In this manuscript, the authors conducted the analysis to the meta-barcoding and shotgun metagenomic data of spontaneous wine fermentation, showing high correlations in abundance measurement. Furthermore, the comparison between the meta-barcoding and shotgun metagenomic data showed that there is strong bias in the meta-barcoding data for the genus Metschnikowia. In general, the manuscript was well written, with appropriate structure and comprehensive description of the methods and results.
Major Comments: 1. About Figure 1: 1)The description about Figure 1 needs improvement. For example, Line 537, "both plots", what are the two plots specifically? (should be A and B, but it should be more clear) Also it seems that plot (B) plot(C) were mislabeled so now the description does not match the labels in the figure. Also the last sentence "Abundance values are presented as in Fig 1A" seems not accurate here, The legend of the values is located at the bottom part of the figure, not in subplot A. 2) In subplot C, how were the nodes about the top 30 genera positioned in the plot? How was the distance between nodes calculated? 2. line 215, the reference genomes used for alignment were "assembled from existing genomic resources for fungal and bacterial genera that were known, or suspected of being wine-associated". What exactly are the genomic resources? On line 408-413 in Methods section, "whole genome sequences were collected, when possible", here is "collected" the same as "assembled"? If it is assembled, what is the specific assembler used here? This is not very clear and may need further clarification. 3. About Figure 2A: "only the abundance measures for species within the Hanseniaspora genus" are depicted. Why this genus is picked? On line 258-260, it is mentioned, the identity values are significantly lower for "Mucor circinelloides, Pseudomonas syringae and Hanseniaspora valbyensis", why not pick these genera to be presented in 2A? 4. Table 2: 1) line 276, "two cases", what are the two cases? 2) In Table2, What does the gray color represent? Also, the boxes for "Total OTUs" column are grey and not grey respectively. Should this be more consistent? 3) Should the "Control mix 1" for "AWRI1498" be "1x10**6" as "AWRI796"?
Minor Comments: 1. line 49, "To the map" -> "To map" 2. line 281, "D1 T1 and T2" , a comma is missing between "D1" and "T1". 3. line 293, "were not within a five-fold range", but on line 290, it is "two-fold". Why "five-fold"? 4. line 560, "to the total the abundance of", is there an extra "the" in the sentence? 5. line 565, "an abundance of S. cerevisiae of 1 million reads per million", what does "per million" mean hear?