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).
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Has reproduction
Metagenomic and Untargeted Metabolomic Analysis of the Effect of Sporisorium reilianum Polysaccharide on Improving Obesity.
PMID 37107373 · PMC10137368 · Foods (Basel, Switzerland) · 2023 · 6 claims · 6 setups
SRP intervention reduces obesity, serum lipid levels, hepatic lipid accumulation, and adipocyte hypertrophy in high-fat-diet rats, especially at high dose.
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Has reproduction
Ligilactobacillus salivarius regulating translocation of core bacteria to enrich mouse intrinsic microbiota of heart and liver in defense of heat stress.
PMID 40276518 · PMC12018310 · Frontiers in immunology · 2025 · 7 claims · 6 setups
Intrinsic microbiota (chiefly genera Burkholderia and Ralstonia) reside in the heart and liver of SPF mice, with the heart having lower bacterial abundance than the liver
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Has reproduction · 24
MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.
PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups
MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics
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Has reproduction · 76
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
Periodontitis significantly alters dental plaque microbial community diversity and structure compared to healthy and treated states
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Has reproduction · 95
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.
PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups
Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns
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Has reproduction · 90
Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.
PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.
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Full-text index only
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.
PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups
CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling
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Has reproduction · 100
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.
PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups
nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.
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Has reproduction · 75
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.
PMID 38860884 · PMC11261899 · Microbial genomics · 2024 · 7 claims · 3 setups
PHA4GE developed a set of standardized contextual data tags (five fields plus controlled-vocabulary terms) for annotating pathogen sequence datasets with known quality issues.
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Full-text index only
Microbial metagenomics.
PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups
Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides
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Has reproduction · 83
Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.
PMID 39227168 · PMC11412076 · FEMS microbiology ecology · 2024 · 5 claims · 8 setups
A near-complete metagenome-assembled genome (MAG) of Dolichospermum lemmermannii (FEM_B0920) was recovered from a Lake Garda bloom and clarified the species' taxonomic position within the genus Dolichospermum and the ADA group.
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Has reproduction · 89
Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.
PMID 40469520 · PMC12130557 · iMeta · 2025 · 8 claims · 8 setups
High pretreatment gut abundance of Lactobacillus (and Bifidobacterium) is strongly associated with the absence of ACRIII in rectal cancer patients undergoing neoadjuvant chemoradiotherapy.
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Has reproduction · 79
Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.
PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups
Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses
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Has reproduction · 56
Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.
PMID 35862823 · PMC9426513 · mSystems · 2022 · 8 claims · 5 setups
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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Has reproduction · 66
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
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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Has reproduction · 68
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
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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Has reproduction · 88
Wochenende - modular and flexible alignment-based shotgun metagenome analysis.
PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups
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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Has reproduction · 76
What the Phage: a scalable workflow for the identification and analysis of phage sequences.
PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups
WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow
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Has reproduction · 59
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
Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes
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Has reproduction · 85
What defines a photosynthetic microbial mat in western Antarctica?
PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups
Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions