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梯度提升回归作为一种工具,揭示了人工酵母群落时间动态的关键驱动因素。

Gradient boosted regression as a tool to reveal key drivers of temporal dynamics in a synthetic yeast community.

机构信息

Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Private Bag X1, Stellenbosch University, Stellenbosch 7600, South Africa.

Centre for Artificial Intelligence Research (CAIR), School for Data-Science & Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa.

出版信息

FEMS Microbiol Ecol. 2024 Jun 17;100(7). doi: 10.1093/femsec/fiae080.


DOI:10.1093/femsec/fiae080
PMID:38777744
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11212668/
Abstract

Microbial communities are vital to our lives, yet their ecological functioning and dynamics remain poorly understood. This understanding is crucial for assessing threats to these systems and leveraging their biotechnological applications. Given that temporal dynamics are linked to community functioning, this study investigated the drivers of community succession in the wine yeast community. We experimentally generated population dynamics data and used it to create an interpretable model with a gradient boosted regression tree approach. The model was trained on temporal data of viable species populations in various combinations, including pairs, triplets, and quadruplets, and was evaluated for predictive accuracy and input feature importance. Key findings revealed that the inoculation dosage of non-Saccharomyces species significantly influences their performance in mixed cultures, while Saccharomyces cerevisiae consistently dominates regardless of initial abundance. Additionally, we observed multispecies interactions where the dynamics of Wickerhamomyces anomalus were influenced by Torulaspora delbrueckii in pairwise cultures, but this interaction was altered by the inclusion of S. cerevisiae. This study provides insights into yeast community succession and offers valuable machine learning-based analysis techniques applicable to other microbial communities, opening new avenues for harnessing microbial communities.

摘要

微生物群落对我们的生活至关重要,但它们的生态功能和动态仍未被充分理解。这种理解对于评估这些系统面临的威胁和利用其生物技术应用至关重要。鉴于时间动态与群落功能有关,本研究调查了葡萄酒酵母群落中群落演替的驱动因素。我们通过实验生成了种群动态数据,并使用梯度提升回归树方法对其进行了可解释的建模。该模型在各种组合的存活物种种群的时间数据上进行了训练,包括二联体、三联体和四联体,并评估了其预测准确性和输入特征重要性。主要发现表明,非酿酒酵母的接种剂量显著影响它们在混合培养物中的表现,而酿酒酵母无论初始丰度如何始终占据主导地位。此外,我们观察到了多物种相互作用,在二联体培养物中,异常威克汉姆酵母的动态受到德巴利酵母的影响,但这种相互作用因包括酿酒酵母而发生了改变。本研究深入了解了酵母群落的演替,并提供了有价值的基于机器学习的分析技术,可应用于其他微生物群落,为利用微生物群落开辟了新途径。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/1a262632face/fiae080fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/625c97ee84d7/fiae080fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/6f27995c4b14/fiae080fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/f17012eb7cac/fiae080fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/1a262632face/fiae080fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/625c97ee84d7/fiae080fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/6f27995c4b14/fiae080fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/f17012eb7cac/fiae080fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f164/11212668/1a262632face/fiae080fig4.jpg

相似文献

[1]
Gradient boosted regression as a tool to reveal key drivers of temporal dynamics in a synthetic yeast community.

FEMS Microbiol Ecol. 2024-6-17

[2]
Impact of oxygenation on the performance of three non-Saccharomyces yeasts in co-fermentation with Saccharomyces cerevisiae.

Appl Microbiol Biotechnol. 2017-3

[3]
Early transcriptional response to biotic stress in mixed starter fermentations involving Saccharomyces cerevisiae and Torulaspora delbrueckii.

Int J Food Microbiol. 2017-1-16

[4]
A Transcriptomic Analysis of Higher-Order Ecological Interactions in a Eukaryotic Model Microbial Ecosystem.

mSphere. 2022-12-21

[5]
Real-time monitoring of population dynamics and physical interactions in a synthetic yeast ecosystem by use of multicolour flow cytometry.

Appl Microbiol Biotechnol. 2020-6

[6]
Linking gene expression and oenological traits: Comparison between Torulaspora delbrueckii and Saccharomyces cerevisiae strains.

Int J Food Microbiol. 2019-2-2

[7]
Yeast population dynamics reveal a potential 'collaboration' between Metschnikowia pulcherrima and Saccharomyces uvarum for the production of reduced alcohol wines during Shiraz fermentation.

Appl Microbiol Biotechnol. 2014-11-12

[8]
An innovative tool reveals interaction mechanisms among yeast populations under oenological conditions.

Appl Microbiol Biotechnol. 2013-1-5

[9]
Interactions between Torulaspora delbrueckii and Saccharomyces cerevisiae in wine fermentation: influence of inoculation and nitrogen content.

World J Microbiol Biotechnol. 2014-7

[10]
Selected non-Saccharomyces wine yeasts in controlled multistarter fermentations with Saccharomyces cerevisiae.

Food Microbiol. 2010-12-10

本文引用的文献

[1]
Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions.

PLoS Comput Biol. 2023-9

[2]
Predictability of the community-function landscape in wine yeast ecosystems.

Mol Syst Biol. 2023-9-12

[3]
Emergent coexistence in multispecies microbial communities.

Science. 2023-7-21

[4]
Synthesizing microbial biodiversity.

Curr Opin Microbiol. 2023-10

[5]
Deep Neural Networks and Tabular Data: A Survey.

IEEE Trans Neural Netw Learn Syst. 2024-6

[6]
Interactions between Culturable Bacteria Are Predicted by Individual Species' Growth.

mSystems. 2023-4-27

[7]
The neglected role of micronutrients in predicting soil microbial structure.

NPJ Biofilms Microbiomes. 2022-12-27

[8]
A Transcriptomic Analysis of Higher-Order Ecological Interactions in a Eukaryotic Model Microbial Ecosystem.

mSphere. 2022-12-21

[9]
Machine Learning Predicts Biogeochemistry from Microbial Community Structure in a Complex Model System.

Microbiol Spectr. 2022-2-23

[10]
Phenotypic characterization of cell-to-cell interactions between two yeast species during alcoholic fermentation.

World J Microbiol Biotechnol. 2021-9-28

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