Key resource table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Human gut microbial DNA from fecal samples | This study | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| RPMI-1640 medium | FUJIFILM Wako Pure Chemical Corporation | 18902025 |
| fetal bovine serum | Cosmobio | 3031 CCP-FBS-BR-500 |
| Penicillin- streptomycin | FUJIFILM Wako Pure Chemical Corporation | 168-23191 |
| nonessential amino acids | FUJIFILM Wako Pure Chemical Corporation | 13915651 |
| interleukin-2 | BioLegend | 589104 |
| succinic semialdehyde | Santa Cruz Biotechnology | sc-281158 |
| Critical commercial assays | ||
| WST-8 method with a Cell Counting Kit | Dojindo | 341-07624 |
| preservation solution kit of fecal sample | Technosuruga | |
| PowerFecal DNA Isolation Kit | QIAGEN | 12830-50 |
| QIAmp DNA Stool | QIAGEN | 51504 |
| Deposited data | ||
| Raw and analyzed gut bacterial DNA sequence data | This paper | DNA Data Bank of Japan (DDBJ) Sequence Read Archive (DRA), DRA016992. |
| Experimental models: Cell lines | ||
| MT-1 | JCRB CELL BANK | JCRB |
| ILT-Mat | RIKEN BRC CELL BANK | RCB0475 |
| ANT | RIKEN BRC CELL BANK | RCB1440 |
| Oligonucleotides | ||
| 16S rRNA-Forward Primer 341F: 5′- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNCCTACGGGNGGCWGCAG-3′ |
Oral Microbiome Center, Taniguchi Dental Clinic | N/A |
| 16S rRNA-Reverse Primer −806R: 5’ – GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNGACTACHVGGGTATCTAATCC-3′ |
Oral Microbiome Center, Taniguchi Dental Clinic | N/A |
| Software and algorithms | ||
| Fastp | Chen et al. [34] | https://github.com/OpenGene/fastp |
| VSEARCH | Rognes et al. [35] | https://github.com/torognes/vsearch |
| SeqKit | Shen et al. [36] | https://github.com/shenwei356/seqkit/releases |
| Deblur | Amir et al. [37] | https://github.com/biocore/deblur |
| SortMeRNA | Kopylova et al. [38] | https://github.com/sortmerna/sortmerna |
| BLASTn | Camacho et al. [39] | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| Cutadapt | Marcel [40] | https://github.com/marcelm/cutadapt |
| Bowtie2 | Langmead et al. [41] | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| MEGAHIT | Li et al. [42] | https://github.com/voutcn/megahit |
| Prodigal | Hyatt et al. [43] | https://github.com/hyattpd/Prodigal |
| MMseqs2 | Steinegger et al. [44] | https://github.com/soedinglab/MMseqs2 |
| Diamond | Buchfink et al. [45] | https://github.com/bbuchfink/diamond |
| MAFFT | Katoh et al. [46] | https://mafft.cbrc.jp/alignment/software/ |
| RAxML | Stamatakis et al. [47] | https://github.com/amkozlov/raxml-ng |
| iTOL | Letunic et al. [48] | https://itol.embl.de/ |
| Enteropathway | Shiroma et al. [23] | https://enteropathway.org/#/ |
| Other | ||
| GTDB | Donovan et al. [49] | https://gtdb.ecogenomic.org/ |
| MGnify | Mitchell et al. [50] | https://github.com/EBI-Metagenomics |
| Python | Python Software Foundation | https://www.python.org/downloads/release/python-376/ |