REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
ZymoBiOMICS Microbial Community standard	Zymo Research	Catalog #D6300
ZymoBIOMICS Microbial Community DNA Standard	Zymo Research	Catalog #D6305
Biological samples
Environmental samples from urban and built-in structures	Participating Consortium members	N/A
Critical commercial assays
QIAGEN QIAseq FX DNA Library Kit	QIAGEN	ID: 180475
Promega DNA extraction Maxwell kit Blood	Promega	AS1400
Promega DNA extraction Maxwell kit Buccal Swab	Promega	AS1640
Zymo DNA/RNA shield	Zymo Research	R1100-250
MoBio PowerSoilR©DNA Isolation Kit	MoBIO	Cat.:12888-100
Agencourt AMPure XP	Beckmann Coulter	Cat.:A63881
Qubit® dsDNA HS Assay	Thermofisher	Q32854
QuantiFluor® ONE dsDNA System	Promega	E4871
Nextera Flex (Now known as Illumina DNA Prep)	Illumina	20018705
Nextera DNA CD Indexes	Illumina	20018708
Deposited data
NCBI/RefSeq Microbial ca. March 2017	NCBI	https://www.ncbi.nlm.nih.gov/refseq/
Hg38 with Alternate Contigs	UCLA	https://hgdownload.cse.ucsc.edu/goldenPath/hg38
Human Microbiome Project	Human Microbiome Project Consortium, 2012	https://www.hmpdacc.org/hmp/resources/download.php
Microbe Directory	Shaaban et al., 2018	https://microbe.directory
UniRef90	Suzek et al., 2007	https://www.uniprot.org/downloads
Integrated Gut Genomes v1.0	Nayfach et al., 2019	https://github.com/snayfach/IGGdb
Genome Taxonomy Database	Parks et al., 2018	https://gtdb.ecogenomic.org/downloads
MetaSUB Sequencing Data	This paper	https://pngb.io/metasub-2021
Software and algorithms
AdapterRemoval v2.17	Schubert et al., 2016	https://github.com/mikkelschubert/adapterremoval
Bowtie2 v2.3.0	Langmead and Salzberg, 2013	https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.0/
BLASTn	Altschul et al., 1990	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
KrakenUniq v0.3.2	Breitwieser et al., 2018	https://github.com/fbreitwieser/krakenuniq
MASH v2.1.1	Ondov et al., 2016	https://github.com/marbl/Mash
HUMAnN2	Franzosa et al., 2018	https://pypi.org/project/humann2/
DIAMOND v0.8.36	Buchfink et al., 2015	https://github.com/bbuchfink/diamond
metaSPAdes v3.8.1	Nurk et al., 2017	https://github.com/ablab/spades/releases/tag/v3.8.1
MegaRes v1.0.1	Lakin et al., 2017	https://megares.meglab.org/download/index.php
MetaBAT2 v2.12.1	Kang et al., 2019	https://anaconda.org/ursky/metabat2
CheckM v1.0.13	Parks et al., 2015	https://github.com/Ecogenomics/CheckM
dnadiff v1.3	Kurtz et al. 2004	https://github.com/mummer4/mummer
GTDB-Tk v1.0.2	Chaumeil et al., 2019	https://github.com/jianshu93/GTDB_Tk
FastTree v2.1.10	Price et al., 2010	https://anaconda.org/bioconda/fasttree
iTOL v5.5	Letunic and Bork 2019	https://itol.embl.de/
CRISPRCasFinder	Couvin et al., 2018	https://github.com/dcouvin/CRISPRCasFinder
SciPy	Virtanen et al., 2020	https://www.scipy.org/
dendextend v1.12.0	Galili 2015	https://github.com/cran/dendextend
MUMmer v3.23	Kurtz et al., 2004	https://github.com/mummer4/mummer
ResistomeAnalyzer (commit 15a52dd)	Lakin et al., 2017	https://github.com/cdeanj/resistomeanalyzer
MetaSUB Core Analysis Pipeline	Danko and Mason 2020	https://github.com/MetaSUB/CAP2
CAPalyzer	Danko and Mason 2020	https://github.com/dcdanko/capalyzer
Figure Generation Code	This paper	https://github.com/MetaSUB/main_paper_figures
Other
Copan Liquid Amies Elution Swab	Copan Diagnostic	Cat.:480C
Isohelix Swabs	Isohelix	Cat.:MS-02
2D Thermo Scientific Matrix	Thermo Scientific	3741-WP1D-BR
ZR BashingBead Lysis Tubes (0.1 & 0.5 mm)	Zymo Research	Cat# S6012-50