Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate

Ziesack, Marika; Karrenbelt, Michiel A P; Bues, Johannes; Schaefer, Elena; Silver, Pamela A.; Way, Jeffrey C.

doi:10.1128/mra.01416-18

Cited by 9 publications

(6 citation statements)

References 12 publications

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“…E. coli NGF-1 is a strain originally isolated from the murine gut, which has proven to be an efficient and persistent colonizer and a reliable platform for the deployment of engineered circuits (3, 12, 16). When grown in the presence of a high concentration (100 ng/ml) of anhydrotetracycline (aTc) inducer, cI DN - triggered strains showed switching to the memory-on state, while cro -triggered strains switched only after a subsequent period of growth in the absence of aTc (Fig.…”

Section: Resultsmentioning

confidence: 99%

Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface

et al. 2019

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Engineering synthetic circuits into intestinal bacteria to sense, record, and respond to in vivo signals is a promising new approach for the diagnosis, treatment, and prevention of disease. However, because the design of disease-responsive circuits is limited by a relatively small pool of known biosensors, there is a need for expanding the capacity of engineered bacteria to sense and respond to the host environment. Here, we apply a robust genetic memory circuit in Escherichia coli to identify new bacterial biosensor triggers responding in the healthy and diseased mammalian gut, which may be used to construct diagnostic or therapeutic circuits. We developed a pipeline for rapid systems-level library construction and screening, using next-generation sequencing and computational analysis, which demonstrates remarkably reliable identification of responsive biosensor triggers from pooled libraries. By testing libraries of potential triggers—each consisting of a promoter and ribosome binding site (RBS)—and using RBS variation to augment the range of trigger sensitivity, we identify and validate triggers that selectively activate our synthetic memory circuit during transit through the gut. We further identify biosensor triggers with increased response in the inflamed gut through comparative screening of one of our libraries in healthy mice and those with intestinal inflammation. Our results demonstrate the power of systems-level screening for the identification of novel biosensor triggers in the gut and provide a platform for disease-specific screening that is capable of contributing to both the understanding and clinical management of intestinal illness. IMPORTANCE The gut is a largely obscure and inaccessible environment. The use of live, engineered probiotics to detect and respond to disease signals in vivo represents a new frontier in the management of gut diseases. Engineered probiotics have also shown promise as a novel mechanism for drug delivery. However, the design and construction of effective strains that respond to the in vivo environment is hindered by our limited understanding of bacterial behavior in the gut. Our work expands the pool of environmentally responsive synthetic circuits for the healthy and diseased gut, providing insight into host-microbe interactions and enabling future development of increasingly complex biosensors. This method also provides a framework for rapid prototyping of engineered systems and for application across bacterial strains and disease models, representing a practical step toward the construction of clinically useful synthetic tools.

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Section: Resultsmentioning

confidence: 99%

Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface

et al. 2019

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“…Escherichia coli NGF-1 was originally isolated from BALB/c mice, has been shown to stably colonize the mouse gut, and can be engineered with standard genetic tools (28–30). Salmonella enterica serovar Typhimurium LT2 ( S. Typhimurium), an attenuated gut pathogen, was rendered further harmless by removing the pathogenicity islands SPI1 and SPI2 and thus causes no disease when administered to mice (31).…”

Section: Resultsmentioning

confidence: 99%

Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium

et al. 2019

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In nature, microbes interact antagonistically, neutrally, or beneficially. To shed light on the effects of positive interactions in microbial consortia, we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wild-type consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments, including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments. IMPORTANCE Microbial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment, and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortium function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us in deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.

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“…Earlier studies of an E. coli strain isolated from mouse fecal samples from a different facility (i.e., NGF-1) (Lasaro et al, 2014;Ziesack et al, 2018) likewise demonstrated long-term colonization (Riglar et al, 2017). However, it was not clear whether undomesticated E. coli strains could be used to study specific bacterial functions, affect the luminal environment, and shape host physiology.…”

Section: Discussionmentioning

confidence: 99%

Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes

Russell

Brown

Siguenza

et al. 2022

Cell

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Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate

Abstract: The genome of the murine commensal strain Escherichia coli NGF-1 contains a 5.03-Mbp chromosome and plasmids of 40.2 kbp and 8.56 kbp. NGF-1 efficiently colonizes the mouse gut and is genetically tractable.

Cited by 9 publications

References 12 publications

Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface

Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface

Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium

Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes

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