Mice lung microbiomes' variable responses to dust exposure
Data files
Oct 12, 2025 version files 186.94 KB
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ReadCountsWIPD.bac.dat.meta.csv
693 B
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README.md
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WIPD.bac.dat.meta_-_WIPD.bac.dat.meta.csv
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Abstract
Inhalation of dust is significant and relevant to health effects. As pollution and climate change worsen in dryland regions, wind currents entrain loose sediment and dust. This potentially disperses toxic geochemical and microbial burdens throughout the region. When inhaled environmental dust and host-associated microbiomes mingle, they pose exposure risks to host respiratory health. The Salton Sea, California’s largest lake, is shrinking thus exposing nearby communities to playa dust. Therefore, we analyze the effect of Salton Sea dust exposure in murine models to relate lung microbial communities and respiratory health. We used an environmental chamber to expose mice to dust filtrate or ambient air and examined the effects of those exposures on lung microbiomes. We found that lung microbial composition varied by dust exposure. Furthermore, dust elicited neutrophil recruitment and immune responses more than mice exposed to ambient air. Sources of dust differentially affected the composition of the lung core microbiome. Lung microbial diversity correlated with neutrophil recruitment as lungs associated with inflammatory responses harbored more diverse microbiomes. Although Salton Sea dust influences dust microbiomes and prevalent taxa, these responses were variable. The composition of lungs exposed to dust collected further from the Sea was more similar to lungs from ambient air exposures; in contrast, dust collected near the Sea yielded lung microbiomes that clustered further from lungs exposed to ambient air. As lakes continue to dry out, we expect greater public health risks in proximal dryland regions, which may correlate with dust microbial dispersal-related changes to lung microbiomes.
Dataset DOI: 10.5061/dryad.95x69p8xh
Description of the data and file structure
These data are metadata related to mouse lung sequences from targeted amplicon sequencing of the marker gene 16S V3-V4 region.
The file WIPD.bac.dat.meta_-_WIPD.bac.dat.meta.csv lists all ASVs and the complete list of taxa in each sample
WIPD.bac.dat.meta has 26 column headings. Below is a list of column headers, including information about the meaning of the data in each column of the dataset. PD stands for Palm Desert, and Wi stands for Wister, which are two locations where dust was collected.
- SampleID = which is the name identifying the sample
- ASV_ID = which is the ASV (i.e., exact sequence variant) Identification code
- Kingdom = Kingdom
- Phylum = Phylum
- Class = Class
- Order = Order
- Family = Family
- Genus = Genus
- Species = Species
- Count = the number of reads that ASV has in that particular sample
- Run.Cont = the abbreviation for the name of that exposure in the chamber; it indicates whether it is a control or a dust-associated exposure
- ShortID = is a short abbreviation of that taxon
- ExposureRun = is the abbreviation for the exposure run, whether it was dust-associated or a contemporaneous control; it is listed as the dust exposure experimental code.
- ExposureMaterial = the specific control air or dust exposure used in the experiment
- ExposureSite = Indicates which site dust was collected from; alternatively, it lists ControlAir if it was a contemporaneous control.l
- DustDeployed = Indicates when dust collectors were deployed at these particular sites
- DustCollected = Indicates when dust collectors were taken to the lab to characterize collected dust.
- DustSeason = Indicates which season dust was collected in
- DustYear = Indicates which year dust was collected in for this experiment
- Chamber = Indicates whether it was a contemporaneous control air exposure or a dust exposure
- MouseSex = Uses F for female or M for male mice, indicates sex of exposed mouse
- MouseGenotype = Indicates the genotype of exposed mice (C57/B6)
- Lobe = Lists the part of the lung that the samples came from (i.e., left, half left, etc.)
- Sample_or_Control = whether the sample was a negative control or if it was from a mouse lung; all listed as False, as they are all samples
- SampleType = all sample types are listed as lung in this column
- RunContColor = color palette used for showing the data in the figures in the manuscript
The file ReadCountsWIPD.bac.dat.meta.csv has a complete list of samples and the reads per sample, as well as the total number of reads across all samples.
Code/software
Excel or R
Access information
Other publicly accessible locations of the data:
- Temporary SubmissionID: SUB15361627
- BioSample accession: SAMN48852837
Data was derived from the following sources:
- 16S targeted amplicon sequencing
- Temporal data on dust
- Demographic data on mice
