The focus on the four VANISH families features prominently throughout the paper, however numerous figures either only shown one (Figure 1A) or a few of these families (Figure 2C). Perhaps it would make sense for consistency and clarity to show all four families throughout, or to at least state why the ones shown were selected.
For Figure 2B, it is not clear how the "30min after butchering Kudo" and "after butchering Kudo" datapoints differ. Is one later in time than the other? Also, although we appreciate that the authors only want to highlight a data for a single individual on this plot, there are a fair number of data points labeled as 'other subjects' (approximate 100, it appears). How do these relate to daily activities? If more daily tracking data is available, this should be incorporated into the analysis to increase rigor.
The authors justify their use of ASVs to identify exact sequence variants for source tracking of microbiota in the environmental analysis. However, it stands to reason that these same methods would have finer resolution for tackling the other analyses in this paper (which use OTUs). For example, did the authors examine the VANISH ASVs in the maize feeding data shown in the final figure in the manuscript?
In the process of reviewing the background material relevant to this article, we found the commentary posted to BioRxiv
here. Although this critique pertains to the lab's previous published work, it struck us that the current manuscript also suffered from a lack of detail in the description of Hadza diet and seasonal data.
The authors report diversity in terms of Observed OTUs, but this metric can be sensitive to very rare OTUs and therefore is highly dependent on data filtering strategies. What filtering steps were carried out, and can other diversity metrics (e.g. Shannon) be used to complement the observed species data?
The data on prevalence of VANISH ASVs in animal stool, bee hives and water that are in the text of the paper might be better presented in a table (see Fig. 1, below, as a suggestion)