Data and code from: Pyrrocidines A and B demonstrate synergistic inhibition of <i>Fusarium verticillioides</i> growth

This dataset contains all raw data and R statistical code needed to reproduce the model fitting, model predictions, and data/model visualizations from the article:Lofton, L.W., Read, Q.D., Hamilton, H.L., Glenn, A.E., Hawkins, J.A., Mitchell, T.R., &amp; Gold, S.E. (2025). Pyrrocidines A and B demonstrate synergistic inhibition of Fusarium verticillioides growth. Front. Microbiol., vol. 15. https://doi.org/10.3389/fmicb.2024.1480920<i>Fusarium verticillioides</i> – a mycotoxigenic fungus and food safety threat – coinhabits maize kernels with <i>Sarocladium zeae</i>. This protective endophyte produces secondary metabolites of interest, pyrrocidines A and B, which inhibit the growth of <i>F. verticillioides</i> and specifically block fumonisin biosynthesis. Here, using pyrrocidine dose-response assays, we discovered a potent synergy between pyrrocidines A and B, where they functioned powerfully together to inhibit <i>F. verticillioides</i> growth. Further, results provided evidence that <i>FvZBD1</i> confers partial tolerance to pyrrocidines, particularly pyrrocidine A, and that pyrrocidine functions through <i>FvZBD1</i> to effectively eliminate fumonisin biosynthesis. Additionally, we showed that the <i>FvABC3</i> (FVEG_11089) mutant, earlier described as hypersensitive to pyrrocidine, is particularly sensitive to pyrrocidine B. Thus, pyrrocidine A and B show different target specificity (<i>FvZBD1 </i>or <i>FvABC3</i>) and synergistic action.The primary data analysis is a Bayesian generalized additive mixed model (GAMM) fit to the optical density data recorded at regular intervals from <i>F. verticillioides </i>strains grown in Bioscreen microtiter plates under different conditions, in a full-factorial design crossing strain (wild-type and two mutant strains) with multiple levels of pyrrocidine A and B concentration. The RMarkdown notebook imports the data, makes plots of the raw observations, fits the model to the data, and uses the posterior samples from the model to make predictions. Predictions are shown in graphical and tabular form, and evidence for effects is assessed using credible intervals of predictions, and Bayesian maximum <i>a posteriori </i>p-values (p_MAP). A secondary analysis is presented of a dose-response assay: this is a frequentist linear model fit to a log-transformed concentration as a function of pyrrocidine type and concentration, followed by post-hoc comparisons within each pyrrocidine type. Again, results are presented in graphical and tabular form.The following files are included:<b>PyrrSynergy_MetaData.pdf</b>: File with column metadata for the data objects listed below<b>bioscreen_data.csv</b>: Primary results of Bioscreen assay<b>bioscreen_data_wt1020.csv</b>: Results of additional Bioscreen assay with concentration levels between 10 and 20<b>AGlenn_Fvzbd1PyrrbFUM.xlsx</b>: Results of dose-response assay 1 of 2<b>LLofton_Fvzbd1PyrrFUM.xlsx</b>: Results of dose-response assay 2 of 2<b>pyrrocidine_bioscreen.html</b>: HTML rendered output of R code notebook containing analysis and visualization of main dataset (Bioscreen assays)<b>fumonisin_synthesis_analysis.html</b>: HTML rendered output of R code notebook containing analysis and visualization of secondary dataset (dose-response assay)<b>pyrrocidine_bioscreen.Rmd</b>: RMarkdown notebook, main analysis<b>fumonisin_synthesis_analysis.Rmd</b>: RMarkdown notebook, secondary analysis<b>splinefit_bioscreen_20240415.rds</b>: Pre-fit model object, created by R package <b>brms</b>, so that notebook may be run to reproduce results without refitting model, which may take days to run<br>本数据集包含复现该论文中模型拟合、模型预测及数据/模型可视化所需的全部原始数据与R统计代码：Lofton, L.W.、Read, Q.D.、Hamilton, H.L.、Glenn, A.E.、Hawkins, J.A.、Mitchell, T.R. 及 Gold, S.E.（2025）。《吡咯菌素A与B协同抑制伏马镰孢（Fusarium verticillioides）生长》，《微生物学前沿》（Front. Microbiol.），第15卷。https://doi.org/10.3389/fmicb.2024.1480920 伏马镰孢是一种产毒真菌且可构成食品安全威胁，其与草枝顶孢（Sarocladium zeae）共同定殖玉米籽粒。这种具有保护作用的内生真菌可产生具有研究价值的次生代谢产物——吡咯菌素A与B，二者能够抑制伏马镰孢的生长，并特异性阻断伏马毒素的生物合成。 本研究通过吡咯菌素剂量响应实验，发现吡咯菌素A与B之间存在显著协同作用：二者联合使用可强力抑制伏马镰孢的生长。进一步研究结果表明，FvZBD1基因可赋予菌株对吡咯菌素（尤其是吡咯菌素A）的部分耐受性，且吡咯菌素通过FvZBD1基因有效消除伏马毒素的生物合成。此外，本研究证实，此前被报道对吡咯菌素敏感的FvABC3（FVEG_11089）突变体对吡咯菌素B尤为敏感。综上，吡咯菌素A与B具有不同的靶点特异性（分别对应FvZBD1或FvABC3）并可发挥协同作用。 本研究的核心数据分析为贝叶斯广义加性混合模型（GAMM），该模型拟合了不同培养条件下，在Bioscreen微孔板中培养的伏马镰孢菌株（野生型及两株突变菌株）经全因子实验设计（设置不同浓度梯度的吡咯菌素A与B）后，定期记录的光密度数据。该RMarkdown文档可导入数据、绘制原始观测值可视化图、对数据拟合模型，并利用模型的后验样本进行预测。预测结果以图表及表格形式呈现，效应显著性通过预测可信区间及贝叶斯最大后验p值（p_MAP）进行评估。 次要分析为一项剂量响应实验：采用频率学派线性模型，以对数转换后的浓度作为吡咯菌素类型与浓度的函数进行拟合，并针对每种吡咯菌素类型开展事后多重比较。结果同样以图表及表格形式呈现。 本数据集包含以下文件： **PyrrSynergy_MetaData.pdf**：包含下述数据对象的列元数据文件 **bioscreen_data.csv**：Bioscreen实验的核心结果数据 **bioscreen_data_wt1020.csv**：额外Bioscreen实验结果，其吡咯菌素浓度梯度介于10至20之间 **AGlenn_Fvzbd1PyrrbFUM.xlsx**：第1组剂量响应实验结果 **LLofton_Fvzbd1PyrrFUM.xlsx**：第2组剂量响应实验结果 **pyrrocidine_bioscreen.html**：R代码文档的HTML渲染结果，包含核心数据集（Bioscreen实验）的分析与可视化内容 **fumonisin_synthesis_analysis.html**：R代码文档的HTML渲染结果，包含次要数据集（剂量响应实验）的分析与可视化内容 **pyrrocidine_bioscreen.Rmd**：核心分析所用的RMarkdown文档 **fumonisin_synthesis_analysis.Rmd**：次要分析所用的RMarkdown文档 **splinefit_bioscreen_20240415.rds**：预拟合的模型对象，由brms包创建，可直接运行文档以复现结果，无需重新拟合模型（重新拟合可能耗时数日）