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).

• Metabolic features that select for Bathyarchaeia in modern ferruginous lacustrine subsurface sediments.

  PMID 39660009 · PMC11631310 · ISME communications · 2024 · 8 claims · 8 setups

  Has reproduction · 50

  Microbial assemblages shift with depth from iron- and sulfate-reducing bacteria to fermentative anaerobes and methanogens, with Bathyarchaeia selected below the sulfate reduction zone as cell densities exponentially decrease

  sediment freeze-dried pore fixed 16s shotgun bulk

• 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

• 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

• Diverse Cyanopeptides follow distinct temporal succession patterns in freshwater harmful algal blooms.

  PMID 41711085 · PMC13196583 · The ISME journal · 2026 · 8 claims · 7 setups

  Full-text index only

  Shifts from Microcystis to Dolichospermum dominance occur later in the bloom season, coinciding with lower temperatures

  natural lake microcystis western shotgun hrms metagenomic

• 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

  Has reproduction · 59

  Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes

  root musa assembled prokka-annotated shotgun culture-free metagenome

• Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

  PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups

  Full-text index only

  The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.

  rumen blood beef metagenome snp longitudinal

• 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

• Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.

  PMID 42007585 · PMC13245728 · The ISME journal · 2026 · 8 claims · 8 setups

  Full-text index only

  Pseudoalteromonas is a symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (Nematoda, Mollusca, and Cnidaria)

  pseudoalteromonas mollusca individual live pangenomic core-genome average

• Transposable elements are driving rapid adaptation of Enterococcus faecium.

  PMID 42020750 · PMC13216065 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  E. faecium has the highest IS density among ESKAPEE pathogens, dominated by replicative ISL3 family elements

  eskapee faecium ncbi single-hospital large-scale chromosome core