A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.
The main results reproduced, with only marginal, non-material deviations.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Any deviation was negligible
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
PARTIAL (in progress). Described well enough to reproduce: YES — the authors ship a complete anvi'o workflow (gitlab.ifremer.fr/rimicaris/..., not the figtree pointer in the registry, which is only the Fig.3 tree viewer) plus an OPEN companion deposit (Ifremer dataref REX_Velo) containing the raw reads, the 6 Megahit assemblies, and the 21 MAGs. Two headline claims already reproduced from metadata/deposit listings WITHOUT compute: C1 (677,134,974 reads ~ reported 677M / 113M avg, exact) and C2 (21 MAGs deposited == reported 21, exact). Remaining claims (C3 dRep->20, C4 GTDB-Tk taxonomy, C5/C6 per-class GC+genome-size, C7 contig counts) require «our HPC» compute on «infra»; scripts staged. BLOCKER: central «our HPC» VPN tunnel is currently down («host» ssh times out) so no «infra» download/compute has run yet; retrying periodically per HARD-RULE-1d (not touching the VPN). NOT attempted: wet-lab/microscopy (FISH/TEM, chromosome spacing) = out of scope. Grades provisional, human-checkable.
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Assessment versions
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v1 current initial assessment Score 64assessed: 2026-06-19 ⛓ 19676afb7d57
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Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-19
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-19no human curator yet
- Last updated
- 2026-07-31
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: opusWhat are the functional roles, genetic potential, and host-symbiont interactions of the bacterial symbionts residing in the foregut and midgut of the deep-sea hydrothermal vent shrimp Rimicaris exoculata, whose digestive symbionts had unknown roles?
- ★ Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut). finding
- ★ Hepatoplasmataceae symbionts have streamlined, reduced genomes capable of using mostly broken-down complex molecules. finding
- ★ Deferribacteres can degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. mechanism
- ★ Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. finding
- ★ Deferribacteres colonize the bacteria-free ectoperitrophic space in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery for division. finding
- ★ Digestive symbionts have key communication and defense roles contributing to overall fitness of the Rimicaris holobiont. mechanism
- A reproducible genome-resolved metagenomics workflow and a collection of MAGs/profiles for Rimicaris gut symbionts are provided as a resource. resource
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Shotgun genome-resolved metagenomics (assembly + binning into MAGs) | Rimicaris exoculata foregut and midgut, three Mid-Atlantic Ridge vent sites (Rainbow, TAG, Snake Pit) | none | Metagenome-assembled genomes, taxonomy, functional/metabolic gene content (COG/KEGG/CAZymes/CRISPR-Cas) | Illumina HiSeq3000, 2×150 bp, TruSeq Nano kit |
| Fluorescence in situ hybridization (FISH) | Rimicaris exoculata midgut and foregut tissue sections (ectoperitrophic space) | none | Localization/identification of Deferribacteres symbiotic lineage | Probe Def1229-Cy3; Zeiss Imager.Z2 microscope with ApoTome.2 and Colibri.7 |
| YOYO-1 DNA-specific fluorescence labeling / chromosome counting | Rimicaris exoculata midgut symbionts (sections) | none | Number of bacterial chromosomes per cell (cell division status) | Zeiss LSM 780 confocal microscope, photon counting |
| Small-subunit rRNA taxonomic profiling (phyloFlash) | Rimicaris exoculata foregut and midgut metagenomes | none | Taxonomic composition of samples / host DNA contamination | phyloFlash v3.4, SILVA 138.1 |
| Differential abundance analysis | Foregut vs midgut MAGs | none | Differentially abundant MAGs between organs | DESeq2; GeTMM normalization |
| Phylogenomic / ANI analysis | Deferribacteres and Hepatoplasmataceae MAGs and related taxa | none | Phylogenetic placement and genome similarity | GTDB-Tk v1.5.0, IQ-TREE v2.0.3, pyANI/dRep |
- – Reconstructed 21 MAGs (≥60% completion, ≤10% redundancy); dereplication to a final collection of 20 MAGs after removing one Hepatoplasmataceae MAG. 21 then 20 MAGs
- – Shotgun sequencing recovered 677 million reads total across six metagenomes. 677 million reads
- – Average reads per metagenome. 113 million reads/metagenome
- – Per-sample assembly yielded contigs longer than 1 kbp. 103K–147K contigs
- – High-quality reads recruited to assembled contigs. average 57.60%
- ▼ High-quality reads mapping to the final MAG collection were low, attributed to host DNA contamination. 1.75–2.61%
- – Deferribacteres symbionts elongate in the ectoperitrophic space but do not divide despite complete division machinery.
- – Hepatoplasmataceae abundant in foregut and Deferribacteres abundant in midgut, with little prior genetic differentiation between organs.
- count 677 million reads (total shotgun reads across six digestive-tract metagenomes)
- mean 113 million reads (average reads per metagenome)
- other 57.60% (average high-quality reads recruited to assembled contigs)
- other 1.75–2.61% (high-quality reads mapped to final MAG collection)
- count 103K to 147K contigs (contigs >1 kbp per sample assembly)
- other padj < 0.01; |log2FC| 1.5 (significance thresholds for differential MAG abundance (DESeq2))
- other ≥99% ANI, 50% coverage threshold (dRep dereplication criteria for MAGs)
- count 20 MAGs (final dereplicated MAG collection (from 21 reconstructed))
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
The study used a genome-resolved metagenomics workflow (anvi'o, Megahit assembly, CONCOCT binning) to reconstruct MAGs from pooled digestive-tract samples (foregut and midgut) collected at three hydrothermal vent sites, with nine to ten specimens' organs pooled per site per organ type due to small tissue size. Differences in MAG relative abundance between organs were assessed statistically using GeTMM-normalized counts analyzed with DESeq2, applying adjusted p-value and log2-fold-change thresholds to call significance. Most other results (genome statistics, phylogenomics, metabolic pathway completeness, CAZyme and CRISPR annotation) were reported descriptively rather than through inferential hypothesis testing.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| DESeq2 (Wald test with GeTMM-normalized counts) | differential abundance of MAGs between foregut and midgut samples | one pooled metagenomic sample per organ per site (3 sites), i.e., samples derived from pooling 9-10 specimens per site | not stated |
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Because of tissue scarcity, organs from 9-10 specimens were pooled into a single metagenomic sample per site per organ, yielding one composite sample per condition rather than multiple independent biological replicates.↳ Could also: A design with multiple independently sequenced (unpooled) biological replicates per site/organ, or explicit reporting of pooling as a limitation alongside site-level replication — Independent biological replicates would allow variance between individuals to be estimated directly, which can strengthen confidence in differential abundance calls beyond what pooled composite samples permit.
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MAG differential abundance between organs was assessed with DESeq2 on GeTMM-normalized counts, using combined padj and log2FC thresholds as the significance criterion.↳ Could also: Alternative differential-abundance frameworks for compositional metagenomic/microbiome count data, such as ALDEx2, ANCOM-BC, or edgeR — These methods use different normalization and compositional-data assumptions and can be used as complementary approaches to cross-check the robustness of differential abundance calls in metagenomic count data.
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Significance for MAG abundance differences is summarized via adjusted p-value and fold-change cutoffs, without reporting exact p-values, confidence intervals, or a dispersion/variance measure for the estimates.↳ Could also: Reporting exact adjusted p-values alongside effect size estimates with confidence intervals (e.g., DESeq2's log2FC standard errors or shrinkage estimates) — Providing effect size with an interval estimate conveys the precision of the fold-change estimate in addition to whether a fixed threshold was crossed.
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Only three sites (Rainbow, TAG, Snake Pit) were sampled, each contributing one pooled sample per organ, and the paper notes that site-level differences could not be statistically investigated due to limited organ samples per site.↳ Could also: A mixed-effects or hierarchical model treating site as a random effect, applied if additional per-site or per-individual samples were available — Such models can partition variance attributable to site versus organ when sufficient replication exists, which the current pooled single-sample-per-site design does not support.
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Taxonomic composition per sample was profiled descriptively with phyloFlash/SILVA rather than through a formal statistical comparison across organs or sites.↳ Could also: A community-level statistical comparison such as PERMANOVA on beta-diversity distances (e.g., Bray-Curtis) across organ/site groups — This would allow a formal test of whether community composition differs significantly between foregut and midgut or between sites, complementing the descriptive taxonomic summaries presented.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
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Reproduction footprint
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