KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Bacterial and virus strains | ||
| C. acnes isolates | This manuscript | N/A |
| C. granulosum isolates | This manuscript | N/A |
| Biological samples | ||
| Skin scrapes and skin pore samples from healthy people | This manuscript | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Brucella Blood Agar | Hardy Diagnostics | A30 |
| QuickExtract buffer | EpiCentre | QE09050 |
| Lysozyme | Millipore Sigma | 62971 |
| PCRClean-DX SPRI beads | Aline Biosciences | C-1003-250 |
| Polyethylene glycol (PEG) 8000 | Hampton Research | HR2-535 |
| Magnesium chloride (MgCl2) | Ambion | AM9530G |
| ReadyLyse Lysozyme Solution | EpiCentre | R1810M |
| KAPA HiFi HotStart ReadyMix | Roche | 7958927001 |
| Reinforced Clostridial Media (RCM) | Oxoid | CM0149 |
| Critical commercial assays | ||
| PureLink Genomic DNA Kit | Invitrogen | K182002 |
| Illumina Tagment DNA TDE1 Enzyme and Buffer Kits | Illumina | 20034198 |
| High-Molecular Weight Genomic DNA Kit | Qiagen | 67563 |
| Ligation Sequencing Kit and Native Barcoding Expansion 1-12 | Oxford Nanopore | SQK-LSK109 and EXP-NBD104 |
| Blackhead Removal Activated Carbon Mask | Mengkou | 4716872044078 |
| Deposited data | ||
| Raw sequencing data | This manuscript | NCBI-SRA BioProject: PRJNA771717 |
| Assembled genomes for each C. acnes lineage | This manuscript | GitHub: https://github.com/arolynconwill/cacnes_biogeo |
| Hybrid assemblies of C. acnes colonies with plasmids | This manuscript | GitHub: https://github.com/arolynconwill/cacnes_biogeo |
| Experimental models: Cell lines | ||
| Experimental models: Organisms/strains | ||
| Oligonucleotides | ||
| 16S V1-V3 forward primer (27F-plex): TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAGAGTTTGATCMTGGCTCAG | Khadka et al., 2021 | N/A |
| 16S V1-V3 reverse primer (534R-plex): GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATTACCGCGGCTGCTGG | Khadka et al., 2021 | N/A |
| Recombinant DNA | ||
| Software and algorithms | ||
| All original code | This manuscript | https://github.com/arolynconwill/cacnes_biogeo |
| Snakemake (v6.4.1) | Mölder et al., 2021 | https://snakemake.readthedocs.io/en/stable/ |
| Matlab (v2015b, v2018a) | Mathworks | https://www.mathworks.com/products/matlab.html |
| Cutadapt (v1.18) | Martin, 2011 | https://cutadapt.readthedocs.io/en/stable/ |
| Sickle (v1.33) | Joshi and Fass, 2011 | https://github.com/najoshi/sickle |
| Bowtie 2 (v2.2.6) | Langmead et al., 2009 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| SAMtools (v1.5) and BCFtools (v1.2) | Li et al., 2009 | https://github.com/samtools/ |
| Kraken 2 (v2.0.7) | Wood et al., 2019 | https://github.com/DerrickWood/kraken2/wiki |
| Bracken (v2.5) | Lu et al., 2017 | https://github.com/jenniferlu717/Bracken |
| BLAST (v2.7.1) | NCBI | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| PHYLIP (v3.69) | Fenselstein, 2005 | https://evolution.genetics.washington.edu/phylip.html |
| FigTree (v1.4.4) | Andrew Rambaut | https://github.com/rambaut/figtree |
| SPAdes (v3.13) | Bankevich et al., 2012 | https://github.com/ablab/spades |
| Prokka (v4.8.1) | Seemann, 2014 | https://github.com/tseemann/prokka |
| CD-HIT (v4.8) | Li et al., 2006; Fu et al., 2012 | http://weizhong-lab.ucsd.edu/cd-hit/ |
| Filtlong (v0.2.0) | Wick, 2018 | https://github.com/rrwick/Filtlong |
| Unicycler (v0.4.8) | Wick et al., 2017 | https://github.com/rrwick/Unicycler |
| SATIVA | Kozlov et al., 2016 | https://github.com/amkozlov/sativa |
| QIIME2 (v2020.11) | Bolyen et al., 2018 | https://qiime2.org |
| DADA2 (v1.18.0) | Callahan et al., 2016 | https://benjjneb.github.io/dada2/index.html |
| Other | ||
| Public C. acnes genomes | NCBI GenBank | Accession: NC_018707.1 |
| Public C. acnes plasmid sequences | NCBI GenBank | CP003294 and CP017041 |
| Public C. granulosum genomes | NCBI GenBank | NZ_LT906441.1 |
| SILVA database (version 132) | Quast et al., 2013 | https://www.arb-silva.de |