REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-1-3 β-glucan	abcam	Cat#ab233743; RRID: AB_2923478
Rabbit polyclonal anti-Aspergillus	abcam	Cat#ab20419; RRID: AB_445571
Mouse monoclonal anti-CD45	Thermo Fisher Scientific	Cat# 14-0459-82; RRID: AB_467274
Mouse monoclonal anti-CD68	Thermo Fisher Scientific	Cat# MA5-12407; RRID: AB_10979558
Biological samples
Ovarian cancer TMA	US Biomax	Cat#OV8010a
Melanoma TMA	US Biomax	Cat#ME804a
Lung cancer TMA	US Biomax	Cat#LC819a
Lung cancer TMA	US Biomax	Cat#LC813b
Breast cancer TMA	US Biomax	Cat#BR1191
Breast cancer TMA	US Biomax	Cat#BC08118a
Pancreatic cancer TMA	US Biomax	Cat#PA961f
Pancreatic cancer TMA	US Biomax	Cat#PA804b
Fungus 4-Tissue Artificial TMA Aspergillus, Candida, Histoplasma and Negative Control	BioSB	Cat#BSB-0335-CS
The resource of the WIS samples cohort was constructed at the Weizmann Institute of Science. All details are in Table S3.	Nejman et al., 2020	N/A
Critical commercial assays
Phusion Hot Start II DNA Polymerase	Thermo Fisher Scientific	Cat# F549L
Qiaquick PCR purification kit	Qiagen	Cat#28104
Agencourt AMPure XP beads	Beckman Coulter	Cat#A63881
MiSeq Reagent Kit v3 (600-cycle)	Illumina	Cat#MS-102-3003
KAPA SYBR FAST qPCR Master Mix (2X) ABI Prism	Kapa Biosystems	Cat#KK4605
Gomori Methenamine-Silver (GMS) Nitrate Stain Kit	abcam	Cat#ab150671
Bond polymer refine detection kit	Leica Biosystems	Cat#DS9800
BOND epitope retrieval solution 1	Leica Biosystems	Cat#AR9961
Deposited data
Raw data from WIS cohort	This paper	PRJNA786764
Datasets
TCGA CIBERSORT immune cell abundances and linked survival data	Thorsson et al., 2018	Table S1
TCGA WGS and RNA-Seq raw data and metadata (processed and/or downloaded from Cancer Genomics Cloud)	Lau et al., 2017	Cancer Genomics Cloud
Hopkins plasma WGS raw data	Cristiano et al., 2019	EGAD00001005339
UCSD plasma WGS raw data	Poore et al., 2020	ENA: ERP119598 (HIV-negative controls); ERP119596 (prostate cancer); ERP119597 (lung cancer and melanoma)
Experimental models: Cell lines
HS-5 human fibroblast cell line	ATCC	Cat# CRL-11882
Oligonucleotides
Forward primer for 1st ITS2 PCR: ITS86F 5’-GTGAATCATCGAATCTTTGAA-3’	Turenne et al., 1999	N/A
Reverse primer for 1st ITS2 PCR: ITS4+rd2 Illumina adaptor 5’-AGACGTGTGCTCTTCCGATCT - TCCTCCGCTTATTGATATGC-3’	ITS4 from White et al., (1990)	N/A
Forward primer for 2nd ITS2 PCR: P5-rd1-ITS86F 5’ - AATGATACGGCGACCACCGAGATCT - ACACTCTTTCCCTACACGACGCTCTTCCGATCT - GTGAATCATCGAATCTTTGAA-3’	ITS86F from Turenne et al., (1999)	N/A
Reverse primer for 2nd ITS2 PCR: 5’- CAAGCAGAAGACGGCATACGAGAT - NNNNNNNN - GTGACTGGAGTTCAGAC GTGTGCTCTTCCGATCT-3’	Nejman et al., 2020	N/A
Forward primer for 5.8S qPCR: ITS3 - 5’-GCATCGATGAAGAACGCAGC-3’	White et al., 1990	N/A
Reverse primer for 5.8S qPCR: ITS86R - 5’- TTCAAAGATTCGATGATTCAC-3’	Turenne et al., 1999	N/A
Probe for 28S fungal FISH: D-205: 5’- ATTCCCAAACAACTCGAC-3’	Inácio et al., 2003	N/A
Probe for 28S fungal FISH: D-223: 5’-CCACCCACTTAGAGCTGC-3’	Inácio et al., 2003	N/A
Probe for 28S fungal FISH: D-260: 5’-TCGGTCTCTCGCCAATATT-3’	Inácio et al., 2003	N/A
Software and algorithms
Python version 3.6	Python Software Foundation	https://www.python.org/
Qiita cloud-enabled microbiome analyses	Gonzalez et al., 2018	https://qiita.ucsd.edu/
Woltka alignment-based taxonomy classification (used by Qiita)	Zhu et al., 2022	https://github.com/qiyunzhu/woltka
ITS2 classification pipeline	This paper	https://github.com/microbiofunc/ITS2-pipeline
Dockerized host depletion pipeline	This paper	https://github.com/knightlab-analyses/mycobiome/tree/master/Docker_host_depletion_pipeline
Per-sample and aggregate genome coverage	Hakim et al., 2022	https://github.com/ucsd-cmi/zebra_filter
MMvec co-occurrence analyses	Morton et al., 2019a	https://github.com/biocore/mmvec
Robust Aitchison beta diversity	Martino et al., 2019	https://github.com/biocore/DEICODE
EMPeror PCoA visualizer	Vázquez-Baeza et al., 2013	https://github.com/biocore/emperor
EukDetect	Lind and Pollard, 2021	https://github.com/allind/EukDetect
metaSPAdes 3.13.1	Nurk et al., 2017	https://github.com/ablab/spades
MaxBin2 2.2.4	Wu et al., 2016	https://sourceforge.net/projects/maxbin2/
MetaBAT2 2.12.1	Kang et al., 2019	https://bitbucket.org/berkeleylab/metabat
Concoct 1.0.0	Alneberg et al., 2014	https://github.com/BinPro/CONCOCT
BowTie2 2.2.3	Langmead and Salzberg, 2012	https://github.com/BenLangmead/bowtie2
SAMtools 0.1.19	Li et al., 2009	https://github.com/samtools/samtools
metaWRAP 1.1.2)	Uritskiy et al., 2018	https://github.com/bxlab/metaWRAP
CheckM (v. 1.0.13)	Parks et al., 2015	https://github.com/Ecogenomics/CheckM
EukCC	Saary et al., 2020	https://github.com/Finn-Lab/EukCC
BUSCO v5.1.2	Simão et al., 2015	https://busco.ezlab.org/
Mfannot	N/A	https://github.com/BFL-lab/Mfannot
PEAR version 0.9.10	Zhang et al., 2014	https://cme.h-its.org/exelixis/web/software/pear/
cutadapt version 1.17	Martin, 2011	https://cutadapt.readthedocs.io/en/v1.17/
QIIME 2 version 2018.8	Bolyen et al., 2019	https://qiime2.org/
ITSx version 1.1b1	(Bengtsson-Palme and Ryberg, 2013	https://microbiology.se/software/itsx/
R version 4.03	R CRAN	www.r-project.org
phyloseq 1.34.0	McMurdie and Holmes, 2013	https://bioconductor.org/packages/release/bioc/html/phyloseq.html
caret 6.0-90	Kuhn, 2008	https://topepo.github.io/caret/
PRROC 1.3.1	Grau et al., 2015	https://cran.r-project.org/web/packages/PRROC/index.html
gbm 2.1.8	Ridgeway, 2007	https://cran.r-project.org/web/packages/gbm/gbm.pdf
xgboost 1.5.0.1	Chen et al., 2015	https://xgboost.readthedocs.io/en/stable/R-package/xgboostPresentation.html
randomForest 4.6-14	Liaw and Wiener, 2002	https://cran.r-project.org/web/packages/randomForest/randomForest.pdf
ANCOM-BC 1.4.0	Lin and Peddada, 2020	https://github.com/FrederickHuangLin/ANCOMBC
decontam 1.14.0	Davis et al., 2018	https://github.com/benjjneb/decontam
limma-voom 3.50.0	Law et al., 2014	https://bioconductor.org/packages/release/bioc/html/limma.html
snm 1.42.0	Mecham et al., 2010	https://www.bioconductor.org/packages/release/bioc/html/snm.html
MATLAB version 2019b with the Statistics and Machine Learning Toolbox	MathWorks	https://www.mathworks.com
Cytoscape 3.8.1	Shannon et al., 2003	https://cytoscape.org/
UNITE database (version 8, dynamic, sh_taxonomy_qiime_ver8_dynamic_04.02.2020.txt)	Nilsson et al., 2019	https://unite.ut.ee/repository.php
scikit-bio 0.5.6	N/A	https://github.com/biocore/scikit-bio
Other
Pannoramic SCAN II automated slide scanner	3D HISTECH	N/A