Engineering Natural Microbiomes Toward Enhanced Bioremediation by Microbiome Modeling

Overview

Journal Nat Commun

Specialty Biology

Date 2024 Jun 1

PMID 38824157

Authors

Zhepu Ruan

Kai Chen

Weimiao Cao

Lei Meng

Bingang Yang

Mengjun Xu

Youwen Xing

Pengfa Li

Shiri Freilich

Chen Chen

Yanzheng Gao

Jiandong Jiang

Xihui Xu

Affiliations

Soon will be listed here.

Abstract

Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.

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