Complete genome sequence of the Gram-negative probiotic Escherichia coli strain Nissle 1917

doi:10.1016/j.jbiotec.2014.07.442

Journal of Biotechnology

Volume 187, 10 October 2014, Pages 106-107

https://doi.org/10.1016/j.jbiotec.2014.07.442 Get rights and content

Highlights

•
We determined the first genome sequence of a probiotic E. coli strain.
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This strain (Nissle 1917) is one of the few probiotics licensed as a medicine.
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190 ORFs are specific for this strain compared to its two closest relatives.

Abstract

Escherichia coli strain Nissle 1917 (EcN) is the active principle of a probiotic preparation (trade name Mutaflor^®) used for the treatment of patients with intestinal diseases such as ulcerative colitis and diarrhea. It has GRAS (generally recognized as save) status and has been shown to be a therapeutically effective drug (Sonnenborn and Schulze, 2009). The complete genomic DNA sequence will help in identifying genes and their products which are essential for the strains probiotic nature.

Genbank/EMBL/DDBJ accession number: CP007799 (chromosome).

Section snippets

Acknowledgement

This work was supported by the company Ardeypharm GmbH, Herdecke, Germany Fonds 824126.

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The probiotic Escherichia coli strain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens
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Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine
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There are more references available in the full text version of this article.

Cited by (63)

Metabolic engineering of the probiotic Escherichia coli Nissle 1917 for lacto-N-triose II production
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Escherichia coli Nissle 1917 (EcN) is a probiotic used to treat gastrointestinal diseases. In recent years, the development of metabolic engineering has promoted the application of EcN in synthetic biology. Lacto-N-triose II (LNT II), as an important component in breast milk, has unique benefits for infant health. This study introduces a metabolic engineering method to produce LNT II in EcN. Firstly, construct promoters with different expression intensities to optimize transcriptional regulation levels and further fine-tune plasmid copy numbers to optimize gene expression levels. The highest titer of LNT II was detected when the lgtA gene was expressed under the tac promoter and pETDuet-1 vector. Secondly, the gene editing efficiency of the EcN strain was improved by knocking out the endA gene (encoding the endonuclease I). Then, a series of engineered strains were constructed by knocking out the wecB gene and cryptic plasmid. It was found that the deletion of the wecB gene increased the titer of LNT II, but the elimination of the cryptic plasmid had no effect. Finally, we validated the production performance of the engineering strain E13 in a 3-L bioreactor with batch feeding culture. The LNT II titer reached 2040 mg/L, which was 6.6 times higher than that of shake flask cultivation and has potential for industrial application.
Next generation probiotics: Engineering live biotherapeutics
2024, Biotechnology Advances
The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, also called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.
Identification of a gene cluster for D-tagatose utilization in Escherichia coli B2 phylogroup
2022, iScience
Citation Excerpt :
In a previous comparative phenome analysis,23 we found that E. coli K-12 MG1655 did not grow using D-tagatose as the sole carbon source, whereas the probiotic EcN did. Thus, we compared the genome sequences of EcN (RefSeq: NZ_CP007799)24 and K-12 MG1655 (RefSeq: NC_000913)25 to identify the EcN-specific genomic region involved in D-tagatose catabolism. The candidate region was completely absent in K-12 and was located between accC (ECOLIN_RS18665) encoding biotin carboxylase and yhdT (ECOLIN_RS18710) encoding a conserved inner membrane protein (Figure 2A).
D-Tagatose is a promising low-calorie sugar-substituting sweetener in the food industry. Most ingested D-tagatose is fermented by intestinal microorganisms. Until now, Escherichia coli has been considered incapable of growing on D-tagatose. Here, we discovered a gene cluster involved in D-tagatose utilization in E. coli. The chromosome of the intestinal probiotic E. coli Nissle 1917 contains a six-gene cluster encoding the ABC transporter, D-tagatose kinase, D-tagatose-bisphosphate aldolase, and putative aldose 1-epimerase. The functionality of the gene cluster was experimentally validated. Based on single-gene deletions, D-tagatose dissimilation occurs via D-tagatose 6-phosphate to D-tagatose 1,6-bisphosphate to D-glyceraldehyde 3-phosphate plus dihydroxyacetone phosphate. Remarkably, this gene cluster was located in 93% of the completely sequenced genomes of the E. coli B2 phylogroup, which contains the majority of extraintestinal pathogenic and adherent-invasive E. coli strains prevalent in patients with inflammatory bowel disease. This highlights the importance of understanding the clinical significance of D-tagatose in microbiota alterations.
Material-based engineering of bacteria for cancer diagnosis and therapy
2021, Applied Materials Today
Citation Excerpt :
EcN has long been used to relieve intestinal symptoms since its first application in Germany to treat diarrhea and ulcerative colitis [165]. The complete genome of EcN was annotated in 2014 by Reister et al. and several regulatory genes of probiotics metabolism were identified [166]. Genes coding for cytolytic enzymes under inducible promoters can be engineered for increased expression and secretion into tumor niche.
Various categories of biomaterials have been utilized for drug delivery, genetic modification, photodynamic and photothermal therapies due to their distinct physicochemical properties, including photothermal convertibility, stimuli-responsiveness, and inherent capability to generate photodynamical radicals. However, successful treatments of cancer are largely hindered by the limited accessibility of nanomaterials into hypoxic or metastatic tumor tissues. Among the various tumor-targeting strategies, bacterial fabrication exhibits particular advantages such as specific hypoxia tropism, high motility, and rapid self-replication. Biomineralization, i.e. bacterial modification, involves the fabrication of bacteria by nanomaterials for precise cancer imaging as well as targeted drug delivery, overcoming the physiological barriers and improving the therapeutic efficiency. Fabrication of bacteria strains can be conducted by various methods, including direct adsorption, electrostatic interaction, covalent ligation, and surface precipitation. In this review, a brief introduction to commonly-utilized biomaterials and bacteria species is provided. A systemic overview of recent advances of bacteria fabrication strategies and techniques are then discussed, followed by future prospective of bacteria-facilitated cancer therapy and diagnostics.
Development of Escherichia coli Nissle 1917 derivative by CRISPR/Cas9 and application for gamma-aminobutyric acid (GABA) production in antibiotic-free system
2021, Biochemical Engineering Journal
Citation Excerpt :
Till now, among all E. coli strains, only EcN is non-pathogenic and functions as a probiotic. The whole genomic sequence of EcN (Accession no. CP007799) is currently available [15], and gene annotation studies indicate that 190 genes are unique and crucial [16]. Interestingly, EcN carried two highly stable cryptic plasmids of pMUT1 and pMUT2 [17].
Escherichia coli Nissle 1917 (EcN) is an endotoxin-free probiotic in the treatment of gastrointestinal diseases. However, two cryptic plasmids are stable in EcN causing metabolic burden, which limits its application in genetic engineering. In this study, two different strategies were employed to enhance the applicability of EcN. First, CRISPR/Cas9-based plasmid curing was designed with two sgRNA targeting sites for each cryptic plasmid. A plasmid-free EcN called EcNP, was successfully and efficiently constructed within one week. EcNP could overexpress sfGFP with high intensity under constitutive promoter J23100. The plasmid copy number (PCN) in EcNP corresponds to the type of replication origin of the plasmid which is in the order of pUC > pMB1 > p15A, consistent with other E. coli. Second, two stable expression vectors based on the cryptic plasmid, pMT1 and pMT2, were developed and showed a high-level expression of sfGFP and RFP, respectively. The stability of pMT1 and pMT2 were superior to other plasmids with 100 % maintenance over 8 passages for every 12 h. Finally, we demonstrated the expression of gadB gene in the stable vector pMT1, and expressed in EcNP, with 17.9 g/L of gamma-aminobutyric acid (GABA) production in an antibiotic-free system. Thus, EcNP and the plasmid pMT1 paved the way to efficiently engineer E. coli Nissle as live therapeutics.
Intein-based thermoregulated meganucleases for containment of genetic material
2024, Nucleic Acids Research

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¹: These authors contributed equally to this work.

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Journal of Biotechnology

Highlights

Abstract

Section snippets

Acknowledgement

References (20)

The probiotic Escherichia coli strain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens

FEMS Immunol. Med. Microbiol.

Probiotics: properties, examples, and specific applications

Cold Spring Harb. Perspect. Med.

Draft genome sequence of Escherichia coli strain Nissle 1917 (serovar O6:K5:H1)

Genome Announc.

Mauve: multiple alignment of conserved genomic sequence with rearrangements

Genome Res.

The probiotic Escherichia coli strain Nissle 1917 (EcN) stops acute diarrhea in infants and toddlers

Eur. J. Pediatr.

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

PLoS Comput. Biol.

CAP3: a DNA sequence assembly program

Genome Res.

Escherichia coli Nissle 1917 (Mutaflor): new insights into an old probiotic bacterium

Dig. Dis.

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Genome Biol.

Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine

Gut

Cited by (63)

Metabolic engineering of the probiotic Escherichia coli Nissle 1917 for lacto-N-triose II production

Next generation probiotics: Engineering live biotherapeutics

Identification of a gene cluster for D-tagatose utilization in Escherichia coli B2 phylogroup

Material-based engineering of bacteria for cancer diagnosis and therapy

Development of Escherichia coli Nissle 1917 derivative by CRISPR/Cas9 and application for gamma-aminobutyric acid (GABA) production in antibiotic-free system

Intein-based thermoregulated meganucleases for containment of genetic material

Short communicationComplete genome sequence of the Gram-negative probiotic Escherichia coli strain Nissle 1917

Highlights

Abstract

Section snippets

Acknowledgement

The probiotic Escherichia coli strain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens

FEMS Immunol. Med. Microbiol.

Probiotics: properties, examples, and specific applications

Cold Spring Harb. Perspect. Med.

Draft genome sequence of Escherichia coli strain Nissle 1917 (serovar O6:K5:H1)

Genome Announc.

Mauve: multiple alignment of conserved genomic sequence with rearrangements

Genome Res.

The probiotic Escherichia coli strain Nissle 1917 (EcN) stops acute diarrhea in infants and toddlers

Eur. J. Pediatr.

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

PLoS Comput. Biol.

CAP3: a DNA sequence assembly program

Genome Res.

Escherichia coli Nissle 1917 (Mutaflor): new insights into an old probiotic bacterium

Dig. Dis.

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Genome Biol.

Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine

Gut

Short communication
Complete genome sequence of the Gram-negative probiotic Escherichia coli strain Nissle 1917