Unbiased and scalable reduction of diverse bacterial genomes
Lipschitz, M.; Quan, B.; Madireddy, I.; Aihara, G.; Bennett, M.; Chou, T.-F.; Wang, K. · synthetic biology · 2026-09-04 · 原文
DOI：10.64898/2026.09.02.748983作者：7 位预印本：bioRxiv (Cold Spring Harbor Laboratory)
The genome is a complex, integrated system where the functions and regulatory interactions of its many components remain poorly understood. Genome minimization aims to reduce genomic complexity by removing non-essential elements to reveal the fundamental building blocks of cellular life. However, current minimization strategies are often slow and species-specific due to a reliance on prior information, and limited to producing single, isolated strains, which obscures the diverse ways a genome can adapt to large-scale DNA removal. Here we show the development and application of Stochastic Lineage-based Iterative Minimization (SLIM) a modular, high-throughput platform for unbiased genome reduction across phylogenetically diverse bacteria. We apply SLIM to generate a library of genome-reduced Escherichia coli lineages. We then interrogate the lineages, identifying both universal and lineage-specific transcriptional and translational reprogramming in response to deletions. We demonstrate that these expression dynamics drive environment-dependent fitness, allowing us to pinpoint a single gene deletion in one genome-reduced lineage as the driver of a measurable environmental growth defec
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1. 人话版
The genome is a complex, integrated system where the functions and regulatory interactions of its many components remain poorly understood.
Genome minimization aims to reduce genomic complexity by removing non-essential elements to reveal the fundamental building blocks of cellular life.
2. 领域脉络
本文类目：synthetic biology，属于其所在研究脉络的最新进展。
3. 机制拆解
Here we show the development and application of Stochastic Lineage-based Iterative Minimization (SLIM) a modular, high-throughput platform for unbiased genome reduction across phylogenetically diverse bacteria.
We apply SLIM to generate a library of genome-reduced Escherichia coli lineages.
4. 证据与数字
摘要未给出量化结果——留意原文的实验与数据。
5. 反例与边界
However, current minimization strategies are often slow and species-specific due to a reliance on prior information, and limited to producing single, isolated strains, which obscures the diverse ways a genome can adapt to large-scale DNA removal.
6. 跨领域连接与意外收获
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7. 可复用方法
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8. 术语表
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