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).

• 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)

  rimicaris quality-filtered dereplicated deferribacteres shotgun ssu differential

• Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.

  PMID 41890980 · PMC13015239 · One health (Amsterdam, Netherlands) · 2026 · 8 claims · 7 setups

  Full-text index only

  Agricultural drainage ditches consistently harbor higher fecal-associated bacterial diversity than mixed-use or forested sites, with pronounced seasonal shifts (higher during spring/fall high-flow periods).

  surface shotgun trimmed co-assembled 16s shotgun short-read

• 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

  Has reproduction · 83

  Phylogenomic analysis of the MAG clarified the taxonomic position of D. lemmermannii within the genus Dolichospermum and the ADA (Anabaena/Dolichospermum/Aphanizomenon) group

  surface bloom environmental dolichospermum shotgun lc-ms metagenome

• metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.

  PMID 34614189 · PMC8643649 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 64

  metaGEM enables end-to-end reconstruction of FBA-ready GEMs directly from metagenomes without relying on reference genomes

  metagenomic prokaryotic reconstructed gut mag genome-scale gem

• metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.

  PMID 41530917 · PMC12818822 · Gut microbes · 2026 · 8 claims · 8 setups

  Full-text index only

  metaFun is an open-source, end-to-end Nextflow/Apptainer pipeline integrating quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomics, network analysis, and strain-level microdiversity analysis into a unified framework

  simulated selected gut mags novo binning pangenome-based

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

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

  Full-text index only

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

  oral saliva noma previously shotgun comparative metagenome

• StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

  PMID 42097292 · PMC13188985 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  StrainMake is a Snakemake-based, Conda-managed workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data.

  cami high-quality recovered gut metagenome metagenomic mag

• 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

  Full-text index only

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

  fecal gut mag mags shotgun alpha differential

• Genomic signatures of migratory preference and historical whaling in eastern South Pacific humpback whales.

  PMID 41986456 · PMC13161203 · Communications biology · 2026 · 7 claims · 8 setups

  Full-text index only

  Nuclear genomic data show no clear population structure among feeding grounds, indicating panmixia despite divergent migratory destinations

  megaptera same unrelated regional whole-genome relatedness population

• Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.

  PMID 41419779 · PMC12858935 · Scientific data · 2025 · 7 claims · 8 setups

  Has reproduction · 87

  A standardized assembly, binning, and dereplication pipeline was used to reconstruct 2,965 non-redundant MAGs from 38 mangrove sediment samples across six sites in Guangxi

  mangrove sediment quality-filtered bacterial whole-genome physicochemical laser

• Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.

  PMID 41594088 · PMC12838372 · Antibiotics (Basel, Switzerland) · 2026 · 8 claims · 7 setups

  Full-text index only

  Anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, increasing their potential as AMR reservoirs.

  bat mag-derived shotgun metagenome arg

• Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

  PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 16s

• Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

  PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient

  gill chemosynthetic host epsilon rna-seq-based metagenomic phylogenomic

• High-resolution metagenomic reconstruction of the freshwater spring bloom.

  PMID 36698172 · PMC9878933 · Microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 69

  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

  freshwater phytoplankton heterotrophic reservoir 16s 18s shotgun

• Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.

  PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  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.

  rhizosphere nematode wtex wolbachia metagenomic pcr comparative

• Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface.

  PMID 39384533 · PMC11650866 · FEMS microbiology ecology · 2024 · 8 claims · 8 setups

  Has reproduction · 85

  Chloroflexota populations are partitioned according to alternative electron acceptors (Anaerolineae) and electron donors (Dehalococcoidia) among respiratory and fermentative metabolites at and below the sediment-water interface

  lake undisturbed chloroflexota 16s shotgun pore

• 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

  fecal horse dominant plasma shotgun taxonomic functional

• The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.

  PMID 42116832 · PMC13157608 · Wellcome open research · 2026 · 7 claims · 8 setups

  Full-text index only

  Aurelia sp. 4 chromosomal genome assembly has a total length of 462.10 Mb with 99.99% of sequence scaffolded into 21 chromosomal pseudomolecules

  aurelia microbial pacbio hi-c rna-seq