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).

• Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.

  PMID 41784373 · PMC13055366 · Microbiology spectrum · 2026 · 8 claims · 6 setups

  Full-text index only

  Significant taxonomic and functional differences exist between the gut microbiota of wild and captive-bred European hares

  fecal gut mag mags shotgun alpha differential

• Gut microbiome signatures associated with depression and obesity.

  PMID 41615149 · PMC13011431 · mSystems · 2026 · 8 claims · 4 setups

  Full-text index only

  Taxonomic gut microbiome profiles classify depressed vs non-depressed subjects with a balanced accuracy of 0.90 using machine learning

  stool subjects shotgun alpha machine

• Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group.

  PMID 35883324 · PMC9312300 · Animals : an open access journal from MDPI · 2022 · 7 claims · 6 setups

  Has reproduction · 84

  Gut microbial diversity (alpha and beta) differs significantly among domestic males, domestic females, and wild male Datong yaks.

  fresh fecal 16s alpha-diversity beta-diversity

• Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.

  PMID 34287005 · PMC8386447 · mSphere · 2021 · 8 claims · 7 setups

  Has reproduction · 76

  Periodontitis significantly alters dental plaque microbial community diversity and structure compared to healthy and treated states

  dental metagenomic taxonomic arg

• Tracing the early bacterial settlers in preterm and very-low birth-weight infants: first report of microbiota dynamics in South American neonates.

  PMID 41563098 · PMC12890024 · Infection and immunity · 2026 · 7 claims · 7 setups

  Full-text index only

  Klebsiella pneumoniae species complex and Escherichia coli dominate the gut microbial composition of VLBW infants

  stool 16s fecal full-length taxonomic alpha

• Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.

  PMID 41594088 · PMC12838372 · Antibiotics (Basel, Switzerland) · 2026 · 8 claims · 7 setups

  Full-text index only

  Anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, increasing their potential as AMR reservoirs.

  bat mag-derived shotgun metagenome arg

• Machine learning reveals microbial interactions driving plastic degradation across plastisphere environments.

  PMID 41657981 · PMC12876002 · Frontiers in microbiology · 2025 · 8 claims · 7 setups

  Has reproduction · 87

  Wastewater plastispheres harbor the most diverse and compositionally even microbial communities among the three habitats studied

  plastisphere otu 16s alpha beta

• geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

  PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 6 setups

  Has reproduction · 75

  geneshot identifies microbial genomic islands consistently associated with ICI response across independent cohorts

  stool deduplicated cag reference gene-level novo co-abundance

• Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.

  PMID 35978648 · PMC9377885 · BioMed research international · 2022 · 7 claims · 5 setups

  Has reproduction · 75

  The composition and relative abundance of intestinal microbiota in three-breed hybrid pigs differ significantly across growth stages (60, 120, 180 days)

  fecal same 16s otu alpha

• Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake.

  PMID 35902092 · PMC9334028 · GigaScience · 2022 · 8 claims · 1 setups

  Has reproduction · 61

  Tourmaline is a Python-based workflow that implements QIIME 2 using the Snakemake workflow management system to automate amplicon sequence analysis.

  bacterial 16s

• Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.

  PMID 35862823 · PMC9426513 · mSystems · 2022 · 8 claims · 5 setups

  Has reproduction · 56

  The vast majority of recovered gene cluster families (GCFs) in sponge microbiomes show no similarity to any characterized BGC, revealing extreme biosynthetic novelty

  microbiomes sponge shotgun nonpareil 16s

• Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.

  PMID 37085932 · PMC10120106 · Environmental microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes

  root musa assembled prokka-annotated shotgun culture-free metagenome

• metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.

  PMID 41530917 · PMC12818822 · Gut microbes · 2026 · 8 claims · 8 setups

  Full-text index only

  metaFun is an open-source, end-to-end Nextflow/Apptainer pipeline integrating quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomics, network analysis, and strain-level microdiversity analysis into a unified framework

  simulated selected gut mags novo binning pangenome-based

• Correlations between gut microbiota and serum metabolomics in patients with neurogenic rosacea.

  PMID 40676500 · PMC12272963 · BMC microbiology · 2025 · 6 claims · 3 setups

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  Patients with neurogenic rosacea exhibit significant gut microbiota dysbiosis compared to healthy controls

  serum fecal paired lc-ms 16s spearman