REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Oropharyngeal swabs, Endotracheal aspirates, Plasma samples, Oral washes, Bronchoalveolar lavage samples	University of Pittsburgh, Division of Pulmonary, Allergy and Critical Care Medicine	Not applicable
Chemicals, peptides, and recombinant proteins
HL-SAN	ArcticZymes	#70910-202
Sputasol	Thermo Scientific	SR0233A
Saponin	Millipore Sigma	S4521
ZymoBIOMICS Microbial Community DNA Standard	Zymo Research	D6305
Critical commercial assays
Dneasy Powersoil DNA Kit	QIAGEN	#12888-100
MiNION Flow Cells R9.4.1	Oxford Nanopore Technologies	FLO-MIN106D
Rapid PCR Barcoding Kit	Oxford Nanopore Technologies	SQK-RPB004
Luminex 10-plex (IL6, IL8, IL10, sRAGE, Ang-2, ST2, sTNFR1, fractalkine, procalcitonin, pentraxin3)	R&D Systems	Custom made
Luminex 2-plex (LBP, sCD14)	R&D Systems	Custom made
ELISA – SPD	Biovendor, LLC	RD194059101
MiSeq Reagent Kit v2 (300-cycles)	Illumina	MS-102-2002
Deposited data
16S rRNA gene sequences	Sequence Resource Archive	PRJNA595346 for biospecimens from ICU patients; PRJNA940725 for Healthy Controls
Software and algorithms
R version v4.2.0	The R Foundation for Statistical Computing	Not applicable
Prism 9 for macOS	GraphPad	Not applicable
ChatGPT	OpenAI.com	Not applicable
EPI2ME – What’s In My Pot (WIMP)	Oxford Nanopore Technologies	Not applicable
Mothur	Mothur.org	Not applicable
Other
Primary Code in R language	GitHub - Zenodo	https://github.com/MicrobiomeALIR/AspirationPneumonia https://doi.org/10.5281/zenodo.7872061