| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Critical commercial assays | ||
| PowerSoil DNA Isolation Kit | QIAGEN, Germany | Catalog No. 12888-50 |
| NexteraXT DNA Library Preparation Kit | Illumina, California, USA | FC-131-1096 |
| Deposited data | ||
| Previously sequenced cohorts in Ethiopia, Ghana, Tanzania | Tett et al.26 | NCBI-SRA BioProject: PRJNA504891; PRJNA529124; PRJNA529400 |
| Previously sequenced cohorts in Italy | Asnicar et al.15; Ferretti et al.16 | NCBI-SRA BioProject: PRJNA352475 |
| Previously sequenced cohort in Sweden | Bäckhed et al.10 | EBI’s Sequence Read Archive: ERP005989 |
| Newly sequenced cohort in Italy | This study | NCBI-SRA BioProject: PRJNA352475 and PRJNA716780 |
| Newly sequenced teff sourdough metagenomes | This study | NCBI-SRA BioProject: PRJNA504891 |
| Software and algorithms | ||
| MEGAHIT (version 1.1.1) | Li et al.65 | RRID: SCR_018551; https://github.com/voutcn/megahit |
| MetaBAT2 (version 2.12.1) | Kang et al.66 | RRID: SCR_019134; https://bitbucket.org/berkeleylab/metabat |
| CheckM (version 1.0.7) | Parks et al.67 | RRID: SCR_016646; https://github.com/Ecogenomics/CheckM |
| CMSeq (version 1.0.0) | Pasolli et al.23 | https://bitbucket.org/CibioCM/cmseq |
| PhyloPhlAn 3 (version 3.0.2) | Asnicar et al.68 | https://github.com/biobakery/phylophlan |
| Mash (version 2.0) | Ondov et al.69 | RRID: SCR_019135; https://github.com/marbl/Mash |
| MetaPhlAn 3 (version 3.0) | Beghini et al.28 | https://github.com/biobakery/MetaPhlAn |
| StrainPhlAn 3 (version 3.0) | Beghini et al.28 | https://github.com/biobakery/MetaPhlAn |
| RAxML (version 8.1.15) | Stamatakis70 | RRID: SCR_006086; https://github.com/stamatak/standard-RAxML |
| SAMtools (version 1.3.1) | Li et al.71 | RRID: SCR_002105; https://github.com/samtools/samtools |
| BEDtools | Quinlan72 | RRID: SCR_006646; https://github.com/arq5x/bedtools2 |
| bowtie2 (version 2.4.0) | Langmead and Salzberg73 | RRID: SCR_016368; https://github.com/BenLangmead/bowtie2 |
| Vegan R package | Oksanen et al.74 | RRID: SCR_011950; https://github.com/vegandevs/vegan |
| ggplot2 (version 3.3.2) | Wickham75 | RRID: SCR_014601; https://github.com/tidyverse/ggplot2 |
| Other | ||
| RefSeq (F. sanfranciscensis genomes) | O’Leary et al. 201676 | RRID: SCR_003496; https://www.ncbi.nlm.nih.gov/refseq/ |
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