Metagenomics analysis of mice gut microbiome to unravel the role of metal exposure and piperine
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The gut and intestinal microbiota consists of trillions of microorganisms inhabiting the human gastrointestinal tract. It plays a crucial role in human health leading to understanding the dynamic crosstalk of host-microbe interaction in the gut and has become necessary for the detection, prevention, or therapy of diseases. Gut microbiota deviations are linked with many diseases, suggesting that various pathways involved in immunity, energy, lipid, and glucose metabolism are affected. Further, it is also altered by external insults such as metal toxicity, antibiotics and pesticides. Heavy metals like arsenic, mercury, cadmium and chromium are some of the well-studied classes of environmental pollutants. Mouse models have become the model of choice for most studies in this emerging field, as they allow perturbations in the gut microbiota to be studied in a controlled experimental setup. Here, we investigate the composition and diversity of intestinal microbes utilizing cecal samples from different intervention groups: arsenic exposure (As(III)), arsenic and piperine co-administration (As +Pp), piperine per se and control group. We obtained DNA samples from these groups and performed PCR amplification and sequencing of the 16S V3-V4 region. The findings showed shift in microbial composition and abundance among different intervention groups, revealing taxa that may contribute to the microbial diversity.
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The work presented is clear and the arguments well formed. This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community.
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The work presented is clear and the arguments well formed. This is a study that would be of interest to the field and community. Please include more rigour criteria and resources in your methods section, as highlighted by the SciScore reports. Including RRIDs and negative statements to explain why things were not performed should increase the rigour and reproducibility of your work. You can find tips on how to improve your article here: https://sciscore.com/reports/Core-Report.php Please deposit the data underlying the work in the Society’s data repository Figshare account here: https://microbiology.figshare.com/submit. Please also cite this data in the Data Summary of the main manuscript and list it as a unique reference in the References section. When you resubmit your article, the Editorial staff will post this data publicly on …
The work presented is clear and the arguments well formed. This is a study that would be of interest to the field and community. Please include more rigour criteria and resources in your methods section, as highlighted by the SciScore reports. Including RRIDs and negative statements to explain why things were not performed should increase the rigour and reproducibility of your work. You can find tips on how to improve your article here: https://sciscore.com/reports/Core-Report.php Please deposit the data underlying the work in the Society’s data repository Figshare account here: https://microbiology.figshare.com/submit. Please also cite this data in the Data Summary of the main manuscript and list it as a unique reference in the References section. When you resubmit your article, the Editorial staff will post this data publicly on Figshare and add the DOI to the Data Summary section where you have cited it. This data will be viewable on the Figshare website with a link to the preprint and vice versa, allowing for greater discovery of your work, and the unique DOI of the data means it can be cited independently.
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Comments to Author
Review for manuscript by Kaur et al "Metagenomics analysis of mice gut to unravel the role of metal exposure and piperine" Kaur et al have done some important study about the effect of arsenic and piperine on gut microbiota. They have used mice and administrated them with arsenic and piperine both individually and in combination. In the mice group fed with arsenic high abundance of arsenic metabolizing bacteria were observed like Desulfovibrio, Salinibacter and Enterococcus and decrease in Bacteroidetes. However, when used in combination with piperine the Bacteroidetes population came back to normal. My concerns Please give the information about various mouse treatment groups in the first paragraph of result section. Give a brief introduction about arsenic and piperine poisoning in humans
Comments to Author
Review for manuscript by Kaur et al "Metagenomics analysis of mice gut to unravel the role of metal exposure and piperine" Kaur et al have done some important study about the effect of arsenic and piperine on gut microbiota. They have used mice and administrated them with arsenic and piperine both individually and in combination. In the mice group fed with arsenic high abundance of arsenic metabolizing bacteria were observed like Desulfovibrio, Salinibacter and Enterococcus and decrease in Bacteroidetes. However, when used in combination with piperine the Bacteroidetes population came back to normal. My concerns Please give the information about various mouse treatment groups in the first paragraph of result section. Give a brief introduction about arsenic and piperine poisoning in humans Please provide legends for all figures Discussion is very brief please give more details in the discussion about why co administration of piprine is making the abundance of Bacteroidetes back to normal. Line 27 change perse to per se at all places (Line 123) Line 38 and 39 italicize all genus names Desulfovibrio Salinibacter Enterococcus, Clostridium and also, at all other places in the manuscript. see comment for line 153. Line 59 Please give reference for this statement "Studies on the gut bacterial community composition shows essential relationship between gut microbiota and good health" Line 65 Change "mice model" to "mouse model" Line 68 Please give reference for this statement 'It is a potential alkaloid that may help in the alteration of gut bacterial communities and dysbiosis". Line 79 what was the age of the mice used in this study? Line 84 what is a perse group do you mean piperine perse? change it to piperine per se group. Figure 3 Change title of third group from perse to piperine perse. also provide legend Figure 4 What is LDA score? provide its full form in result section Line 114 Please reframe the sentence "Metal exposure through its manipulation of gut flora, can adversely affect human health" to "Dysbiosis of gut flora by metal exposure can adversely affect human health" Line 114 also provide reference for the above statement Line 132 In the statement you claim "In our studies, bacterial diversity at the phylum level showed very less Firmicutes relative abundance in As(III) group as compared to other" however, Figure 4 shows high abundance of Firmicutes why you are mentioning very less Firmicutes relative abundance in text. The abundance of Bacteroidetes are going down in this group Line 150 Please provide reference for the statement "Functionally it also contribute to the metabolism of lipids, choline, and bile acid". Line 152 Change bacterias to bacteria Line 153 italicize all genus names Salinibacter, similarly Arsenicitalea (line 156), Clostridium (line 157) Line 156 Please provide reference for the statement "Recently, a new genus Arsenicitalea of the family Hyphomicrobiaceae, which is arsenic resistant bacterium, was isolated from the high-arsenic sediment". Line 158 Please provide reference for the statement "Clostridia as a group have been demonstrated to induce beneficial immune responses, in part via their ability to produce short-chain fatty acids that can attenuate gut inflammation"
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Strongly 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 study investigates the composition and diversity of intestinal microbes in different intervention groups and aims to unravel the role of metal exposure and piperine. 1. Methodological rigour, reproducibility and availability of underlying data. Lines 93-94: "Raw reads up 94 to ~150 Mb per sample with an average read length of 2×250bp were generated". Please check the sentence. The read length of the fragments in the libraries should be provided as single fragment and not paired-end. Is there any other reason? Could the authors provide more information about the data availability? Are the raw sequencing data be deposited in a public database? 2. Presentation of results. Considering that the Lefse plot presented the results at the Genus level, could the author present at the same taxonomic level also …
Comments to Author
The study investigates the composition and diversity of intestinal microbes in different intervention groups and aims to unravel the role of metal exposure and piperine. 1. Methodological rigour, reproducibility and availability of underlying data. Lines 93-94: "Raw reads up 94 to ~150 Mb per sample with an average read length of 2×250bp were generated". Please check the sentence. The read length of the fragments in the libraries should be provided as single fragment and not paired-end. Is there any other reason? Could the authors provide more information about the data availability? Are the raw sequencing data be deposited in a public database? 2. Presentation of results. Considering that the Lefse plot presented the results at the Genus level, could the author present at the same taxonomic level also the relative abundance of bacterial diversity? 3. How the style and organization of the paper communicates and represents key findings. The manuscript is well-organized, with clear sections and flow. 4. Literature analysis or discussion. While the authors have provided a thorough discussion of their findings, it would be beneficial to include a discussion of the limitations of the study. For example, are there any limitations related to the mouse model used, the methods of data analysis, or the interpretation of the results? The authors could discuss more about the implications of their findings for future research. For example, what are the potential avenues for further investigation? How could these findings inform the development of interventions to mitigate the effects of heavy metal exposure on the gut microbiota? It would be beneficial to include a brief conclusion at the end of the discussion section, summarizing the main findings and their implications. 5. Any other relevant comments. It would be interesting to see if the authors have considered other factors that could influence the gut microbiota, such as the diet of the mice.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Very good
To what extent are the conclusions supported by the data?
Strongly 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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