Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.
Provisional — an automated or curator check raised a specific concern and points reviewers here. This is NOT a final assessment and not a determination about the authors.
Part of the results reproduced; minor but material deviations remained.
- Nothing in this column.
- 🔴Could not use the authors’ exact input data
- 🔴Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🔴A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
This paper has a computational component, but its primary data is legally or ethically access-restricted — identifiable patient cohorts, rare-disease genomes, or controlled-access biobanks that cannot be openly shared. The reproduction therefore could not be attempted. That is a neutral verdict: it does not mean the result is wrong or that the authors fell short — only that, for legitimate privacy reasons, it cannot be independently checked from public data. We deliberately do NOT assign a 0–100 score here, because a low number would wrongly read as a failed reproduction.
▸Reproduction agent’s raw note
DROP (data_unavailable) for the paper's central, code-derived contribution. The TSS atlas requires the Alteromonas macleodii Te101 dRNA-seq reads run through GRPutils (segemehl mapping -> replicate-assisted background subtraction -> classify). The paper cites BioProject PRJNA237745 for these 'primary transcriptomic reads', but PRJNA237745 holds ONLY 5 RNA-Seq runs, all Trichodesmium erythraeum IMS101 (the partner organism), not Alteromonas dRNA-seq. The genome BioProject PRJNA355640 links to exactly 1 SRA run (PacBio genome SRR5067210); the Te101 taxid (529120) has only 30 unrelated paired-end runs from 2019/2024 projects; no single-end HiSeq-2000 dRNA/minus/Mischung Alteromonas libraries (~18-40M reads) are findable in SRA/ENA. So the reads underpinning every transcriptome result (2,280 TSS and category counts, 5'-UTR stats, 138 sRNAs, DE genes) are effectively unavailable and were NOT attempted. Secondary code gap: GRPutils' tss_analysis_pipline.sh is a fully-commented demo that hard-codes the author's local paths and a 'Mischung' reference grp, and its classify step needs ../genomes/TE101.gff & pTE101a.gff annotations not shipped in the repo (docs_insufficient). PARTIAL POSITIVE: the deposited genome assembly GCA_002849875.1 is public, so the Table 1 genome-statistics rows were reproduced 1:1 on «our HPC» («job»): chromosome 4,630,082 bp / GC 44.68% and plasmid pTE101a 237,311 bp / GC 41.66% -- both exact vs the paper (44.7% / 41.7% within rounding). No fabrication indicators in the genome stats; the TSS values cannot be assessed for fabrication because their source reads are not locatable. Not attempted: full TSS pipeline, sRNA detection, promoter motifs, differential expression -- all blocked by the missing reads.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessmentassessed: 2026-06-16 ⛓ 2b601770ba88
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
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
- 2026-06-16
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-16no human curator yet
- Last updated
- 2026-08-05
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: opusHow does the copiotrophic heterotroph Alteromonas macleodii respond transcriptomically to the rapid, transient nutrient changes that occur when its associated cyanobacterium Trichodesmium declines and crashes in co-culture?
- ★ Increasing salinity to >=43 ppt inhibits Trichodesmium growth/increases mortality while stimulating growth of associated Alteromonas, shifting community dominance to the heterotroph finding
- ★ A consistent set of genes (fliA, rpoS, flagellar assembly, growth-related and biosynthetic genes) is activated in Alteromonas when Trichodesmium growth declines, indicating increased motility, growth, and biosynthesis finding
- ★ A CsrA-CsrB/C-like regulatory mechanism (three small RNAs Aln1a-c analogous to CsrB-C/RsmX-Z plus the CsrA homolog Te101_05290) is at the heart of the Alteromonas response to Trichodesmium decay mechanism
- ★ The genome of Alteromonas Te101 comprises a 4.63 Mb chromosome and a single 237 kb plasmid (pTE101), with conserved synteny and 14 chromosomal flexible genomic islands resource
- ★ dRNA-Seq mapped 2280 active transcription start sites at single-nucleotide resolution, defining the primary transcriptome architecture of Alteromonas Te101 method
- The primary transcriptome architecture of Alteromonas Te101 differs from other bacteria, with an unusually high share of gene-TSSs (~57.7%) and low share of antisense-TSSs (~6%) finding
- Alteromonas Te101 shares >95% ANI (98.1% with strain 'English Channel 673') with other A. macleodii strains and clusters phylogenomically with them finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| differential RNA-seq (dRNA-Seq, TEX-treated, single-nucleotide TSS mapping) | Alteromonas macleodii str. Te101 in non-axenic co-culture with Trichodesmium erythraeum IMS101 | increased salinity (37 ppt vs 43 ppt by adding NaCl to 736 mM) | transcription start sites and differential gene expression | Illumina HiSeq 2000, 100 nt single-end |
| bulk RNA-seq / metatranscriptome (TEX omitted, pooled) | co-culture of Alteromonas Te101 and Trichodesmium IMS101 | salinity 37 vs 43 ppt | full-length transcript coverage and hierarchical taxonomic read assignment (community composition) | Illumina HiSeq 2000 |
| whole-genome sequencing (SMRT/PacBio, HGAP assembly, PGAAP annotation) | Alteromonas macleodii str. Te101 (axenic isolate) | none | complete chromosome and plasmid sequence and annotation | PacBio RS II, large SMRTbell 10-kb insert |
| chlorophyll a extraction and spectrophotometry / spectral pigment scan | Trichodesmium IMS101 cultures | salinity gradient (30, 37, 43, 48 ppt) | chlorophyll a concentration and cell growth rate | Cary 300 (Agilent) spectrophotometer |
| 16S rRNA gene sequencing | Alteromonas Te101 isolate from Trichodesmium IMS101 culture | none | species identification | — |
| comparative genomics (reciprocal BLASTN/TBLASTX, ANI, COG, phylogenomics) | Alteromonas Te101 genome vs other Alteromonas genomes | none | flexible genomic islands, synteny, ANI, core-proteome phylogeny | JSpecies v1.2.1, FastTree, Kalign |
- – At 37 ppt ~90% of assignable reads were Trichodesmium with 4.6% and 8.4% Alteromonas; at 43 ppt Trichodesmium share dropped (14.1% rep1, 65.4% rep2) and Alteromonas rose to 70.6% (rep1) and 19.5% (rep2) Alteromonas up to 70.6%
- ▼ Trichodesmium grew exponentially at 30/37 ppt, declined in growth rate (biomass still increasing) at 43 ppt, and was severely growth-inhibited at 48 ppt
- ▲ Parallel activation of fliA, rpoS, flagellar assembly, and growth/biosynthesis genes in Alteromonas as Trichodesmium declined
- ▲ Three small RNAs Aln1a-c had the highest expression in the dataset, identified as CsrB-C/RsmX-Z analogs controlling expression via the CsrA homolog Te101_05290
- – 2280 TSSs identified (57.7% gTSS, 27.6% iTSS, 8.3% nTSS, 6.4% aTSS); 2008 active at 43 ppt and 1431 at 37 ppt
- – 14 flexible genomic islands detected in the chromosome harboring ~8% (298/3920) of all genes 298/3920 genes
- – Phylogenomic tree from 1015 concatenated core proteins confirms clustering with A. macleodii strains (ANI >95%) ANI 98.1% to strain 673
- count 4,630,082 bp chromosome; 237,311 bp plasmid (genome size of Alteromonas Te101)
- count 2280 total TSSs (active TSSs on chromosome plus plasmid in at least one condition)
- other 57.7% gTSS, 27.6% iTSS, 8.3% nTSS, 6.4% aTSS (distribution of TSS types)
- other 70.6% (rep1) and 19.5% (rep2) Alteromonas reads at 43 ppt vs 4.6%/8.4% at 37 ppt (relative metatranscriptome read share by salinity)
- other ANI 98.1% (Te101 vs A. macleodii 'English Channel 673')
- count 298/3920 genes in 14 fGIs (~8%) (flexible genomic island gene content)
- other median 5'-UTR 63 nt; 10 leaderless transcripts; 34 long 5'-UTRs >200 nt (transcript architecture)
- count >40 million and 18 million reads (reads per dRNA-Seq and minus library respectively)
Statistical methods review
Model: opusA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This is primarily a descriptive genomics/transcriptomics study combining PacBio genome assembly, comparative genomics, and differential RNA sequencing (dRNA-Seq) of Alteromonas Te101 under two salinity conditions (37 vs 43 ppt). The main inferential statistic was differential expression of transcription start site (TSS) counts, computed in edgeR using TMM normalization, qCML dispersion estimation, and the exactTest, with an adjusted p-value cutoff of 0.05. Growth data were summarized with error bars (standard errors for chlorophyll a, standard deviations for growth rates), and most other analyses (genome features, phylogeny, TSS classification, motif/binding-site searches) were reported as counts, percentages, or bioinformatic thresholds rather than formal hypothesis tests.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| edgeR exactTest (negative-binomial, qCML dispersion) on TSS counts | differential expression of TSSs between 43 ppt and 37 ppt conditions (Fig. 2b) | two replicate libraries per condition (37 and 43 ppt treated as replicates for dispersion) | not stated |
| FastTree maximum likelihood (JTT+CAT model, gamma) with bootstrap values | phylogenomic tree of 1015 concatenated core proteins (Fig. 2a) | 1015 concatenated core proteins | na |
| Average Nucleotide Identity (ANI) calculation (JSpecies) | pairwise genome similarity between Alteromonas strains | — | na |
| BLASTN/TBLASTX and COG homology searches with e-value/coverage/identity thresholds | fGI detection, conserved protein/synteny identification | — | na |
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Differential expression was assessed with the edgeR exactTest using two replicate libraries per condition.↳ Could also: A generalized linear model framework (edgeR glmQLFTest) or DESeq2 with shrinkage estimators, and/or limma-voom, could also be applied. — GLM/quasi-likelihood and empirical-Bayes shrinkage approaches share information across features, which can stabilize dispersion and effect-size estimates when the number of replicates is small.
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Two biological replicates per salinity condition were used for the transcriptomic comparison.↳ Could also: Additional biological replicates, or an explicit a priori description of the detectable effect size, could also accompany the design. — More replicates increase statistical power and the precision of dispersion estimates in count-based RNA-Seq, and stating the targeted effect size helps readers interpret sensitivity.
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The adjusted p-value cutoff of 0.05 was the reported criterion for calling differentially expressed TSSs.↳ Could also: Reporting exact adjusted p-values alongside log2 fold-change thresholds (or an effect-size filter such as treatCSAT) could also be presented. — Showing the continuous adjusted p-values and combining significance with a fold-change threshold conveys both statistical and biological relevance of each feature.
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Growth measurements were summarized using standard errors (chlorophyll a) and standard deviations (growth rates).↳ Could also: Reporting 95% confidence intervals, or consistently using SD with the n displayed, could also convey spread. — Confidence intervals or a single consistent dispersion measure with explicit n make the precision and variability of small-sample estimates directly comparable across panels.
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Salinity effects on growth were described primarily descriptively with error bars across treatments.↳ Could also: A model such as ANOVA or a mixed-effects model on growth rate by salinity (with post-hoc comparisons) could also be fit. — A formal model would provide a single family-wise-controlled test of the salinity effect and quantify the magnitude and uncertainty of differences among treatment levels.
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The phylogenomic tree reported bootstrap support values from a maximum-likelihood reconstruction.↳ Could also: Complementary support metrics such as approximate likelihood-ratio test (aLRT/SH-aLRT) values or Bayesian posterior probabilities could also be reported. — Multiple independent support measures give a fuller picture of node reliability in the inferred relationships.
Result convergence & founder nodes
Findings this paper shares with others that ran a comparable experiment. A node’s strength is how many independent papers report it (replication breadth) — not how often it is cited, so a heavily-replicated but under-cited founder still stands out.
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14 flexible genomic islands identified in Alteromonas Te101 chromosome, encoding approximately 8% (298/3920) of all protein-coding geneslong-read-DNA alteromonas macleodii te101 2018×1papers★ This paper is the founder (earliest)
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Trichodesmium erythraeum growth rate declined at 43 ppt NaCl and was severely inhibited at 48 ppt, validating the salinity-stress demise perturbation used in co-culture experimentsother trichodesmium erythraeum ims101 culture down 2018×1papers★ This paper is the founder (earliest)
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Small RNAs Aln1a-c were the highest-expressed transcripts in Alteromonas Te101 and function as CsrB/RsmZ analogs regulating the CsrA homolog Te101_05290RNA-seq alteromonas macleodii te101 trichodesmium co-culture up 2018×1papers★ This paper is the founder (earliest)
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Alteromonas Te101 relative transcript fraction rose to up to 70.6% in metatranscriptome at 43 ppt while Trichodesmium share collapsed, reflecting bloom opportunism during host demiseRNA-seq alteromonas macleodii te101 trichodesmium co-culture up 2018×1papers★ This paper is the founder (earliest)
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fliA, rpoS, flagellar assembly genes, and growth/biosynthesis genes were co-upregulated in Alteromonas Te101 as Trichodesmium declined at 43 ppt salinityRNA-seq alteromonas macleodii te101 trichodesmium co-culture up 2018×1papers★ This paper is the founder (earliest)
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2280 transcription start sites mapped genome-wide in Alteromonas Te101; more TSSs active at 43 ppt (2008) than 37 ppt (1431), with gTSS the dominant class (57.7%)RNA-seq alteromonas macleodii te101 trichodesmium co-culture 2018×1papers★ This paper is the founder (earliest)
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Phylogenomic analysis of 1015 concatenated core proteins confirms Alteromonas Te101 clusters within A. macleodii (ANI 98.1% to strain 673, >95% to all A. macleodii strains)WGS alteromonas macleodii te101 2018×1papers★ This paper is the founder (earliest)
Citation network
Where this publication sits in the reproducibility-weighted citation graph — what it is built on, and what is built on it. Citation data from OpenAlex.
No assessed neighbours yet — the network grows as more papers are assessed.
Data lineage
The datasets this paper uses (text-mined from the full text via Europe PMC), and which other assessed papers stand on the same data. A shared dataset is a factual link — not a judgement.
Downstream reach in the literature
1 downstream papers · 2 datasetsHow widely the datasets deposited by this paper are reused across the whole literature (Europe PMC), beyond our assessed set. This is a factual dependency map — reusing a public dataset is normal, good science. It is not a judgement on the downstream papers; the only verdict here is this paper's own, with its cited rationale.
- The primary transcriptome of the marine diazotroph T... 2014 · 41 cites
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-29335641
Paper: Hou et al. 2018, ISME J — "Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise." DOI 10.1038/s41396-017-0034-4 · PMCID PMC5864184.
Code: https://github.com/housw/GRPutils (GRPutils — dRNA-seq → TSS prediction
toolkit; grptools/tptools + tss_analysis_pipline.sh).
Data (as cited by paper): genome PRJNA355640; "primary transcriptomic reads"
PRJNA237745.
Pipeline-derived results in the paper
| Result | Pipeline | In scope? |
|---|---|---|
| Genome size: chromosome 4,630,082 bp; plasmid pTE101 237,311 bp (Table 1) | PacBio HGAP assembly → deposited GCA_002849875.1 | YES (assembly is public) |
| GC%: 44.7% chrom / 41.7% plasmid (Table 1) | same | YES |
| CDS counts: 3,920 chrom / 239 plasmid; 72 tRNA, 16 rRNA (Table 1) | genome annotation | partial (annotation differs by tool; see note) |
| Total 2,280 TSS (chrom 2,181 + plasmid 99); gTSS 1,282 / iTSS 595 / nTSS 174 / aTSS 130 (Table 1) | segemehl mapping of dRNA-seq → GRPutils replicate-assisted background subtraction → classify | NO — data unavailable |
| Condition-specific TSS (37 vs 43 ppt), 5′-UTR median 63 nt, leaderless/long-UTR counts | same dRNA-seq → GRPutils | NO — data unavailable |
| 138 sRNAs (127+11); promoter -10/-35 motifs | dRNA-seq → GRPutils + motif analysis | NO — data unavailable |
| 504 up / 56 down DE genes (43 vs 37 ppt) | classical RNA-seq counts → DE | NO — data unavailable |
| 126/161 CsrA targets; 154 peptidases; 14 fGIs | sequence/annotation analyses | out of scope (annotation/manual) |
Decisive blocker — dRNA-seq raw reads are not retrievable
The paper's central, code-derived contribution is the TSS atlas (GRPutils on the Te101 dRNA-seq libraries). Reproducing it requires the 4 dRNA-Seq + 4 minus + 1 pooled classical ("Mischung") single-end HiSeq-2000 libraries (~18–40 M reads each, 37 ppt & 43 ppt, labelled S3/S4/S5/S6). These were searched for exhaustively:
- PRJNA237745 (the accession the paper gives for "primary transcriptomic reads") contains only 5 RNA-Seq runs, all Trichodesmium erythraeum IMS101 (SRR1178963–66, SRR1181644) — the partner organism's transcriptome, not Alteromonas dRNA-seq. (NCBI eLink bioproject 237745 → 5 SRA ids; ENA filereport → 5 rows, all Trichodesmium.) Wrong project cited.
- PRJNA355640 (genome) links to exactly 1 SRA run — the PacBio genome run SRR5067210 (WGS, 163,482 subreads). No transcriptome.
- Te101 taxid 529120 in SRA = 30 runs, all paired-end RNA-seq from unrelated later projects (PRJNA591216, 2019; PRJNA1184977, 2024). None is the 2018 single-end dRNA-seq.
- Alteromonas species taxid 28108, HiSeq-2000: no single-end RNA-seq library named dRNA/minus/Mischung/37ppt/43ppt with ~18–40 M reads.
- Free-text "Te101" across ENA read_run: only unrelated hits.
→ The dRNA-seq reads underpinning every transcriptome result are effectively
data_unavailable (accession resolves to the wrong organism; the actual data
cannot be located in any public archive). Per BRIEF rule 6 this is a valid drop;
no compute is spent chasing it and no value is fabricated.
Code caveats (secondary)
Even with reads, full reproduction would be hard: tss_analysis_pipline.sh is an
example with every stage commented out, hard-codes the author's local paths
(«path», the Mischung reference grp), and the classify
step needs ../genomes/TE101.gff / pTE101a.gff annotations that are not
shipped in the repo. (docs_insufficient would also apply — recorded as a
secondary note; the primary, decisive drop_reason is data_unavailable.)
What we DID reproduce (salvageable, public)
The deposited genome assembly GCA_002849875.1 (ASM284987v1) is public, so the genome-statistics rows of Table 1 are verifiable 1:1. One small «our HPC» job (seqkit on the deposited FASTA) checks per-replicon length + GC. This is a genome-ass
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.