Understanding Camellia sinensis using Omics Technologies along with Endophytic Bacteria and Environmental Roles on Metabolism: A Review
, Khayalethu Ntushelo 1, Fhatuwani Nixwell Mudau 1, Bahare Salehi 2,*, Mehdi Sharifi-Rad 3,*, Natália Martins 4,5,*, Miquel Martorell 6 and Javad Sharifi-Rad 7,8,*Round 1
Reviewer 1 Report
The review article on the application of the "omics" technologies to the study of Camellia sinensis is well organized and well presented. A minor suggestion:
lines 199 -200 where the authors mention the PCA and PLS-DA statistical analysis, specify the statistical analysis principle and differences.
Author Response
The review article on the application of the "omics" technologies to the study of Camellia sinensis is well organized and well presented. A minor suggestion:
lines 199 -200 where the authors mention the PCA and PLS-DA statistical analysis, specify the statistical analysis principle and differences.
Reply: Thanks for assessing our efforts. We inserted the suggestion information in the text.
Reviewer 2 Report
Tshikhudo et al provided a comprehensive review about Camellia sinensis from the following aspects: multi-omics (transcriptomics, proteomics, and metabolomics), role of endophytic bacteria, antioxidant and antimicrobial properties, as well as environmental stress tolerance. In general, the review is well-written and conveyed clear opinions and ideas. However, I have the following suggestion which can improve the quality of the manuscript:
1. Line 72-73: the authors listed the main chemical compositions in green teas. In addition, in metabolomics part, the authors mentioned similar contents again. As a review, it may be a good idea to list all the detected/analyzed chemical compounds in green teas from literature so far in a table, in order to give a comprehensive overview about the main metabolites appeared in green teas.
2. Line 143-144: the authors mentioned several search engines, but they neither listed the details about these searching engines, nor gave any reference
3. Last paragraph in Proteomics part: the authors should try to provide more applications with more examples, instead of spending many lines of words on explaining limited papers.
4. Line 198-199: “score plot and loading plot analyses” should be pattern recognition.
5. The authors focused on secondary metabolites in green teas, which is totally fine. But it may be also helpful to have a short and brief description about primary metabolites in green tea samples
6. The last three paragraphs in metabolomics part: the authors listed several papers about green tea quality, different growing areas, plucking positions, seasonal variations, etc. Have the authors compared the biomarkers detected for each factor/study? Did they have some overlapping biomarkers for different cases? If so, what could be the possible reasons?
7. Line 276 but not Line 290 is the first place to mention SAR, should give the full name and abbreviation.
8. Line 276-277: could you elaborate more about finding new isomers, and give the reference?
9. Line 342, 343: no need to list all authors, you can use et al.
10. The authors may considered to have a summarized figure to integrate multi-omics with other topics they commented in this manuscript to have a complete story.
11. About the title: the title seems long, in addition, it seemed the topics that the authors mentioned in the text are more than “quality parameters” and “defense mechanism”. I would suggest the authors to re-consider a concise and proper title.
Author Response
Tshikhudo et al provided a comprehensive review about Camellia sinensis from the following aspects: multi-omics (transcriptomics, proteomics, and metabolomics), role of endophytic bacteria, antioxidant and antimicrobial properties, as well as environmental stress tolerance. In general, the review is well-written and conveyed clear opinions and ideas. However, I have the following suggestion which can improve the quality of the manuscript:
Reply: Thank you very much for your comments to improve our manuscript.
1. Line 72-73: the authors listed the main chemical compositions in green teas. In addition, in metabolomics part, the authors mentioned similar contents again. As a review, it may be a good idea to list all the detected/analyzed chemical compounds in green teas from literature so far in a table, in order to give a comprehensive overview about the main metabolites appeared in green teas.
Reply: According to the suggestion, we inserted Table 1. Chemical compounds in green tea.
2. Line 143-144: the authors mentioned several search engines, but they neither listed the details about these searching engines, nor gave any reference
Reply: We inserted two new references:
Verheggen, K.; Martens, L.; Berven, F.S.; Barsnes, H.; Vaudel, M. Database Search Engines: Paradigms, Challenges and Solutions. Advances in experimental medicine and biology 2016, 919, 147-156.
Chi, H.; Liu, C.; Yang, H.; Zeng, W.-F.; Wu, L.; Zhou, W.-J.; Wang, R.-M.; Niu, X.-N.; Ding, Y.-H.; Zhang, Y., et al. Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine. Nature biotechnology 2018, 36, 1059-1061.
3. Last paragraph in Proteomics part: the authors should try to provide more applications with more examples, instead of spending many lines of words on explaining limited papers.
Reply: In this paragraph, we inserted the importance of proteomics in the characterization of posttranslational modifications.
4. Line 198-199: “score plot and loading plot analyses” should be pattern recognition.
Reply: According to the suggestion, we changed it.
5. The authors focused on secondary metabolites in green teas, which is totally fine. But it may be also helpful to have a short and brief description about primary metabolites in green tea samples
Reply: We inserted this information in metabolomics section.
6. The last three paragraphs in metabolomics part: the authors listed several papers about green tea quality, different growing areas, plucking positions, seasonal variations, etc. Have the authors compared the biomarkers detected for each factor/study? Did they have some overlapping biomarkers for different cases? If so, what could be the possible reasons?
Reply: According with the suggestion, we included a conclusion in metabolomics part explaining the importance of temperature, length of daytime or stronger sunlight in phenolic composition.
7. Line 276 but not Line 290 is the first place to mention SAR, should give the full name and abbreviation.
Reply: We changed it.
8. Line 276-277: could you elaborate more about finding new isomers, and give the reference?
Reply: We elaborated more this information and inserted the following reference:
Tanaka, T.; Mine, C.; Watarumi, S.; Fujioka, T.; Mihashi, K.; Zhang, Y.J.; Kouno, I. Accumulation of epigallocatechin quinone dimers during tea fermentation and formation of theasinensins. Journal of natural products 2002, 65, 1582-1587.
9. Line 342, 343: no need to list all authors, you can use et al.
Reply: We used et al.
10. The authors may considered to have a summarized figure to integrate multi-omics with other topics they commented in this manuscript to have a complete story.
Reply: According to the suggestion, we inserted Figure 1.
11. About the title: the title seems long, in addition, it seemed the topics that the authors mentioned in the text are more than “quality parameters” and “defense mechanism”. I would suggest the authors to re-consider a concise and proper title.
Reply: We changed the title.
Reviewer 3 Report
The proposed article is presented in a nice way.
It would be better to use also tables in your manuscript, describing and comparing somehow some of the referenced articles.
Please use more recent references.
1) Line 38: Please rewrite “In this sense, the present study aims to provide a comprehensive review of the various methods of transcriptomic, …”
2) Line 62-64: What is the connection with this study?
3) Line 209: 1H NMR please superscript
4) Mine 273: Please check the sentence “This bacterium was also able to reduce tea root tea caused by P. hypobrunnea”. Tea is referred 2 times, is it OK?
5) Line 423: Please check “photosynthesis rate, , transpiration rate”. Please delete the second comma.
6) Lines 440-446: Why there is special reference to “Athrixia phylicoides” in the last paragraph?
Author Response
1) Line 38: Please rewrite “In this sense, the present study aims to provide a comprehensive review of the various methods of transcriptomic, …”
Reply: This sentence was revised.
2) Line 62-64: What is the connection with this study?
Reply: This sentence was removed.
3) Line 209: 1H NMR please superscript
Reply: This aspect was revised throughout the manuscript.
4) Mine 273: Please check the sentence “This bacterium was also able to reduce tea root tea caused by P. hypobrunnea”. Tea is referred 2 times, is it OK?
Reply: This sentence was revised.
5) Line 423: Please check “photosynthesis rate, , transpiration rate”. Please delete the second comma.
Reply: This sentence was revised.
6) Lines 440-446: Why there is special reference to “Athrixia phylicoides” in the last paragraph?
Reply: Thanks for the reviewer comment. A special reference was given to bush tea (Athrixia phylicoidesDC.) because this is a shrub indigenous to South Africa, naturally grows in Limpopo, Mpumalanga, Eastern Cape and KwaZulu-Natal provinces of the country. Its leaves have been traditionally used as herbal/medicinal brew for cleansing blood and treating ailments, such as boils, headaches, infested wounds and coughs. So, this plant is gaining popularity countrywide as a healthy beverage.
Reviewer 4 Report
The manuscript entitled "Understanding Camellia sinensis quality parameters and defense mechanism using omics technologies along with endophytic bacteria role on metabolism: a review" reports extensive information regarding Camellia sinensis. The most interesting part is the role of endophitic bacteria in its metabolism. The description of the transcriptomics, proteomics and metabolomics is too long and extended. Please reduce/summarize this part, since in the Conclusion these aspects are only shortly mentioned. Conclusions should be rewritten and extended inclusing Authors perspective opinion on the topic: e.g. metabolomics is currently studied with NMR, so the line 444 should be rewritten. Some other comments. Line 350 reference related to cathechins is missing; line 356-357 the mechanism of action should be cleared and references added. English phrasing/grammar is to be checked by a native English speaking.
Author Response
The manuscript entitled "Understanding Camellia sinensis quality parameters and defense mechanism using omics technologies along with endophytic bacteria role on metabolism: a review" reports extensive information regarding Camellia sinensis. The most interesting part is the role of endophitic bacteria in its metabolism.
Reply: Thank you for considering our efforts.
The description of the transcriptomics, proteomics and metabolomics is too long and extended. Please reduce/summarize this part, since in the Conclusion these aspects are only shortly mentioned.
Reply: According with the reviewer suggestion, transcriptomics, proteomics and metabolomics sections were reduced.
Conclusions should be rewritten and extended inclusing Authors perspective opinion on the topic: e.g. metabolomics is currently studied with NMR, so the line 444 should be rewritten.
Reply: Conclusion section was completely restructured.
Some other comments.
Line 350 reference related to cathechins is missing;
Reply: We inserted a new reference:
Reygaert, W.C. Green Tea Catechins: Their Use in Treating and Preventing Infectious Diseases. BioMed research international 2018,2018, 9105261-9105261.
line 356-357 the mechanism of action should be cleared and references added.
Reply: We inserted mechanism of action and reference:
Reygaert, W.C. Green Tea Catechins: Their Use in Treating and Preventing Infectious Diseases. BioMed research international 2018,2018, 9105261-9105261.
English phrasing/grammar is to be checked by a native English speaking.
Reply: We checked grammar.
Round 2
Reviewer 3 Report
1) Figure 1: Please name the 2 columns
2) Line 150: Please delete the comma after e.g.
3) Line 453-456: Please use some references
4) Please use also tables in your manuscript, describing and comparing somehow some of the referenced articles.
5) Please use more recent references throughout the manuscript.
Author Response
1) Figure 1: Please name the 2 columns
Answer: Figure 1 was revised accordingly.
2) Line 150: Please delete the comma after e.g.
Answer: The required change was done.
3) Line 453-456: Please use some references
Answer: We inserted the following new references:
Joubert, E.; Gelderblom, W.C.; Louw, A.; de Beer, D. South african herbal teas: Aspalathus linearis, cyclopia spp. And athrixia phylicoides--a review. Journal of ethnopharmacology 2008, 119, 376-412.
Lerotholi, L.J.; Chaudhary, S.K.; Chen, W.; Veale, C.G.L.; Combrinck, S.; Viljoen, A.M. Identification, isolation and determination of biomarkers for quality control of bush tea (athrixia phyllicoides). Planta medica 2018, 84, 902-912
4) Please use also tables in your manuscript, describing and comparing somehow some of the referenced articles.
Answer: According to the suggestion, we inserted Table 1 about roles of Roles of endophytic bacteria from Camellia sinensis.
5) Please use more recent references throughout the manuscript.
Answer: We inserted the following new references:
Shan, W.; Zhou, Y.; Liu, H.; Yu, X. Endophytic actinomycetes from tea plants (camellia sinensis): Isolation, abundance, antimicrobial, and plant-growth-promoting activities. BioMed research international 2018, 2018, 1470305.
Wang, M.; Zhang, X.; Li, Q.; Chen, X.; Li, X. Comparative transcriptome analysis to elucidate the enhanced thermotolerance of tea plants (camellia sinensis) treated with exogenous calcium. Planta 2018.
Liu, L.; Li, Y.; She, G.; Zhang, X.; Jordan, B.; Chen, Q.; Zhao, J.; Wan, X. Metabolite profiling and transcriptomic analyses reveal an essential role of uvr8-mediated signal transduction pathway in regulating flavonoid biosynthesis in tea plants (camellia sinensis) in response to shading. BMC plant biology 2018, 18, 233.
Lerotholi, L.J.; Chaudhary, S.K.; Chen, W.; Veale, C.G.L.; Combrinck, S.; Viljoen, A.M. Identification, isolation and determination of biomarkers for quality control of bush tea (athrixia phyllicoides). Planta medica 2018, 84, 902-912.
Azevedo, R.S.A.; Teixeira, B.S.; Sauthier, M.; Santana, M.V.A.; Dos Santos, W.N.L.; Santana, D.A. Multivariate analysis of the composition of bioactive in tea of the species camellia sinensis. Food chemistry 2019, 273, 39-44.
Akroum, S. Antifungal activity of camellia sinensis crude extracts against four species of candida and microsporum persicolor. Journal de mycologie medicale 2018, 28, 424-427.
