Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing

IF 4.6 2区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

iScience Pub Date : 2024-10-28 DOI:10.1016/j.isci.2024.111249

Simon Klaes , Shobhit Madan , Darja Deobald , Myriel Cooper , Lorenz Adrian

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引用次数: 0

Abstract

Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-prototyping-based stable isotope probing (GroEL-SIP), that uses GroEL as a taxonomic marker protein to identify bacterial taxa (GroEL-proteotyping) coupled to SIP directly linking identified taxa to substrate consumption. GroEL-SIP’s main advantages are that (1) it can be performed with a sample-independent database and (2) sample complexity can be reduced by enriching GroEL proteins, increasing sensitivity and reducing instrument time. We applied GroEL-SIP to pure cultures, synthetic bicultures, and a human gut model using ²H-, ¹⁸O-, and ¹³C-labeled substrates. While ²H and ¹⁸O allowed assessing general activity, ¹³C enabled differentiation of substrate source and utilized metabolic pathways. GroEL-SIP offers fast and straightforward protein-SIP analyses of highly abundant families in mixed bacterial communities, but further work is needed to improve sensitivity, resolution, and database coverage.

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通过基于 GroEL 蛋白分型的稳定同位素探测揭示混合细菌群落的分类、活性和底物同化作用

基于蛋白质的稳定同位素探测（protein-SIP）可以将微生物类群与底物同化联系起来。传统上，蛋白质-SIP 需要一个特定于样本的元基因组数据库，用于未知成分的样本。在这里，我们介绍了基于GroEL-prototyping的稳定同位素探针（GroEL-SIP），它使用GroEL作为分类标记蛋白来识别细菌类群（GroEL-proteotyping），并结合SIP直接将已识别的类群与底物消耗联系起来。GroEL-SIP 的主要优点是：(1) 可使用与样品无关的数据库；(2) 可通过富集 GroEL 蛋白降低样品的复杂性，提高灵敏度并缩短仪器时间。我们使用 2H、18O 和 13C 标记的底物将 GroEL-SIP 应用于纯培养物、合成双培养物和人体肠道模型。2H 和 18O 可以评估一般活性，而 13C 则可以区分底物来源并利用代谢途径。GroEL-SIP为混合细菌群落中的高丰度家族提供了快速、直接的蛋白质-SIP分析，但还需要进一步的工作来提高灵敏度、分辨率和数据库覆盖率。

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来源期刊

iScience Multidisciplinary-Multidisciplinary

CiteScore

7.20

自引率

1.70%

发文量

1972

审稿时长

6 weeks

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