Engineering synthetic spatial patterns in microbial populations and communities

Barbier, Içvara; Kusumawardhani, Hadiastri; Schaerli, Yolanda

doi:10.1016/j.mib.2022.102149

Cited by 13 publications

(10 citation statements)

References 67 publications

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“…In fact, certain bacteria naturally produce spatially ordered structures when exposed to alternating dark/light cycles e.g., (Kahl et al, 2022). As recently reviewed (Barbier et al, 2022), the patterning of microbial communities gains traction and appears suited for diverse applications in synthetic biology and biotechnology. Although not the only means of organizing bacterial populations in space, see e.g., (Frangipane et al, 2018;Chen and Wegner, 2020;Barbier et al, 2022), light-regulated gene expression appears particularly straightforward, versatile, and efficient.…”

Section: Bacterial Photography and Structured Materialsmentioning

confidence: 99%

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Ohlendorf

Möglich²

2022

Front. Bioeng. Biotechnol.

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Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.

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Section: Bacterial Photography and Structured Materialsmentioning

confidence: 99%

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Ohlendorf

Möglich²

2022

Front. Bioeng. Biotechnol.

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show abstract

“…Interestingly, our heterogeneous stripe test demonstrates consortium behavior can be controlled through the consortium’s spatial organization alone. Combined with a rise in experimental methods for controlling spatial organizations in consortia ( 20 , 23 , 24 , 38 ), this opens an interesting avenue for regulating consortium dynamics in the future ( 36 ).…”

Section: Discussionmentioning

confidence: 99%

“…We used this principle here to design a consortium that oscillated synchronously on the half that contained small stripes and asynchronously on the half that contained large stripes. Combined with a growing number of experimental approaches for designing consortia with specific spatial arrangements, including optogenic, seeding, and other approaches ( 20 , 22 , 23 , 24 ), modulating consortium dynamics through spatial organization is becoming more practical. Since the underlying numerical scheme used to solve our reaction-diffusion equation model has routinely been applied in higher dimensions ( 39 , 40 , 41 , 42 ), our framework is well suited to interrogate the effects of the more complex spatial organizations implemented by these experimental methods ( 23 , 43 , 44 , 45 ).…”

Section: Discussionmentioning

confidence: 99%

“…Substantial tools exist for controlling a particular consortium’s behavior genetically using synthetic regulatory circuits ( 16 , 17 , 18 , 19 ), and tools for engineering a consortium’s spatial organization have also begun to be developed ( 20 ). For example, Romano et al.…”

Section: Introductionmentioning

confidence: 99%

“…demonstrated that the number of subpopulation bands in an extended microfluidic device can be regulated through the seeding of the trap. Other methods for regulating the spatial organization of consortia including adhesion, cell-communication, and motility are also being developed ( 20 , 22 , 23 , 24 , 25 , 26 ). With previous studies demonstrating that the spatial organization of a consortium can significantly alter its dynamics ( 18 , 27 ), these experimental methods are enabling an additional layer of control for engineering microbial consortia.…”

Section: Introductionmentioning

confidence: 99%

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The space between us: Modeling spatial heterogeneity in synthetic microbial consortia dynamics

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Synthesis of queuine by colonic gut microbiome via cross‐feeding

Yan,

Xiang,

Shi

et al. 2023

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Queuine (Que) is an essential micronutrient, and its deficiency will lead to errors in tRNA modification and protein misfold, further to diseases. Meanwhile, the content of Que in food will be further reduced due to the modern planting pattern and processing. In this study, an idea, synthetic biology of gut microbiome, was introduced to meet people's demand for Que. Further, various food can be used as a media for promoting the growth of synthetic biology of flora and the concentrations of Que. Through this research, gut bacteria (Escherichia coli K12, Bacteroides fragilis ATCC25285, and Lactobacillus reuteri DSM20058) with abilities of Que independent synthesis in vitro were selected, and higher productivity of Que was fulfilled through the above three strains cocultivation via cross‐feeding. Moreover, the effect of Que on the structure of microbiome was also studied, in order to figure out the continuous synthesis of Que by this coculture system in colonic situation. Que could enhance bacterial α‐diversity, increase the abundance of Limosilactobacillus, Pediococcus, and Lactobacillus, while decrease the abundance of Eschi‐Shigella. Three bacteria combination intervention changed intestinal microbial composition, and distribution of enzymes transglycozyme, QueA, and QueG that involved in last three steps of Que synthesis in microorganisms was significantly changed. These results provide an experimental basis for colonic synthesis of Que via food intervention to solve the deficiency Que in human body. Here, we regard gut microbes as a fermentation system in human body, providing a constant supply of tiny but important substance that humans need.

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Engineering synthetic spatial patterns in microbial populations and communities

Cited by 13 publications

References 67 publications

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

The space between us: Modeling spatial heterogeneity in synthetic microbial consortia dynamics

Synthesis of queuine by colonic gut microbiome via cross‐feeding

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