Microbiome composition modulates secondary metabolism in a multispecies bacterial community.
Microbiome composition modulates secondary metabolism in a multispecies bacterial community.
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DOI：
10.1073/pnas.2212930119
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发表时间：
2022-10-18
影响因子：
11.1
通讯作者：
中科院分区：
文献类型：
--
作者：
微生物群落与人类和植物疾病有关，对全球生物地球化学循环至关重要。然而，我们可靠地改变这些社区的能力受到对推动社区进程的网络的理解不足的限制。本研究的目的是了解社区成员如何改变在一个模型微生物群落的次生代谢。我们发现，群落物种组成影响生物合成基因的表达和代谢产物的丰度。当一种代谢产物koreenceine的生物合成基因簇被删除时，观察到了巨大的变化，这表明种间相互作用网络可能是由次级代谢产物驱动的。这项工作提供了一种方法来解剖通过社区的信息流，这可能会导致操纵社区功能的策略。细菌次级代谢产物是抗生素和其他生物活性化合物的主要来源。在微生物群落中，这些分子可以介导物种间的相互作用和对环境变化的反应。尽管次级代谢产物在人类健康和微生物生态学中的重要性，但对它们在多物种群落中的作用和调控知之甚少。在一个简化的模型组成的蜡状芽孢杆菌，黄杆菌johnsoniae，和假单胞菌koreensis根际，我们表明，次生代谢的动态取决于社区物种组成和种间相互作用。比较元转录组学和代谢组学揭示，丰富的生物合成基因簇（BGC）和代谢组学的分子特征的转录本之间的单培养或双文化和三方社区不同。在两个和三个成员的共培养物中，P. koreensis修改了B中的两性霉素、petrobactin和其他次级代谢产物的BGC的表达。cereus和F. johnsoniae中的BGC转录响应，而P. koreensis本身的社区是最小的。与P. koreensis的成对和三重共培养物显示出似乎是lokisin衍生物的独特分子特征，表明物种之间的代谢平衡。删除另一种朝鲜青霉代谢物朝鲜霉素的BGC，改变了整个群落的转录物和代谢物谱，包括B中petrobactin和bacillibactin BGC的显著上调。cereus，这表明朝鲜霉素抑制铁载体的生产。该模型社区的结果表明，细菌BGC表达和化学输出取决于共培养伙伴的身份和生物合成能力，这表明社区组成和微生物组相互作用可能会影响自然界中次生代谢的调节。
Microbial communities have been implicated in human and plant disease and are essential to global biogeochemical cycles. However, our ability to reliably alter these communities is limited by insufficient understanding of the networks that drive community processes. The goal of this study was to understand how community membership alters secondary metabolism in a model microbial community. We found that community species composition affects expression of biosynthetic genes and abundance of metabolites. Dramatic changes were observed when the biosynthetic gene cluster of one metabolite, koreenceine, was deleted, suggesting that interspecies interaction networks may be driven by secondary metabolites. This work offers an approach to dissecting the flow of information through communities, which could lead to strategies for manipulating community function. Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions and responses to environmental change. Despite the importance of secondary metabolites in human health and microbial ecology, little is known about their roles and regulation in the context of multispecies communities. In a simplified model of the rhizosphere composed of Bacillus cereus, Flavobacterium johnsoniae, and Pseudomonas koreensis, we show that the dynamics of secondary metabolism depend on community species composition and interspecies interactions. Comparative metatranscriptomics and metametabolomics reveal that the abundance of transcripts of biosynthetic gene clusters (BGCs) and metabolomic molecular features differ between monocultures or dual cultures and a tripartite community. In both two- and three-member cocultures, P. koreensis modified expression of BGCs for zwittermicin, petrobactin, and other secondary metabolites in B. cereus and F. johnsoniae, whereas the BGC transcriptional response to the community in P. koreensis itself was minimal. Pairwise and tripartite cocultures with P. koreensis displayed unique molecular features that appear to be derivatives of lokisin, suggesting metabolic handoffs between species. Deleting the BGC for koreenceine, another P. koreensis metabolite, altered transcript and metabolite profiles across the community, including substantial up-regulation of the petrobactin and bacillibactin BGCs in B. cereus, suggesting that koreenceine represses siderophore production. Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
DOI：
10.1073/pnas.0803622105
发表时间：
2008-08-12
影响因子：
11.1
作者：
Chng, Chinping;Lum, Amy M.;Kao, Camilla M.
通讯作者：
Kao, Camilla M.
DOI：
10.1198/016214501753382129
发表时间：
2001-12-01
影响因子：
3.7
作者：
Efron, B;Tibshirani, R;Tusher, V
通讯作者：
Tusher, V
影响因子：
4.4
作者：
Caldera, Eric J.;Chevrette, Marc G.;Currie, Cameron R.
通讯作者：
Currie, Cameron R.
影响因子：
4
作者：
Acharya, Deepa;Miller, Ian;Bugni, Tim S.
通讯作者：
Bugni, Tim S.