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).

• Gut microbiome signatures associated with depression and obesity.

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

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

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• The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.

  PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups

  Has reproduction · 86

  Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.

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• RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

  PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.

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• Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.

  PMID 41636304 · PMC12918712 · Environmental science & technology · 2026 · 7 claims · 6 setups

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  Reclaimed effluents show lower AMR exposure (<0.5 ARGs/cell) than typically reported for secondary effluents

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• 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

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

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• What defines a photosynthetic microbial mat in western Antarctica?

  PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups

  Has reproduction · 85

  Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions

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• Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

  PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla

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• Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

  PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups

  Has reproduction · 88

  Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life

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• A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

  PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

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• 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

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• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 8 claims · 7 setups

  Has reproduction · 64

  Reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut-associated) and Deferribacteres (midgut-associated)

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• sedimix: a workflow for the analysis of hominin nuclear DNA sequences from sediments.

  PMID 41512286 · PMC12866666 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  sedimix is a snakemake workflow that processes raw sediment DNA sequencing reads (fastq) through filtering, taxonomic classification, mapping, and duplicate/quality filtering to output hominin-derived BAM files and summary statistics.

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• Diverse Cyanopeptides follow distinct temporal succession patterns in freshwater harmful algal blooms.

  PMID 41711085 · PMC13196583 · The ISME journal · 2026 · 8 claims · 7 setups

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  Shifts from Microcystis to Dolichospermum dominance occur later in the bloom season, coinciding with lower temperatures

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• 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

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• 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

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• Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

  PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups

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  Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.

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• Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota.

  PMID 41741451 · PMC13046836 · NPJ biofilms and microbiomes · 2026 · 6 claims · 6 setups

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  High inulin supplementation (4%) significantly altered caecal microbial composition and promoted broader microbial metabolic adaptations, indicating a strong fermentative response to soluble fibre

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• Water mass specific genes dominate the Southern Ocean microbiome.

  PMID 41803086 · PMC12972064 · Nature communications · 2026 · 8 claims · 8 setups

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  The Southern Ocean microbial gene catalog is highly original and largely distinct from existing marine gene catalogs

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• Shotgun metagenomic analysis of the oral microbiomes of children with noma.

  PMID 41860897 · PMC13029773 · PLoS neglected tropical diseases · 2026 · 8 claims · 6 setups

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  Noma oral microbiomes show marked dysbiosis with significant enrichment of Treponema, Porphyromonas, and Bacteroides, and depletion of Streptococcus and Rothia, compared to healthy controls

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• Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

  PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups

  Has reproduction · 65

  eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.

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