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 · 8 claims · 4 setups
SRP reduces body weight gain and improves serum lipid levels (TG, TC, LDL-c, HDL-c) and liver enzyme function (ALT, AST) in HFD rats, especially at the high dose
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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 abundance of Lactobacillus (and Bifidobacterium) in gut microbiota correlates with absence of ACRIII in rectal cancer patients
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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 · 6 claims · 6 setups
Intrinsic microbiota (dominated by Burkholderia and Ralstonia) resides in the heart and liver of healthy SPF mice
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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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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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Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.
PMID 28789673 · PMC5549432 · BMC research notes · 2017 · 7 claims · 7 setups
Gene and transcript abundances of bacterial type III secretion system (T3SS) genes are positively correlated with methane yield in sheep
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Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.
PMID 41594088 · PMC12838372 · Antibiotics (Basel, Switzerland) · 2026 · 8 claims · 7 setups
Anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, increasing their potential as AMR reservoirs.
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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
Reclaimed effluents show lower AMR exposure (<0.5 ARGs/cell) than typically reported for secondary effluents
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Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.
PMID 41854267 · PMC13098197 · mSystems · 2026 · 8 claims · 6 setups
SPF scalably and robustly estimates the fraction of bacterial and archaeal reads in a metagenome using detection of prokaryotic single-copy marker genes, without requiring eukaryotic or viral reference genomes
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nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.
PMID 42057295 · PMC13141149 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups
nf-core/viralmetagenome is a Nextflow pipeline that automates untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation-capture data.
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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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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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2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.
PMID 41609375 · PMC12915991 · mSystems · 2026 · 8 claims · 1 setups
Pipeline selection for MAG reconstruction is a nontrivial decision that must align user needs with workflow factors such as sequencing data type, analytical functions, and computational environment.
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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 · 7 claims · 8 setups
Phylogenomic analysis of the MAG clarified the taxonomic position of D. lemmermannii within the genus Dolichospermum and the ADA (Anabaena/Dolichospermum/Aphanizomenon) group
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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.