REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Metagenomic sequences of longitudinal samples	This paper	SRA: PRJEB41102
Deposited data
Gene catalogue nucleotide and amino acid sequences	This paper	http://vm-lux.embl.de/∼hildebra/Drama_GC
Kushugulova et al., 2018	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJEB17632
Willmann et al., 2015	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJEB10391
Bäckhed et al., 2015	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJEB6456
Chu et al., 2017	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA322188
Asnicar et al., 2017	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA339914
Lee et al., 2017	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA353655
Heintz-Buschart et al., 2016	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA289586
Human Microbiome Project Consortium, 2012	HMP webpage	N/A
Kostic et al., 2015	https://diabimmune-17.ltdk.helsinki.fi/	N/A
Yassour et al., 2016	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA290381
Vatanen et al., 2016	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA290380
Ferretti et al., 2018	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA352475
Mehta et al., 2018	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA354235
Zeevi et al., 2015	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJEB11532
Bengtsson-Palme et al., 2015	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJEB7369
Raymond et al., 2016	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJEB8094
Palleja et al., 2018	https://www.ebi.ac.uk/ena/browser/home	SRA: ERP022986
Yassour et al., 2018	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA475246
Scholz et al., 2016, Ward et al., 2016	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJNA63661
Li et al., 2016	https://www.ebi.ac.uk/ena/browser/home	SRA: PRJEB12357
Software and algorithms
R version 3.6.2	R Core Team 2017	https://www.r-project.org/
Rarefaction scripts	Saary et al., 2017	https://github.com/hildebra/Rarefaction
Shotgun metagenomic data processing pipeline	Hildebrand et al., 2019	https://github.com/hildebra/MATAFILER
Read depth windows calculation	Hildebrand et al., 2019	https://github.com/hildebra/rdCover
Frameshifts fixing in MSAs program	This paper	https://github.com/hildebra/MSAfix
MetaBAT2 version 2.15	Kang et al., 2019	https://bitbucket.org/berkeleylab/metabat/src/master/
sdm version 1.47	Hildebrand et al. 2014	https://github.com/hildebra/sdm
MegaHit version 1.2.3 beta	Li et al. 2015	https://github.com/voutcn/megahit
Prodigal version 2.6.1	Hyatt et al., 2010	https://github.com/hyattpd/Prodigal
Bowtie2 version 2.3.4.1	Langmead and Salzberg, 2012	https://github.com/BenLangmead/bowtie2
Samtools version 1.3.1	Li et al., 2009	http://www.htslib.org/
BedTools version 2.21.0	Quinlan and Hall, 2010	https://github.com/arq5x/bedtools2
CD-HIT version 4.6.1	Fu et al., 2012	http://weizhongli-lab.org/cd-hit/
MMseqs2 Version f5a1cdb44c9 96d6be229226b09ecc687646c0c12	Steinegger and Söding, 2017	https://github.com/soedinglab/MMseqs2
CheckM version 1.0.11	Parks et al., 2015	https://ecogenomics.github.io/CheckM/
MAFFT version 7.245	Katoh and Standley, 2013	https://mafft.cbrc.jp/alignment/software/
Trimal version 1.4.rev22	Capella-Gutiérrez et al., 2009	http://trimal.cgenomics.org/
IQ-TREE version 1.6.3a	Nguyen et al., 2015	https://github.com/iqtree/iqtree2
iTOL	Letunic and Bork, 2016	https://itol.embl.de/
GTDB-TK version 1.3.0	Parks et al., 2018	https://github.com/Ecogenomics/GTDBTk
Kraken2 version 2.0.9-beta	Wood et al., 2019	http://ccb.jhu.edu/software/kraken2/
Lambda version 1.9.3	Hauswedell et al., 2014	https://seqan.github.io/lambda/
EggNOG-mapper version 2.0.0	Huerta-Cepas et al., 2019	https://github.com/eggnogdb/eggnog-mapper
Diamond version 0.9.24.125	Buchfink et al., 2015	https://github.com/bbuchfink/diamond
Bcftools mpileup version 1.9	Li, 2011	https://samtools.github.io/bcftools/howtos/variant-calling.html
Vegan R package	Oksanen et al., 2014	https://cran.r-project.org/web/packages/vegan/index.html
FUBAR	Murrell et al., 2013	http://www.hyphy.org/
APE	Paradis et al., 2004	https://cran.r-project.org/web/packages/ape/index.html