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 · 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 · 59
The effect of 16S rRNA region choice on bacterial community metabarcoding results.
PMID 30720800 · PMC6362892 · Scientific data · 2019 · 8 claims · 8 setups
The V2-V3 16S rRNA fragment has higher resolution for lower-rank taxa (genera and species) than V3-V4, enabling more precise distance-based OTU clustering.
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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
Germ-free C57BL/6J mice can be stably and heritably colonized with a human fecal microbiota, reproducing much of the donor's bacterial diversity.
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Has reproduction · 50
Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition.
PMID 34434657 · PMC8362670 · PeerJ · 2021 · 8 claims · 6 setups
Elevation and soil type influenced baseline soil biogeochemical indicators
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Has reproduction · 62
The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.
PMID 38537644 · PMC11063626 · Cell reports · 2024 · 8 claims · 8 setups
The natural (non-sterilized) Clue Field soil microbiome reduces Striga attachment to sorghum roots compared to gamma-sterilized soil
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Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture.
PMID 34248892 · PMC8264503 · Frontiers in microbiology · 2021 · 7 claims · 6 setups
Natural seasonality is the primary driver of aquatic bacterial community structure in the fishponds and reservoir
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Has reproduction · 84
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
Gut microbial diversity (alpha and beta) differs significantly among domestic males, domestic females, and wild male Datong yaks.
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Has reproduction · 55
Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).
PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups
The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation
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How bacterial communities expand functional repertoires.
PMID 17238278 · PMC1750926 · PLoS biology · 2006 · 8 claims · 7 setups
The human microbiome contains roughly 100 times as many genes as does the human genome
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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 · 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 · 95
Spatial patterns of benthic biofilm diversity among streams draining proglacial floodplains.
PMID 36003939 · PMC9393633 · Frontiers in microbiology · 2022 · 7 claims · 8 setups
Benthic biofilms in tributaries develop higher biomass than those in glacier-fed streams along the lateral chronosequence
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Has reproduction · 62
Metatranscriptomics of the human oral microbiome during health and disease.
PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups
Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.
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Has reproduction · 93
Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract.
PMID 31608047 · PMC6769089 · Frontiers in microbiology · 2019 · 7 claims · 5 setups
Five amplicon sequence variants (unclassified Flavobacteriales, Fusibacter, Planktotalea, Algicola, and Vibrio) were consistently enriched in disease lesions across three coral species (M. cavernosa, D. labyrinthiformis, D. stokesii)
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Has reproduction · 61
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
Tourmaline is a Python-based workflow that implements QIIME 2 using the Snakemake workflow management system to automate amplicon sequence analysis.
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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 · 75
Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.
PMID 35978648 · PMC9377885 · BioMed research international · 2022 · 7 claims · 5 setups
The composition and relative abundance of intestinal microbiota in three-breed hybrid pigs differ significantly across growth stages (60, 120, 180 days)
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Has reproduction · 100
Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments.
PMID 36988509 · PMC10128000 · mBio · 2023 · 7 claims · 7 setups
SRB modify niches (e.g., pH) to affect species coexistence during organic matter degradation
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Has reproduction · 87
Machine learning reveals microbial interactions driving plastic degradation across plastisphere environments.
PMID 41657981 · PMC12876002 · Frontiers in microbiology · 2025 · 6 claims · 7 setups
Wastewater plastispheres harbor the most diverse and compositionally even microbial communities among the three habitats.
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Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups
The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.