枯草芽孢杆菌的泛基因组尺度代谢模型揭示了功能上截然不同的群体。

IF 5 2区 生物学 Q1 MICROBIOLOGY
mSystems Pub Date : 2024-11-19 Epub Date: 2024-10-04 DOI:10.1128/msystems.00923-24
Maxwell Neal, William Brakewood, Michael Betenbaugh, Karsten Zengler
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引用次数: 0

摘要

枯草芽孢杆菌(Bacillus subtilis)是一种重要的工业和环境微生物,众所周知,它占据着许多生态位,并能产生许多令人感兴趣的化合物。虽然枯草芽孢杆菌是研究得最好的生物之一,但包括重建基因组尺度代谢模型在内的大部分研究重点都放在了几个关键的实验室菌株上。在这里,我们将这些先前的模型大幅扩展到泛基因组规模,代表了具有 2,315 个同源基因簇、1,874 个代谢物和 2,239 个反应的 481 个枯草芽孢杆菌基因组。此外,我们还纳入了八个菌株的碳利用实验数据,以完善和验证其代谢预测。这种全面的泛基因组模型能够评估菌株之间在营养物质利用、发酵产出、稳健性和其他代谢方面的差异。利用该模型和表型预测,我们将枯草芽孢杆菌菌株分为五组,这五组菌株具有与这些特征相关的不同行为模式。泛基因组模型深入揭示了枯草杆菌在不同环境下的新陈代谢,并让人们了解不同菌株是如何适应动态生境的:随着基因组数据量和计算能力的增加,基因组尺度代谢模型的数量也在增加。这些模型囊括了特定生物体的全部代谢功能。枯草芽孢杆菌 168 菌株是最早重建代谢网络的细菌之一。从那时起,该模型微生物的代谢网络已多次更新重建。在这里,我们将单一菌株的代谢模型扩展为一个泛基因组规模的模型,其中包括 481 株枯草芽孢杆菌的单个模型。通过评估这些菌株之间的差异,我们确定了五个不同的菌株群,从而可以对任何特定菌株进行快速分类。此外,将菌株分为五组有助于快速确定适合任何应用的菌株。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Pan-genome-scale metabolic modeling of Bacillus subtilis reveals functionally distinct groups.

Bacillus subtilis is an important industrial and environmental microorganism known to occupy many niches and produce many compounds of interest. Although it is one of the best-studied organisms, much of this focus including the reconstruction of genome-scale metabolic models has been placed on a few key laboratory strains. Here, we substantially expand these prior models to pan-genome-scale, representing 481 genomes of B. subtilis with 2,315 orthologous gene clusters, 1,874 metabolites, and 2,239 reactions. Furthermore, we incorporate data from carbon utilization experiments for eight strains to refine and validate its metabolic predictions. This comprehensive pan-genome model enables the assessment of strain-to-strain differences related to nutrient utilization, fermentation outputs, robustness, and other metabolic aspects. Using the model and phenotypic predictions, we divide B. subtilis strains into five groups with distinct patterns of behavior that correlate across these features. The pan-genome model offers deep insights into B. subtilis' metabolism as it varies across environments and provides an understanding as to how different strains have adapted to dynamic habitats.

Importance: As the volume of genomic data and computational power have increased, so has the number of genome-scale metabolic models. These models encapsulate the totality of metabolic functions for a given organism. Bacillus subtilis strain 168 is one of the first bacteria for which a metabolic network was reconstructed. Since then, several updated reconstructions have been generated for this model microorganism. Here, we expand the metabolic model for a single strain into a pan-genome-scale model, which consists of individual models for 481 B. subtilis strains. By evaluating differences between these strains, we identified five distinct groups of strains, allowing for the rapid classification of any particular strain. Furthermore, this classification into five groups aids the rapid identification of suitable strains for any application.

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来源期刊
mSystems
mSystems Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
10.50
自引率
3.10%
发文量
308
审稿时长
13 weeks
期刊介绍: mSystems™ will publish preeminent work that stems from applying technologies for high-throughput analyses to achieve insights into the metabolic and regulatory systems at the scale of both the single cell and microbial communities. The scope of mSystems™ encompasses all important biological and biochemical findings drawn from analyses of large data sets, as well as new computational approaches for deriving these insights. mSystems™ will welcome submissions from researchers who focus on the microbiome, genomics, metagenomics, transcriptomics, metabolomics, proteomics, glycomics, bioinformatics, and computational microbiology. mSystems™ will provide streamlined decisions, while carrying on ASM''s tradition of rigorous peer review.
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