Dear Editor,
Dear authors,

The article entitled, “The Mycobiomes and Bacteriomes of the Lower Respiratory Tract and Home Dust “ (by Niemeier-Walsh et al.), compare the mycobiomes and bacteriomes between three sample types: home dust, saliva, and sputum samples from the same participants (40 adolescents). The authors found that home dust had a very low bacterial load and a very high fungal load compared to the lower respiratory tract. Future studies should examine the relationship between the taxa found in the indoor environment and the taxa found in the lower respiratory tract.
General comments:
- Introduction, results and discussion are well written; the bibliography is quite up-dated.
However, recent publications: “DNA metabarcoding to assess indoor fungal communities: Electrostatic dust collectors and Illumina sequencing.” by Rocchi et al. 2017 and “Indoor microbiome, environmental characteristics and asthma among junior high school students in Johor Bahru, Malaysia.” By Fu X, et al. 2020 should be added and taken into account during the discussion.

• The authors present the data as an exploration of lower respiratory tract while only saliva, and induced sputum samples have been used. This is overstated and need to be modified.

• Regarding methodology, it could of interest to compare Basidiomycota/Ascomycota ratio between the 3 types of samples, as proposed in “Fungal microbiota dysbiosis in IBD” by Sokol H et al. 2017, and discuss this ratio taking into account the highly prevalence of medically relevant fungi in Ascomycota.
  Moreover, it would be of interest to characterize and compare the microbial core of each type of samples, by using Venn Diagram (for example this function is implemented in RAM package).
  It is not clear if any relative abundance cut-off (OTU abundance) has been used.

Specific comments:
- Page 18, lines 38-42: Why the authors discussed how the growth conditions may impact bacterial load differences between the oral cavity and the lower respiratory tract, without connecting this item with the fungal load. Fungal growth requires nutrients as well.
- Figures 2, S4 and S6: p values should be added to each graph.
- Figure 4: Results of the betadisper function should be added.

In conclusion, the reviewer recommends to ask for substantial revisions of this study version.
Sincerely yours

The authors have adequately responded to all of my comments, but further revision is needed regarding the response pasted below.
- The betadisper tests (Figure 4) are significant ; this point has to be discussed since it
tests for homogeneity of multivariate dispersions (i.e. deviations from centroids) among groups.
- The Title of the Supporting Information has to be up-dated.