KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Bacterial and Virus Strains
Cowpea mosaic virus	Dr. Dinesh Kumar, UC Davis	N/A
Biological Samples
NATtrol Respiratory Validation Panel (RVP) (Qualitative)	ZeptoMetrix Corporation	NATRVP-3
Chemicals, Peptides, and Recombinant Proteins
Pyridine	FISHER SCIENTIFIC	AC131780500
Octanoic acid	Sigma	C2875–10ML
Hexanoic acid	Sigma	53745–2.5G
Decanoic acid	Sigma	C1875–100G
N,N-diethyl-m-toluamide (DEET)	Fisher Scientific	AC114571000
Tangeretin	Fisher Scientific	505943
Nobiletin (Hexamethoxyflavone)	Fisher Scientific	505360
Phthalate	Sigma	90677–100ML
Diethylene glycol	Sigma	03128–5ML-F
Omethoate	Sigma	36181–100MG
Critical Commercial Assays
The Ovation RNA-Seq System V2	NuGEN	7102–32
PowerWater® DNA kit	Qiagen-Mo Bio	14900–100-NF
PowerWater® RNA kit	Qiagen-Mo Bio	14700–100-NF
REPLI-g Single Cell Kit	Qiagen	150343; 150345
HyperPlus library kit	Roche-Kapa Biosystems	KK8514
Deposited Data
Raw sequencing reads for DNA and RNA	This study	NCBI Bioproject PRJNA421162
Co-assembled contigs for DNA and RNA	This study	NCBI Bioproject PRJNA421162
Experimental Models: Cell Lines
Experimental Models: Organisms/Strains
Oligonucleotides
Recombinant DNA
Software and Algorithms
Moves App	ProtoGeo Oy	N/A
R analysis script	This study	Data File 1
PAVA	PMID: 21937731	https://www.ncbi.nlm.nih.gov/pubmed/21937731
Rstudio	https://www.rstudio.com	https://www.rstudio.com
Bioconductor package	https://www.bioconductor.org/	https://www.bioconductor.org/
DESeq2	PMID: 25516281	https://genomebiology.biomedcentral.com/articles/10.1186/s13059–014-0550–8
phyloseq	PMID: 23630581	https://www.ncbi.nlm.nih.gov/pubmed/23630581
reshape2	https://www.rdocumentation.org/packages/reshape2/versions/1.4.3	https://www.rdocumentation.org/packages/reshape2/versions/1.4.3
ggplot2	https://github.com/hadley/ggplot2-book	https://github.com/hadley/ggplot2-book
edgeR	PMID: 19910308	https://www.ncbi.nlm.nih.gov/pubmed/19910308
NMF	PMID: 20598126	https://www.ncbi.nlm.nih.gov/pubmed/20598126
RcolorBrewer	https://cran.r-project.org/web/packages/RColorBrewer/index.html	https://cran.r-project.org/web/packages/RColorBrewer/index.html
vegan	https://cran.r-project.org/web/packages/vegan/index.html	https://cran.r-project.org/web/packages/vegan/index.html
factoextra	https://cran.r-project.org/web/packages/factoextra/index.html	https://cran.r-project.org/web/packages/factoextra/index.html
glmnet	PMID: 20808728	https://www.ncbi.nlm.nih.gov/pubmed/20808728
e1071	https://cran.r-project.org/web/packages/e1071/index.html	https://cran.r-project.org/web/packages/e1071/index.html
relaimpo	https://cran.r-project.org/web/packages/relaimpo/index.html	https://cran.r-project.org/web/packages/relaimpo/index.html
ade4	https://www.jstatsoft.org/article/view/v022i04	https://www.jstatsoft.org/article/view/v022i04
ViromeScan	PMID: 29492895	https://www.ncbi.nlm.nih.gov/m/pubmed/29492895/
PubChem	PMID: 15879180	https://pubchem.ncbi.nlm.nih.gov
phyloT	PMID: 27095192	https://phylot.biobyte.de
iTOL	PMID: 27095192	https://itol.embl.de
megahit	PMID: 25609793	https://github.com/voutcn/megahit
bbtools	https://jgi.doe.gov/data-and-tools/bbtools/	https://jgi.doe.gov/data-and-tools/bbtools/
Bwa-mem	https://arxiv.org/abs/1303.3997	http://bio-bwa.sourceforge.net
Gephi	https://www.aaai.org/ocs/index.php/ICWSM/09/paper/view/154	https://gephi.org
XCalibur	Thermo-Fisher Scientific	https://www.thermofisher.com/order/catalog/product/OPTON-30487
SIMCA	Umetric	https://umetrics.com/products/simca
Other
ODP2 HP-4B (LC column)	Shodex	F009121
OPD2 HPG-4A (LC guard column)	Shodex	G207063
Information and statistics on classified contigs of Rotifer and Apicomplexa	This Study	Data File 2
MicroPEM Personal Aerosol Exposure Monitor v3.2A	RTI International	N/A
Teflo Air Sampling Filters	PALL Life Science	R2P1025
Polyethersulfone Membrane Filters	STERLITECH Corporation	PES0825100
The TSI Mass Flowmeter	TSI Inc	Model 4143 D
Bioanalyzer	Agilent	G2939BA
Illumina HiSeq 4000 platform	Illumina Inc.	https://www.illumina.com/systems/sequencing-platforms/hiseq-3000–4000.html
Molecular Sieve Adsorben Sigma 20304	Sigma-Aldrich Corp., St. Louis, MO USA	https://www.sigmaaldrich.com/catalog/product/supelco/20304?lang=en&region=US
Structural database of allergenic proteins (SDAP)	PMID: 12520022	http://fermi.utmb.edu
Protein Family database (Pfam)	PMID: 26673716	https://pfam.xfam.org
Gene Ontology database (GO)	PMID: 10802651	http://www.geneontology.org
Cluster of orthologous groups database (COG)	PMID: 10592175	https://www.ncbi.nlm.nih.gov/COG/
Metlin database	PMID: 16404815	https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage