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).

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 8 setups

  Has reproduction · 78

  INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types

  testis young testicular invade-seq histology sperm

• A qualitative assessment of direct-labeled cDNA products prior to microarray analysis.

  PMID 15762992 · PMC1079821 · BMC genomics · 2005 · 5 claims · 5 setups

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  The Agilent 2100 Bioanalyzer can be used in a novel assay to assess the quality/quantity of direct-labeled Cy-dye cDNA prior to microarray hybridization

  mcf-7 same 16lu bioanalyzer agarose cdna

• 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

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  The types of vaginal bacterial communities found in Japanese women closely resemble those previously found in White and Black North American women.

  vaginal japanese t-rflp clone cluster

• Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

  PMID 19853919 · PMC2787966 · Molecular immunology · 2009 · 7 claims · 6 setups

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  OAS2 is identified as a novel NOD2-binding partner in THP-1 cells by tandem affinity purification and mass spectrometry

  thp-1 hek293 tandem co-immunoprecipitation oas2

• Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

  PMID 42098796 · PMC13154700 · Microbiome · 2026 · 8 claims · 5 setups

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  Poly(A)-enriched mRNA-seq can reliably reconstruct microbiome composition, validated against a quantitative mock community standard and metagenomic analysis

  zymobiomics vls-vscc vulvar subset mrna-seq rna-seq poly

• Colorectal microenvironment determines the prognosis of colorectal cancer.

  PMID 41495419 · PMC12868731 · Experimental & molecular medicine · 2026 · 8 claims · 7 setups

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  The colorectal microenvironment (classified via NBT gene expression as tumor-supportive vs healthy) can serve as a prognostic biomarker predicting cancer invasiveness and recurrence

  paired nbt slide bulk bulk 16s single-cell

• Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

  PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups

  Has reproduction · 69

  Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis

  colon gut single-cell 16s western

• Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models.

  PMID 36536288 · PMC9762025 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 4 setups

  Has reproduction · 93

  Structural equation models can decompose the total genetic effect on a production trait into a direct host genetic effect and an indirect effect exerted through the microbiota.

  rabbits cecal host bayesian 16s snp

• On the holobiont 'predictome' of immunocompetence in pigs.

  PMID 37127575 · PMC10150480 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 8 setups

  Has reproduction · 40

  Holobiont (combined genotype + microbiome) models performed better than partial models (genotype-only or microbiome-only) overall

  duroc fecal plasma serum snp 16s immunoglobulin

• Thermophilic and mesophilic sulfate reduction by rare biosphere bacteria in acidic metal-bearing mine wastes from the temperate climate zone.

  PMID 41345487 · PMC12739157 · Scientific reports · 2025 · 7 claims · 8 setups

  Has reproduction · 52

  Sulfate reduction rates (SRR) at in-situ ambient temperature in acidic Bom-Gorkhon tailings sediments are unexpectedly high, up to 9.86 µmol SO4 cm-3 day-1.

  acidic water bu28s pure radioactive 16s shotgun

• Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility.

  PMID 34021225 · PMC8140134 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 70

  Sulfate-reducing Desulfovibrio are the key players responsible for H2S production in swine manure slurry

  manure sediment desulfovibrio solid-liquid radioactive 16s shotgun

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• 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

• Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.

  PMID 36925474 · PMC10011098 · Frontiers in microbiology · 2023 · 8 claims · 8 setups

  Has reproduction · 74

  The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.

  cupriavidus stm taiwanensis genome 16s average

• Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

  PMID 18820594 · PMC2905378 · Pharmacogenetics and genomics · 2008 · 7 claims · 8 setups

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  The tRNA-Thr G15927A mutation has a potential modifier role that increases penetrance and expressivity of A1555G-associated deafness.

  blood genomic lymphoblastoid same pcr-rflp mitochondrial northern

• Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition.

  PMID 41634153 · PMC12929062 · Nature plants · 2026 · 8 claims · 8 setups

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  Multi-omics integration of root transcriptome, rhizosphere 16S microbiome and root/shoot ionome across 175 B. napus accessions at two field sites links host gene expression to microbiome assembly and nutrient traits

  lateral rhizosphere shoot napus sequencing 16s ionomic

• Correlations between gut microbiota and serum metabolomics in patients with neurogenic rosacea.

  PMID 40676500 · PMC12272963 · BMC microbiology · 2025 · 6 claims · 3 setups

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  Patients with neurogenic rosacea exhibit significant gut microbiota dysbiosis compared to healthy controls

  serum fecal paired lc-ms 16s spearman

• 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

  Has reproduction

  Intrinsic microbiota (dominated by Burkholderia and Ralstonia) resides in the heart and liver of healthy SPF mice

  heart ileum metagenomic culturomics 16s

• 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

• Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.

  PMID 15799778 · PMC1080126 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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  Dart shooting introduces an allohormone that inhibits digestion of donated sperm, increasing the amount reaching the spermathecae and fertilizing eggs, thereby manipulating the mating partner's sperm storage.

  dart-possessing same land cantareus 28s shimodaira-hasegawa principal