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 · 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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Full-text index only
Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.
PMID 16091627 · PMC1184225 · Nucleic acids research · 2005 · 8 claims · 5 setups
Headloop PCR: a 5' primer extension homologous to internal amplicon sequence causes hairpin formation after incorporation, suppressing further amplification of the matching sequence while unaffected sequences amplify normally
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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 · 69
High-resolution metagenomic reconstruction of the freshwater spring bloom.
PMID 36698172 · PMC9878933 · Microbiome · 2023 · 8 claims · 8 setups
High-frequency metagenomic sampling (57 samples, 3 filter sizes, 2 depths, 37 days) recovers thousands of prokaryotic, eukaryotic, and viral genomes tracking spring bloom succession in fine detail
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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 · 59
The effect of 16S rRNA region choice on bacterial community metabarcoding results.
PMID 30720800 · PMC6362892 · Scientific data · 2019 · 8 claims · 6 setups
The V2-V3 16S rRNA fragment has higher resolution for lower-rank taxa (genera and species) than V3-V4, allowing more precise distance-based clustering of reads into species-level OTUs.
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Has reproduction · 61
Unraveling the role of bacteria with heritable versus non-heritable relative abundance in the gut on boar semen quality.
PMID 41199168 · PMC12590650 · Genetics, selection, evolution : GSE · 2025 · 6 claims · 7 setups
39 heritable and 91 non-heritable bacterial genera were identified in the boar gut based on heritability of relative abundance
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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
Unlocking the microbial studies through computational approaches: how far have we reached?
PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups
Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.
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Has reproduction · 99
Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.
PMID 29590198 · PMC5874073 · PloS one · 2018 · 8 claims · 8 setups
Verrucomicrobia is highly prevalent in north-temperate freshwater lakes, on average the 4th most abundant phylum (range 1.7–41.7%).
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Has reproduction · 78
Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.
PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 7 setups
INVADE-seq simultaneously captures host and bacterial transcripts to map bacteria-host interactions across diverse testicular cell types at single-cell resolution
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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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The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.
PMID 19912342 · PMC2868947 · FEMS immunology and medical microbiology · 2010 · 7 claims · 5 setups
The types of vaginal bacterial communities found in Japanese women closely resemble those previously found in White and Black North American women.
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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 soil microbiome reduces Striga attachment to sorghum roots at the post-germination stage by interfering with haustorium initiation rather than seed germination
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Has reproduction · 77
Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.
PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 6 claims · 7 setups
Electroacupuncture reshapes microbial co-occurrence network topology and drives keystone species in AD-related BPSD, with R. gnavus emerging as a likely keystone species post-intervention.
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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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Has reproduction · 100
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.
PMID 35910650 · PMC9326479 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis.
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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.
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Has reproduction · 36
A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.
PMID 35019679 · PMC8754136 · Microbiology spectrum · 2022 · 8 claims · 9 setups
Microbulbifer sp. YX04 shows high algicidal activity against P. globosa, peaking at 93.2% in the declining growth phase
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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)