{"id":32596240,"url":"https://github.com/schlosslab/schubert_abxd01_mbio_2015","last_synced_at":"2025-10-30T04:58:26.971Z","repository":{"id":15898630,"uuid":"18640063","full_name":"SchlossLab/Schubert_AbxD01_mBio_2015","owner":"SchlossLab","description":"Reproducible workflow for Schubert et al. 2015 mBio","archived":false,"fork":false,"pushed_at":"2015-06-11T21:08:28.000Z","size":62289,"stargazers_count":2,"open_issues_count":0,"forks_count":3,"subscribers_count":8,"default_branch":"master","last_synced_at":"2023-05-15T12:35:16.735Z","etag":null,"topics":["reproducible-paper"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/SchlossLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-04-10T14:46:39.000Z","updated_at":"2021-12-16T14:04:12.000Z","dependencies_parsed_at":"2022-09-09T16:51:56.426Z","dependency_job_id":null,"html_url":"https://github.com/SchlossLab/Schubert_AbxD01_mBio_2015","commit_stats":null,"previous_names":[],"tags_count":1,"template":null,"template_full_name":null,"purl":"pkg:github/SchlossLab/Schubert_AbxD01_mBio_2015","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SchlossLab%2FSchubert_AbxD01_mBio_2015","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SchlossLab%2FSchubert_AbxD01_mBio_2015/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SchlossLab%2FSchubert_AbxD01_mBio_2015/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SchlossLab%2FSchubert_AbxD01_mBio_2015/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SchlossLab","download_url":"https://codeload.github.com/SchlossLab/Schubert_AbxD01_mBio_2015/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SchlossLab%2FSchubert_AbxD01_mBio_2015/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281748722,"owners_count":26554822,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-30T02:00:06.501Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["reproducible-paper"],"created_at":"2025-10-30T04:58:10.941Z","updated_at":"2025-10-30T04:58:26.966Z","avatar_url":"https://github.com/SchlossLab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"README\n======\n\nPerturbations to the gut microbiota can result in a loss of colonization resistance against gastrointestinal pathogens such as *Clostridium difficile*. Although *C. difficile* infection is commonly associated with antibiotic use, the precise alterations to the microbiota associated with this loss in function are unknown. We used a variety of antibiotic perturbations to generate a diverse array of gut microbiota structures, which were then challenged with *C. difficile* spores. Across these treatments we observed that *C. difficile* resistance was never attributable to a single organism, but rather it was the result of multiple microbiota members interacting in a context-dependent manner. Using relative abundance data, we built a machine learning regression model to predict the levels of *C. difficile* that were found 24 hours after challenging the perturbed communities. This model was able to explain 77.2% of the variation in the observed number of *C. difficile* per gram of feces. This model revealed important bacterial populations within the microbiota, which correlation analysis alone did not detect. Specifically, we observed that populations associated with the *Porphyromonadaceae*, *Lachnospiraceae*, *Lactobacillus*, and *Alistipes* were protective and populations associated with *Escherichia* and *Streptococcus* were associated with high levels of colonization. In addition, a population affiliated with *Akkermansia* indicated a strong context dependency on other members of the microbiota. Together, these results indicate that individual bacterial populations do not drive colonization resistance to *C. difficile*. Rather, multiple diverse assemblages act in concert to mediate colonization resistance.\n\n\n\nOverview\n--------\n\n    project\n    |- README          # the top level description of content\n    |\n    |- doc/            # documentation for the study\n    |  |- notebook/    # preliminary analyses (dead branches of analysis)\n    |  +- paper/       # manuscript(s), whether generated or not\n    |\n    |- data            # raw and primary data, are not changed once created\n    |  |- references/  # reference files to be used in analysis\n    |  |- raw/         # raw data, will not be altered\n    |  +- process/     # cleaned data, will not be altered once created\n    |\n    |- code/           # any programmatic code\n    |- results         # all output from workflows and analyses\n    |  |- tables/      # text version of tables to be rendered with kable in R\n    |  |- figures/     # graphs, likely designated for manuscript figures\n    |  +- pictures/    # diagrams, images, and other non-graph graphics\n    |\n    |- scratch/        # temporary files that can be safely deleted or lost\n    |\n    |- study.Rmd       # executable Rmarkdown for this study, if applicable\n    |- study.md        # Markdown (GitHub) version of the *Rmd file\n    |- study.html      # HTML version of *.Rmd file\n    |\n    +- Makefile        # executable Makefile for this study, if applicable\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fschlosslab%2Fschubert_abxd01_mbio_2015","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fschlosslab%2Fschubert_abxd01_mbio_2015","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fschlosslab%2Fschubert_abxd01_mbio_2015/lists"}