Common principles and best practices for engineering microbiomes

Abstract

Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries on the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyze microbiome function. These approaches can be used to NRMICRO-19-067V3 2 harness microbiomes for broad applications related to medicine, agriculture, energy, and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture, and enabling the bioeconomy.

Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes

“…Recent studies have shown that a small class of key groups are present in the rhizosphere microbial community, and they play a leading role in promoting disease occurrence (Berg and Smalla 2009;Liu et al 2016;Berendsen et al 2012;Lawson et al 2019). Therefore, we extracted 16S rRNA and 18S rRNA genes from the total DNA of perennial diseased and perennial healthy tobacco rhizosphere soils to further analyze the rhizosphere microbial composition under natural conditions.…”

Multiplexed biosensors for precision bacteria tropism in vivo

“…Main Text: Microbiome research continues to demonstrate the abundance of microorganisms in various environments (1-3). An emerging focus in synthetic biology engineers microbes to integrate within specific niches in nature, artificial infrastructure and the human body (4)(5)(6)(7)(8)(9)(10)(11). Since genetic programming of bacteria enables them to sense and respond to physiological conditions in situ, this approach is poised to change existing paradigms for diagnosing and treating diseases such as inflammation (12,13), infection (14,15), and cancer (16)(17)(18).…”

Limitation by a shared mutualist promotes coexistence of multiple competing partners

“…Within mutualistic communities, coexistence of many species within a partner mutualist guild creates functional redundancy, which is important in the face of disturbances because redundancy can protect mutualistic communities from collapse 5,31 . Knowledge of ways to preserve functional redundancy might aid efforts to design stable microbial communities for applications in health and industry 32 .…”