Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

  PMID 20368178 · PMC2894525 · Science translational medicine · 2009 · 7 claims · 6 setups

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  Germ-free C57BL/6J mice can be stably and heritably colonized with a human fecal microbiota, reproducing much of the donor's bacterial diversity.

  fecal postnatal luminal pooled 16s shotgun body

• What the Phage: a scalable workflow for the identification and analysis of phage sequences.

  PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

  Has reproduction · 76

  WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

  assembled illumina phage-predicted predicted multitool metagenome gene

• Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility.

  PMID 41638211 · PMC13091097 · Cell systems · 2026 · 8 claims · 7 setups

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  A complex, intact gut microbiome is necessary for the steady-state transcriptional landscape of all major brain-resident cell types, with myelinating oligodendrocytes and immune cells showing the largest microbiome-dependent transcriptional response.

  hippocampus cd11b+ intestinal brain single-nucleus bulk multiplex

• Microbiota-derived IPA protects against colitis by regulating intestinal HMGCS2-mediated ketogenesis to facilitate mucosal healing.

  PMID 41651833 · PMC12988232 · Nature communications · 2026 · 8 claims · 8 setups

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  IPA is consistently depleted in IBD/colitis patients and in murine colitis models relative to healthy controls

  fecal c57bl germ-free mice quasi-targeted dss-induced tnbs-induced