Yeast and Lactic Acid Bacteria Dominate the Core Microbiome of Fermented ‘Hairy’ Tofu (Mao Tofu)

Round 1

Reviewer 1 Report

excellent work... please consider to revise the conclusion and include limitations and future direction.... Best of luck

Author Response

Thank you for your comments. We have included a paragraph about the limitations of the study and future directions as requested.

Author Response File: Author Response.pdf

Reviewer 2 Report

The paper entitled "Yeast and lactic acid bacteria dominate the core microbiome of fermented 'hairy' tofu (Mao tofu)" reports a study on bacterial and fungal communities evaluated through the metagenomic sequencing of ITS, LSU and 16 S rDNA of DNA extracted from sample of Mao tofu picked up in four markets in Yunnan (China).

Althoug interesting because it deals with a subject  that has not studied so far, it has major scientific shortcomings, some of which are listed below.

-The research work on microbial communities did not concern also cultivable microorganisms, but only the sequencing of the DNA belonging to microorganisms linked to the history of each sample, however many of them are not viable, therefore of no interest for the consumer of Mao tofu.

The cornerstone of a scientific work is based on the possibility of demostrating the same results, repeating the tests in any area even by different researcher. In the specific case, the physico-chemical composition of the samples are completely unknown, therefore they are anonymous, in fact, it is not possible correlate the different results obtained in the samples taken in different markets with their chemical and physical composition.

-The Material and Methods section is lacking: it does not report any information on the production technologies used in the various area of origin of the tofu samples.

-The lack of reference related to the physico-chemical characteristics of the starting material and of the production technologies, linked to the territory, make the predictive models reported in the work less unreliable.

Other important shortcomings are not reported for the sake of brevity.

Minor point:

The title of the paper refers to Mao tofu, in the text instead it is also treated the stinky tofu wich is different (see Introduction section).

Author Response

1) Thank you for this comment. Our goal was to characterize the fungal and bacterial microbial communities present in Mao tofu. We chose to use culture independent methods for this pursuit, rather than succumbing to the well-known biases of culture-based assays. Microbial viability was not tested either. Most of the fungi and bacteria are likely culturable, but doing would have been a significant undertaking and beyond the scope of this work.

2) The production technologies were not available to us, unfortunately. See above.

3) Our results serve as a baseline for understanding microbial communities associated with Mao Tofu. Other studies focused on physico-chemical, productive technologies, and cultured members of the community will surely follow and will be of interest to the field of traditional fermentation.  

It is important to consider that our study aimed to interpret microbiome data and identify relationships between microbial communities of Mao Tofu and markets (region).

4) We corrected the text accordingly. Our samples are now correctly referred to as Mao tofu, not stinky tofu.

Author Response File: Author Response.pdf

Reviewer 3 Report

The text of fig. 5 is difficult to read because the color of the letters is gray and the contrast is low. Recommendation - please reformat the figure and adjust the color of the letters to black!
You could support this microbiological study with some biochemical studies (amino acid and fatty acid analysis) of different fermented tofu samples. An organoleptic study of the properties of the finished product would also be interesting. This would enrich the study and expand the circle of readers.
I recommend doing similar research in other Asian countries that have a tradition of tofu making.

Author Response

1) We corrected Figure 5 as recommended.

2) We agree that investigating the microbiological and biochemical characteristics of Mao tofu would be interesting. These are all great follow up studies to this initial culture-independent characterization of the microbial communities living in and on Mao tofu.

Author Response File: Author Response.pdf

Reviewer 4 Report

The article presented to me for review answers to important and current scientific problems is related to the poorly studied microbiota of fermented products like fermented hairy tofu. There is a need for more in-depth corrections of English grammar and style. The article can be published after the correction of English. A high percent (20%) of plagiarism was detected in the abstract. Metagenomic analyzes have been made methodologically correct. The discussion and conclusions correspond to the results. Аccept after revision.

 

Comments for author File: Comments.pdf

Author Response

1) Thank you for this comment. We have corrected all the grammar and typos throughput the manuscript text. We reworked the abstract as suggested.

2) We are not sure what the plagiarism was, perhaps of a preprint of this article? In any event, we have rewritten the abstract.

Response to additional comments (those in the PDF file)

- we refer to as ‘yogurt’: https://en.wikipedia.org/wiki/Yogurt

- We now include the suggested reference in the introduction section.

-To clarify, the correct spelling for the““rarecurve”, specnumber” and “diversity” R functions  do not contain an “-”.

- We have used an active, as is currently recommended for science writing.

See:

- https://www.science.org/content/article/how-write-scientist

- Plotnick J. How to use active voice in the sciences. University College Writing Centre, University of Toronto, Canada. Available from: http://www.writing.utoronto.ca/advice/specific-types-of-writing/active-voice-in-science [Accessed 20th June 2016].

- The Writer’s Handbook. Use the active voice. The Writing Centre, University of Wisconsin, USA. Available from: http://writing.wisc.edu/Handbook/CCS_activevoice.html [Accessed 20th June 2016].

- We corrected all the grammar errors reported by the reviewers as requested.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

No additional comments to those already expressed previously.