KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse Mucin 2 Antibody (H-300) | Santa Cruz Biotechnology | sc-15334 |
| Alexa Fluor® 488-AffiniPure Donkey Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | 711-545-152 |
| Bacterial and Virus Strains | ||
| Bacteroides thetaiotaomicron VPI-5482 | ATCC | ATCC 29148 |
| Bacteroides fragilis NCTC 9343 | ATCC | ATCC 25285 |
| Bacteroides vulgatus ATCC 8482 | ATCC | ATCC 8482 |
| Bacteroides distasonis ATCC 8503 | ATCC | ATCC 8503 |
| Bacteroides caccae ATCC 43185 | ATCC | ATCC 43185 |
| Bacteroides ovatus ATCC 8483 | ATCC | ATCC 8483 |
| Bacteroides uniformis ATCC 8492 | ATCC | ATCC 8492 |
| Bacteroides intestinalis DSM 17393 | DSMZ | DSM 17393 |
| Bacteroides cellulosilyticus CL02T12C19 | BEI (HMP) | HM-726 |
| Bacteroides salyersiae CL02T12C01 | BEI (HMP) | HM-725 |
| Bacteroides stercoris CC31F | BEI (HMP) | HM-1036 |
| Bacteroides vulgatus CL09T03C04 | BEI (HMP) | HM-720 |
| Bacteroides vulgatus (humanized mouse 1, D0) | This study | |
| Bacteroides vulgatus (humanized mouse 1, D4) | This study | |
| Bacteroides vulgatus (humanized mouse 1, D12) | This study | |
| Bacteroides caccae (humanized mouse 1, D12) | This study | |
| Bacteroides vulgatus (humanized mouse 1, D16) | This study | |
| Bacteroides salyersiae (humanized mouse 2, D0) | This study | |
| Bacteroides stercoris (humanized mouse 2, D0) | This study | |
| Bacteroides xylanisolvens (humanized mouse 2, D0) | This study | |
| Bacteroides intestinalis (humanized mouse 2, D0) | This study | |
| Bacteroides intestinalis (humanized mouse 2, D0) | This study | |
| Bacteroides uniformis (humanized mouse 2, D0) | This study | |
| Bacteroides uniformis (humanized mouse 2, D10) | This study | |
| Bacteroides uniformis (humanized mouse 2, D10) | This study | |
| Bacteroides vulgatus (humanized mouse 2, D16) | This study | |
| Bacteroides caccae (humanized mouse 2, D22) | This study | |
| Bacteroides uniformis (humanized mouse 2, D22) | This study | |
| Bacteroides uniformis (humanized mouse 2, D22) | This study | |
| Bacteroides vulgatus (conventional mouse 1, day 0) | This study | |
| Bacteroides vulgatus (conventional mouse 1, day 0) | This study | |
| Bacteroides acidifaciens (conventional mouse 1, day 0) | This study | |
| Bacteroides uniformis (conventional mouse 1, day 0) | This study | |
| Bacteroides vulgatus (conventional mouse 1, day 11) | This study | |
| Bacteroides acidifaciens (conventional mouse 1, day 11) | This study | |
| Bacteroides uniformis (conventional mouse 1, day 11) | This study | |
| Bacteroides sp. D1 (H2 microbiota mouse 1, day 11) | This study | |
| Bacteroides sp. D1 (H2 microbiota mouse 1, day 11) | This study | |
| Bacteroides salyersiae (H2 microbiota mouse 1, day 11) | This study | |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Rhodamine-labeled Ulex Europaeus Agglutinin I | Vector Labs | Cat# RL-1062 |
| Bacteroides Bile Esculin Agar/Laked Brucella Blood Agar with Kanamycin and Vancomycin (BBE/LKV) | Anaerobe Systems | AS-242 |
| BD Difco™ Brain Heart Infusion Agar | BD | 241830 |
| Standard MAC-rich diet | Purina | LabDiet 5010 |
| Defined low-MAC diet | Harlan | TD.86489 |
| Critical Commercial Assays | ||
| PowerSoil HT DNA Isolation Kit | Qiagen | 12955 |
| UltraClean 96 PCR Cleanup Kit | Qiagen | 12596-4 |
| Quant-iT™ dsDNA Assay Kit, high sensitivity | Invitrogen | Q33120 |
| Deposited Data | ||
| 16S and whole genome sequencing datasets | Stanford Digital Repository | https://purl.stanford.edu/rm696bw4911 |
| Experimental Models: Organisms/Strains | ||
| Swiss Webster Mice – Germ Free | Taconic | SW GF |
| Swiss Webster Mice – Restricted Flora | Taconic | SW RF |
| Software and Algorithms | ||
| QIIME v.1.8 | (Caporaso et al., 2010) | N/A |
| BacSpace | (Earle et al., 2015) | N/A |
| FastQC v. 0.11.4 | FastQC | N/A |
| R v. 3.2.1 | (Ihaka and Gentleman, 1996) | N/A |
| MATLAB 2017a | Mathworks | N/A |
| bowtie2 v. 2.3.09 | (Langmead and Salzberg, 2012) | N/A |
| dbCAN2 meta server | (Zhang et al., 2018) | N/A |
| ResFinder | (Zankari et al., 2012) | N/A |
| Diamond v. 0.8.18 | (Buchfink et al., 2015) | N/A |
| MCL | (van Dongen and Abreu-Goodger, 2012) | N/A |
| Trimmomatic 0.36 | (Bolger et al., 2014) | N/A |
| Anvi’o v. 3 | (Eren et al., 2015) | N/A |