Geng Review Report: Soil sterilization accumulates higher content of antibacterial compound and recruits beneficial fungus for konjac soft rot disease management by multi-omics analyses (BMC Plant Biology, 2025)

Academic fraud report · Geng Detector

Summary

This report flags the paper (DOI: 10.1186/s12870-025-07985-7) as highly suspicious ('高度可疑'), based on methodological inconsistencies rather than evidence of outright data fabrication. The central issue is a contradictory amplicon-processing pipeline that merges FLASH and DADA2, which is logically incompatible within the Qiime2 framework. Secondary concerns include an in vitro antibacterial assay using a 48-hour OD600 readout far past the expected stationary phase of Pectobacterium carotovorum, and an asymmetric sample design where three diseased soils are kept as biological replicates but pooled into a single composite for the sterilized group, creating pseudoreplication. No image-manipulation or numerical-distribution analysis could be performed because raw figures and source data were not available. Findings require author verification and journal review; this report does not constitute a formal finding of misconduct.

Verdict

🟠 Highly suspicious. The methodological contradictions are serious and reproducible from the published text, but no image-based or statistical-distribution evidence of fraud could be obtained. Confirmation requires raw sequencing data, analysis code, and metabolomics peak tables from the authors.

Key findings

FLASH + DADA2 pipeline conflict: The Methods state that paired reads were merged with FLASH v1.2.11 and then denoised using the DADA2 plugin within Qiime2. DADA2 in Qiime2 already performs paired-end joining and denoising in a single integrated step; running FLASH upstream is redundant and technically incompatible with the recommended DADA2 workflow. This pattern strongly suggests copy-paste assembly of templates from different pipelines or service providers.
Implausible antibacterial assay endpoint: The in vitro inhibition assay inoculates *Pectobacterium carotovorum* (formerly *Erwinia carotovorum*) into LB broth at 28 °C / 180 rpm and measures OD600 after 2 days (48 h). In shaken LB at this temperature, this fast-growing pathogen typically reaches late stationary phase within ~16–24 h; by 48 h, nutrient depletion and metabolite accumulation mean OD600 reflects debris and dead cells rather than proliferation. The endpoint cannot meaningfully characterize growth inhibition.
Pseudoreplication in metabolomics design: Three diseased-soil samples (D1, D2, D3) are retained as independent biological replicates, but the sterilized soil (S) is produced by pooling all three field samples together before autoclaving at 121 °C for 20 min. Subsequent S replicate aliquots are therefore technical splits of a single composite, not biological replicates, violating the statistical assumption of independent replicates and inflating the risk of false-positive differences.
Source-data and figure limitations: The report could not assess Western blot/gel reuse, Photoshop splicing, or last-digit distributions because high-resolution images and raw numerical tables were not accessible from the available text.

Evidence highlights

Direct quote from Methods: "…merged with FLASH (v1.2.11) [23] and then were de-noised using DADA2 [24] plugin in the Qiime2 [25] pipeline with recommended parameters…"
Direct quote from Methods: "…inoculated into 100 mL LB liquid medium… incubated at 28 °C, 180 rpm for 2 days, then OD600 was measured…"
Direct quote from Methods: soil from the three diseased fields was combined for sterilization, while the corresponding diseased soils were kept separate.
DOI: 10.1186/s12870-025-07985-7 (BMC Plant Biology, 2025).

Notes

All three primary findings are considered confirmed (✅) based on the published text; the image/data limitation is marked as insufficient evidence (⚠️).
The FLASH/DADA2 incompatibility is a documented common artifact in outsourced microbiome analyses and is not by itself proof of misconduct, but the combination with the other issues raises the probability of a non-rigorous or template-driven write-up.
Recommended actions: request raw FASTQ files, Qiime2 commands, and metabolomics peak tables from the corresponding author; raise a PubPeer comment; notify the BMC Plant Biology editorial office.
This report is AI-assisted and intended for academic discussion only; final determination of misconduct requires institutional investigation.