Applying the design-build-test paradigm in microbiome engineering

doi:10.1016/j.copbio.2017.03.021

Current Opinion in Biotechnology

Volume 48, December 2017, Pages 85-93

https://doi.org/10.1016/j.copbio.2017.03.021 Get rights and content

Highlights

•
Recent progress in microbiome engineering is reviewed.
•
Design principles to engineer the human microbiome are reviewed.
•
Methods to engineer microbiome with desired functions are reviewed.
•
The ‘design-build-test’ cycle can expedite microbiome engineering.

The recently discovered roles of human microbiome in health and diseases have inspired research efforts across many disciplines to engineer microbiome for health benefits. In this review, we highlight recent progress in human microbiome research and how modifications to the microbiome could result in implications to human health. Furthermore, we discuss the application of a ‘design-build-test’ framework to expedite microbiome engineering efforts by reviewing current literature on three key aspects: design principles to engineer the human microbiome, methods to engineer microbiome with desired functions, and analytical techniques to examine complex microbiome samples.

Graphical abstract

Introduction

Recent discoveries on the roles of the human gut microbiome in health and diseases have inspired novel means for prophylactic and therapeutic intervention against disease onset and progression. The engineering of human microbiome for health benefits and related applications could be observed across many disciplines in nanotechnology, chemistry, and biology. Nanoscale instruments are being fabricated to interface with human microbiome for real-time monitoring of health status, or for on-site protection against early disease onset [1]. Chemical microbiome modifiers, such as prebiotics, probiotics, and antibiotics, have long been prescribed by doctors for disease treatment [2]. With the advent of DNA sequencing and metabolomics tools allowing data analysis at higher resolution and throughput, interests to develop biological modifiers for in situ precision engineering of the human microbiome are increasingly gaining momentum [3, 4••, 5]. Synthetic biology envisages microbiome engineering as one of the grand frontiers of precision medicine. Genetic programs have been installed into single-species microbial communities to perform diagnostic and therapeutic operations, such as regulating glucose level in the blood, or detecting liver metastasis in urine [6, 7]. Alongside these developments, there is emerging global interest to expand the said conceptual frameworks for the development of synthetic cellular consortia that could enable targeted engineering of the human microbiome and deliver the corresponding health benefits [5]. The ‘design-build-test’ (DBT) cycle is an engineering paradigm that is widely practiced among engineering disciplines for the design of experiments and the rational optimization of technology. In this review, we aim to demonstrate how the DBT cycle can be strategically applied to expedite microbiome engineering efforts. To support this proposition, we herein assess the status of human gut microbiome engineering with a focus on three key aspects: design principles to engineer the human microbiome, methods to reassemble microbiome with desired functions, and analytical techniques to examine complex microbiome samples.

Section snippets

Design

Harnessing the design principles of natural microbiome represents a pioneering step for rational microbiome engineering. In this section, we review the current knowledge on fundamental design features of natural human gut microbiome, including the composition and dynamics, biogeography, and metabolic activity (Figure 1). Examples illustrating the application of these understanding to modify microbiome are presented.

Build

Current microbiome engineering methods aim to introduce specific perturbation to cause the intentional shift and transition of the human microbiota. Subsequently, the composition and metagenome of the re-assembled microbiota could be correlated with host physiology changes to identify and augment microbial functions that contribute to specific health conditions [4^••]. Ongoing efforts to engineer the microbiome can be classified as either abiotic perturbation, including drug treatment and

Test

Possessing the capability to analyze complex microbial samples in high-throughput workflows is critical in advancing current knowledge and application in microbiome engineering. In this section, we survey the status of contemporary tools for microbiome testing and analysis, particularly on cutting-edge tools for transcriptomics, metagenomics, proteomics, and metabolomics (Figure 3).

Conclusion

In this review, we describe various aspects of the human microbiome and how modifications to the composition and functionality of the microbiome can result in implications to human health. Understanding these fundamental mechanisms allow us to formulate design principles and strategies to enable rational engineering and analysis of the human microbiome at multi-species community levels. Despite the rapid advancement of human microbiome knowledge, it is critical to acknowledge that the

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

• of special interest
•• of outstanding interest

Acknowledgements

This work was supported by the Synthetic Biology Initiative of the National University of Singapore (DPRT/943/09/14), the Summit Research Program of the National University Health System (NUHSRO/2016/053/SRP/05), the Ministry of Defence of Singapore (MINDEF, RE2016-074), the Singapore Ministry of Education (MOE/2014/T2/2/128), the US Air Force (AOARD, FA2386-14-1-4060) and the U.S. Defense Threat Reduction Agency (DTRA, HDTRA1-13-0037).

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The world’s coral reefs are threatened by the cumulative impacts of global climate change and local stressors. Driven largely by a desire to understand the interactions between corals and their symbiotic microorganisms, and to use this knowledge to eventually improve coral health, interest in coral microbiology and the coral microbiome has increased in recent years. In this review, we summarize the role of the coral microbiome in maintaining a healthy metaorganism by providing nutrients, support for growth and development, protection against pathogens, and mitigation of environmental stressors. We explore the concept of coral microbiome engineering, that is, precise and controlled manipulation of the coral microbiome to aid and enhance coral resilience and tolerance in the changing oceans. Although coral microbiome engineering is clearly in its infancy, several recent breakthroughs indicate that such engineering is an effective tool for restoration and preservation of these valuable ecosystems. To assist with identifying future research targets, we have reviewed the common principles of microbiome engineering and its applications in improving human health and agricultural productivity, drawing parallels to where coral microbiome engineering can advance in the not-too-distant future. Finally, we end by discussing the challenges faced by researchers and practitioners in the application of microbiome engineering in coral reefs and provide recommendations for future work.
Quorum sensing-mediated microbial interactions: Mechanisms, applications, challenges and perspectives
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Microbial community in natural or artificial environments playes critical roles in substance cycles, products synthesis and species evolution. Although microbial community structures have been revealed via culture-dependent and culture-independent approaches, the hidden forces driving the microbial community are rarely systematically discussed. As a mode of cell-to-cell communication that modifies microbial interactions, quorum sensing can regulate biofilm formation, public goods secretion, and antimicrobial substances synthesis, directly or indirectly influencing microbial community to adapt to the changing environment. Therefore, the current review focuses on microbial community in the different habitats from the quorum sensing perspective. Firstly, the definition and classification of quorum sensing were simply introduced. Subsequently, the relationships between quorum sensing and microbial interactions were deeply explored. The latest progressives regarding the applications of quorum sensing in wastewater treatment, human health, food fermentation, and synthetic biology were summarized in detail. Finally, the bottlenecks and outlooks of quorum sensing driving microbial community were adequately discussed. To our knowledge, this current review is the first to reveal the driving force of microbial community from the quorum sensing perspective. Hopefully, this review provides a theoretical basis for developing effective and convenient approaches to control the microbial community with quorum sensing approaches.
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Although currently none of these tools involve microbial communities, these tools could be of great value for future microbiome research. To further understand the impact of microbiome modulation, current microbiome engineering methods can be used to introduce a specific perturbation to cause intentional shifts in human studies [46]. Such perturbations can be either biotic (microbial transplants, probiotics, phages) or abiotic (dietary changes, antibiotics/xenobiotics use).
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Microbiome engineering for controllable outcomes requires computational models that enable integrating the high dimensionality of microbiome data to propose optimal intervention or design strategies [15,16]. Rational microbiome engineering can be framed to follow a design-build-test-learning cycle [17••,18], among which the ‘design’ step is a critical part that can greatly benefit from predictive mathematical modeling and data integration. The utility of computational models in microbiome design, particularly those enabling accurately predicting microbial interactions, has been highlighted through a recently proposed workflow, termed Biological Computer-Aided Design of Interactions (BioCADi) [19].
Microbiome engineering aims to manipulate, control, and design community-level properties through targeted interventions of existing microbial communities or the construction of new synthetic consortia. These efforts often lead to unexpected or undesirable outcomes because of highly complex input-output relationships that are primarily ascribable to adaptive responses of interspecies interactions to perturbation. Therefore, accurate prediction of microbial interaction networks and context-specific organization will aid success in future microbiome engineering efforts. Here, we review state-of-the-art modeling approaches to evaluate their scope of prediction as in silico tools for microbiome design. We highlight the utility of advanced models for predicting context-dependent interactions, multi-omics data integration, and combined use of complementary modeling and computational tools for enhanced prediction and eventual facilitation of in silico microbiome design.
A designed whole-cell biosensor for live diagnosis of gut inflammation through nitrate sensing
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In particular, probiotics have been actively serving as a chassis and have been reprogrammed through genetic circuits to sense disease biomarkers and to deliver therapeutics efficiently with site specificity (Singh et al., 2017). Similar to commensal bacteria in the gut, these designer probiotics can also sense, respond to, and control the gut environment (Hwang and Chang, 2020; Pham et al., 2017). The mammalian gut is home to a diverse community of commensal, symbiotic, and even pathogenic microbes (Mimee et al., 2016) and plays active roles in human health, including metabolism (Fischbach and Sonnenburg, 2011), immunity (Belkaid and Hand, 2014), and the gut-brain axis (Sampson and Mazmanian, 2015).
Microbes reprogrammed using advanced genetic circuits are envisaged as emerging living diagnostics for a wide range of diseases and play key roles in regulating gut microbiota to treat disease-associated symptoms in a non-invasive manner. Here, we developed a designer probiotic Escherichia coli that senses and responds to nitrate, a biomarker of gut inflammation. To this end, we first employed the NarX-NarL two-component regulatory system in E. coli to construct a nitrate-responsive genetic circuit. Next, we optimized the nitrate biosensor for the best performance using measures of sensitivity and specificity. We then introduced this genetic circuit into a probiotic E. coli Nissle 1917. We demonstrated that the designed biosensor can sense elevated nitrate levels during gut inflammation in mice with native gut microbiota. Moreover, using Boolean AND gate, we generated a genetically encoded biosensor for simultaneous sensing of the thiosulfate and nitrate biomarkers, thus increasing the tool's specificity for diagnosing gut inflammation. The nitrate-responsive genetic circuit will enable new approaches for non-invasive diagnostics of inflammation-associated diseases.

View all citing articles on Scopus

^*: These authors contributed equally to this work.

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Applying the design-build-test paradigm in microbiome engineering

Highlights

Graphical abstract

Introduction

Section snippets

Design

Build

Test

Conclusion

References and recommended reading

Acknowledgements

Trends Genet.

Science

Nat. Rev. Immunol.

Nat. Rev. Microbiol.

Cell

Cell Host Microbe

Nat. Rev. Microbiol.

Cell Host Microbe

Am. J. Gastroenterol.

Gastroenterol

Mol. Syst. Biol.

Proc. Natl. Acad. Sci. U. S. A.

J. Clin. Invest.

Tools for the microbiome: nano and beyond

ACS Nano

The antibiotics market

Nat. Rev. Drug Discov.

Drugging the gut microbiome

Nat. Biotechnol.

Microbiome therapeutics—advances and challenges

Adv. Drug Deliv. Rev.

Programmable probiotics for detection of cancer in urine

Sci. Transl. Med.

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Proc. Natl. Acad. Sci. U. S. A.

Antibiotics in early life alter the murine colonic microbiome and adiposity

Nature

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Appl. Environ. Microbiol.

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Nature

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Science

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Nature

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Sci. Transl. Med.

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Proc. Natl. Acad. Sci. U. S. A.

Composition of the gut microbiota modulates the severity of malaria

Proc. Natl. Acad. Sci. U. S. A.

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Nature

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Science

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Curr. Biol.

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Gastroenterol

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Cell Syst.

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Nat. Neurosci.

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Nature