
-
Comments to Author
ACMI-D-24-00114: Potential role of Gut Bacteria in the development of hepatocellular carcinoma Overall: The manuscript aims to identify microbes and their metabolic pathways that potentially play a role in hepatocellular carcinoma. The author collected fecal samples from normal individuals and patients with hepatocellular carcinoma. Shotgun genome sequencing was performed and analyzed using conventional bioinformatics tools. Although the proposal is relevant to the field, the manuscript does not show originality. In the last years, several manuscripts have described the potential role of specific microbes in this type of cancer, the authors should have brought this up in the introduction. They only briefly mention two studies in the discussion. In addition, the text lacks scientific rigor and …
Comments to Author
ACMI-D-24-00114: Potential role of Gut Bacteria in the development of hepatocellular carcinoma Overall: The manuscript aims to identify microbes and their metabolic pathways that potentially play a role in hepatocellular carcinoma. The author collected fecal samples from normal individuals and patients with hepatocellular carcinoma. Shotgun genome sequencing was performed and analyzed using conventional bioinformatics tools. Although the proposal is relevant to the field, the manuscript does not show originality. In the last years, several manuscripts have described the potential role of specific microbes in this type of cancer, the authors should have brought this up in the introduction. They only briefly mention two studies in the discussion. In addition, the text lacks scientific rigor and organization. The figures need improvement in resolution, font size, and labels. The legends poorly describe the figure's components, such as statistic metrics, color scale, and number of samples per group. Major comments: The Material and Methods section needs improvement. It needs a better description of how samples were collected and stored till processing. DNA extraction method needs a reference. The code used in the analysis should be available on an online platform, like github. It is impossible to know if Lefse analysis was performed online or using the command line version. The WGCNA analysis description lacks reference, and it is a bit off. All the method explanations should be moved to results. Results titles should describe the main results from that section, not only the approach. The sequencing result should present a supplementary table describing each sample, group, number of sequences by sample (before and after quality control), and, if possible, the metadata (gender, age, group, clinical data). Diversity analysis is very poorly explained. In lines 128-120, the authors say: "alpha diversity (Observe, Pielou, and Shannon) of the patient group was smaller than that of the control group, which proved that the gut bacteria of hepatocellular carcinoma patients had changed." Changed how? What does that mean? Beta diversity was brought up in the methods, but no analysis was shown. All species names should be in italic. Remove the underline and use scientific notation. Only when looking at Figure 2 the reader will know the number of samples by group. The analysis is very unbalanced since the authors have 15 patients and only 5 controls. Looking at the percentage of "other" in taxa classification. It is unclear if this is all assigned microbes with a very low number of reads or unassigned reads. Please include that in the text. For community composition and WCGNA analysis, the author keeps saying "high/low expression." They don't have gene expression data, at least it is not described in the methods. They have relative abundance of DNA sequencing data. All this misuse of terms made their text very confusing. For heatmap analysis. Have the authors performed any axis clustering approach? The discussion is very shallow. The authors say the flora is more complex. Complex how? Without previous analysis or mention of antibiotic use, or if clinical data was collected during the study, the author justified part of their findings based on antibiotic use. Text and analysis need improvement. Do they have clinical data for that? Performed any analysis? Minor comments: Line 24: Liver Cancer should be written in lowercase. Line 36: Fix reference. Line 43: Fix "----" typo Line 65: Material and Method. Missing "s" in Methods Figure 1: Show sample dots overlapping boxplots. Add the statistic threshold in the legend. Line 140-143: Text needs improvement for clarity. The results are poorly described. Figure 2: It is "taxa", not "taxo". Why use capital letters for all first words in the legend? Figure 5: What * and ** mean? Most readers know it might be the pvalue levels, but it should be described in the legend. Figure 6: Font labels too small. Figure 6: Add color scheme label
Please rate the manuscript for methodological rigour
Poor
Please rate the quality of the presentation and structure of the manuscript
Poor
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
No: It is impossible to know. The authors did not mention ethical agreement.
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