REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-Involucrin	Novus Biologicals	cat# NBP2-16981; RRID:AB_2936950
DAPI	Novus Biologicals	cat# NBP2-31156; RRID:DAPI Solution
Alexa Fluor® 647 Phalloidin	ThermoFisher	cat# A22287; RRID:AB_2620155
Goat anti-Rabbit IgG (H + L) Secondary Antibody, Alexa Fluor® 488 conjugate	ThermoFisher	cat# A11008; RRID:AB_143165
Bacterial and Virus Strains
Lactobacillus crispatus bacteria type strain	DSMZ	DSM20584
Prevotella amnii bacteria type strain	DSMZ	DSM23384
Gardnerella vaginalis bacteria type strain, strain designation 594	ATCC	ATCC14018
Mobiliuncus mulieris bacteria type strain, strain designation SV175, SV17J	DSMZ	DSM25311
Chemicals, Peptides, and Recombinant Proteins
Imidazolepropionic acid	Millipore Sigma	77951-250MG
Critical Commercial Assays
LavaPep’s Fluroescent Peptide and Protein Quantification Kit	Gel Company, CA, USA	LP022010
RNeasy Fibrous Tissue Mini Kit	Qiagen	Cat. No. ID: 74704
Cell Proliferation Reagent WST-1	Millipore Sigma	5015944001
Deposited Data
Transcriptomics of vaginal biopsies	GEO	Accession number: GSE139655
Metabolomics of vaginal swab elutions	MetaboLights	Accession number: MTBLS7087
Proteomics/metaproteomics of vaginal swab elutions	PRIDE	Accession numbers: PXD040895 and PXD040280
Experimental Models: Cell Lines
VK2/E6E7 immortalized human epithelial vaginal cell line	ATCC	Cat# CRL-2616; RRID: CVCL_6471
HEC-1-A immortalized human epithelial endometrium cells	ATCC	Cat# HTB-112; RRID: CVCL_0293
Software and Algorithms
Mascot v2.4.0	Matrix Science	RRID:SCR_014322
Progenesis	Nonlinear Dynamics	RRID:SCR_018923
R programming software	R Foundation for Statistical Computing	RRID:SCR_001905
R Studio	Posit Software, PBC	Version 2022.12.0 + 353
R NMF package	BMC Bioinformatics	RRID:SCR_023124
R ColorBrewer package	Erich Neuwirth	RRID:SCR_016697
R ggplot2	Springer-Verlag	RRID:SCR_014601
R COMBAT	Minghui Wang and Yiyuan Liu and Shizhong Han	RRID:SCR_010974
R reshape2 package	Hadley Wickham	RRID:SCR_022679
R plyr	Hadley Wickham	https://www.jstatsoft.org/v40/i01/
R ggfortify package	Yuan Tang and Masaaki Horikoshi and Wenxuan Li	https://doi.org/10.32614/RJ-2016-060
R survival package	Terry M Therneau	RRID:SCR_021137
R vegan package	Jari Oksanen	RRID:SCR_011950
DAVID	DAVID bioinformatics team (LHRI/ADRD at Frederick National Laboratory)	RRID:SCR_001881
Ingenuity Pathway Analysis	Ingenuity	RRID:SCR_008653
Gene Set Enrichment Analysis	Broad Institute	RRID:SCR_003199
FlowJo	LLC	RRID:SCR_008520
Adobe Photoshop CC	Adobe	RRID:SCR_014199
MATLAB	Mathworks	R2021a
Partial Least Squares Path Modeling	This Work	https://doi.org/10.5281/zenodo.7810345