Escherichia coli
Microbiome CRO Services

Creative Biolabs delivers end-to-end Escherichia coli microbiome solutions—strain access, engineering, mechanism-of-action studies, safety profiling, and scalable bioprocessing—so academic and biotech teams can generate decision-ready data, reduce risk, and move confidently from exploratory ideas to robust, reproducible results.

Preferred by Leading Microbiome Programs

Chosen by R&D teams that need mechanism-first analytics, standardized wet-lab workflows, and transparent project management tailored to E. coli research.

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Why Engage a Dedicated E. coli Microbiome CRO?

E. coli spans commensal, engineered, and probiotic lineages, demanding platform methods that align genetic design, fermentation performance, and host-interaction biology. An experienced partner connects these layers into coherent datasets and clear, comparable readouts.

Creative Biolabs integrates genetic stability, MoA screening, advanced epithelial/co-culture models, and scale-aware fermentation under one roof—accelerating iteration cycles while mitigating biosafety and antimicrobial resistance (AMR) concerns common to E. coli programs. Evidence generation includes siderophore/microcin-linked competitive effects and barrier-relevant outcomes.

Service Portfolio for E. coli Research

One-stop Solutions for E. coli Nissle 1917

Comprehensive support for E. coli Nissle 1917 (EcN): authenticated strain access, identity confirmation, fermentation process development, stabilization and formulation, and mechanism-aligned in vitro evaluation. Packages span feasibility to pilot scale with QC gates, enabling EcN programs to benchmark colonization-adjacent traits and microcin/siderophore-associated competitive effects with consistent, comparable data.

Probiotics Engineering and Optimization Services

Engineering for E. coli includes CRISPR/recombineering, promoter/operon tuning, vector selection, auxotrophy/safety-switch design, and chassis fitness optimization. We couple genotype to phenotype via multiplex growth and expression profiling, mapping burden, copy-number effects, and stress responses to measurable outputs that guide construct pruning and scale-up readiness across E. coli backgrounds.

Gene Integration Stability Test

For engineered E. coli, we quantify segregational and structural stability across serial passages with and without selection pressure, track copy number and expression, and screen for off-target events via WGS/targeted panels. Results pinpoint circuit fragilities, plasmid addiction needs, or integration-site effects to de-risk downstream fermentation and host-interaction experiments.

Functional and MoA Screening

We build mechanism-relevant assays for E. coli: competitive exclusion against pathobionts, siderophore/microcin-linked effects, metabolite outputs, and barrier integrity or cytokine shifts. Data packages include orthogonal readouts (e.g., CFU dynamics, TEER, reporter panels) to anchor claims in quantifiable biology and enable apples-to-apples comparisons across variants.

Host-Microbe Interaction Tests

Using epithelial monolayers (Caco-2/HT29-MTX), primary/organoid-derived intestinal models, and immune-competent co-cultures, we assess E. coli adhesion/colonization, tight junction markers, mucus interactions, and host response signatures. These models provide barrier-relevant endpoints without overfitting to a single cell line, supporting iterative design and formulation refinement.

Microbial Fermentation Services

We translate E. coli bench runs to robust fed-batch/continuous regimes by optimizing carbon feed, DO, pH, and temperature, then scale by transfer-ready criteria (e.g., kLa, oxygen uptake rate). Deliverables balance biomass/viability with expression targets and link upstream parameters to downstream stability, drying, and packaging needs.

Biological Safety Test Services

For E. coli lines, we screen virulence genes and mobile elements, evaluate prophage/lysogeny risk, and quantify endotoxin and residual DNA per harmonized test chapters. Outputs support internal risk management and communication with oversight bodies in research contexts.

Antimicrobial Susceptibility Testing

We provide MIC/MLC panels for E. coli using current CLSI methods and breakpoints, complemented by AMR-gene profiling and cross-resistance interpretation. Results contextualize selective markers and environmental exposures, informing strain stewardship and documentation for research governance.

Workflow for E. coli Services

1

Scoping & Risk Mapping

Define goals, strain background, design constraints, and biosafety/AMR considerations; align on decision thresholds and timelines.

2

Strain Access & Identity

Source or receive E. coli, authenticate, and establish seed stocks; baseline genotype/phenotype.

3

Assay Design & Pilot

Prototype stability, MoA, and host-interaction assays; confirm signal windows and QC metrics.

4

Process & Scale-Up

Optimize fermentation (feed/DO/pH), establish CPPs and sampling plans, and bridge to downstream steps.

5

Integrated Safety Panel

Run genetic element screens, endotoxin/residual-DNA tests, and prophage assessments; compile risk notes.

6

Reporting & Tech Transfer

Deliver annotated protocols, raw/processed data, and recommendations; support internal replication.

Advantages of Our E. coli CRO Services

End-to-End Integration

One coordinated program connects strain work, assay development, safety analytics, and bioprocessing for a seamless path from concept to dataset.

Flexible, Model-Agnostic Platforms

A broad menu of epithelial, co-culture, and advanced in vitro systems is configured to match goals, timelines, and budgets.

Scale-Aware Execution

Methods, controls, and sampling plans are designed to translate smoothly from bench experiments to pilot-ready processes.

Quality, Traceability, and Compliance

Standardized protocols, audited documentation, and reproducible workflows support consistent results and confident internal review.

Modular Engagement

Pick only the modules you need; transparent checkpoints keep scope, deliverables, and timelines aligned throughout the project.

Decision-Ready Reporting

Concise summaries, annotated data, and practical next-step recommendations enable faster go/no-go decisions across R&D teams.

Applications of E. coli in Modern Research

Recombinant Proteins & Hormones

Engineered E. coli supports high-yield expression of insulin analogs, somatropin, enzymes, and peptides, enabling process development, comparability studies, and mechanism assays with traceable quality controls from bench-scale screening to scalable upstream operations.

Vaccine Antigen & VLP Production

Optimized E. coli strains produce antigens and VLP components for immunogenicity models, epitope mapping, and formulation screening, accelerating design–build–test cycles and standardized analytics across bacterial and viral targets with reproducible, lot-to-lot performance.

Engineered Probiotic Chassis

Non-pathogenic E. coli, including Nissle 1917, can be engineered as living biosensors or competitive strains to study microenvironmental sensing, metabolite modulation, pathogen suppression, colonization dynamics, and barrier-relevant host responses in controlled models.

Genetics, CRISPR & Synthetic Genomes

E. coli remains the canonical chassis for genetic circuits, CRISPR tool development, codon-reduced genomes, and pathway prototyping—advancing studies of replication, gene regulation, and burden, while de-risking constructs before scale-up or formulation optimization.

Antibiotic Resistance & Small-Molecule Discovery

Pathogenic and engineered E. coli panels power high-throughput screening, susceptibility profiling, and mode-of-action studies, clarifying targets and resistance mechanisms while informing stewardship strategies and experimental design for antibacterial research programs.

Industrial Biomanufacturing & Biomaterials

Pathway-optimized E. coli converts renewable feedstocks or waste-derived intermediates into organic acids, alcohols, platform chemicals, and biopolymers, enabling carbon-flux control, stress mapping, and robustness criteria that translate from microtiter screens to pilot-scale runs.

E. coli in microbiome service (Creative Biolabs Original)

Collaborate with our experts to accelerate your E. coli research.

Case Study: Construction of a 3HB-Producing E. coli Nissle 1917 Strain

Creative Biolabs successfully engineered E. coli Nissle 1917 (EcN) to biosynthesize (R)-β-hydroxybutyrate (3HB), a key ketone body metabolite with physiological relevance. Using CRISPR/Cas9-mediated genome editing, specific genes (tB–pA–pB) were integrated into the malEK locus, while lA was deleted to optimize carbon flux toward 3HB formation. PCR and sequencing verified correct gene insertion and knockout events, and antibiotic sensitivity profiling confirmed strain stability.

This engineered EcN strain demonstrates how probiotic chassis organisms can be transformed into efficient microbial factories for value-added metabolite production, bridging synthetic biology with next-generation probiotic applications.

EcN knock-in gene identification (Creative Biolabs Original)Fig.1 Identification of gene knock-out.
EcN knock-in gene identification (Creative Biolabs Original)Fig.2 Identification of genes knock-in.
Construction of a 3HB-producing probiotic EcN strains brochure (Creative Biolabs Original)

Download the case study brochure from Creative Biolabs to see the step-by-step construction, validation data, and deliverables for a 3HB-producing E. coli Nissle 1917 chassis.

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E. coli Related Products

Below is a curated list of related research-use products to support ongoing E. coli studies

Product Name Catalog No. Target Product Overview Size Price
Escherichia coli Nissle 1917 LBSX-0522-GF116 Escherichia A probiotic strain with proven efficacy in inducing and maintaining remission of ulcerative colitis.
Escherichia coli -10^3 LBGF-0926-GF57 Escherichia coli Each instant-dissolve pellet delivers 10–100 CFU per 0.1 mL and provides 6 hours of stability after rehydration.
Escherichia coli -10^5 LBGF-0926-GF58 Escherichia coli Each instant-dissolve pellet delivers 10^3-10^4 CFU per 0.1 mL and provides 6 hours of stability after rehydration.
Escherichia coli -10^8 LBGF-0926-GF59 Escherichia coli Each instant-dissolve pellet delivers 10^6-10^7 CFU per 0.1 mL and provides 6 hours of stability after rehydration.
Escherichia coli Nissle 1917 △pMUT1△pMUT2 LBGF-0324-GF1 Escherichia Gene-modified strain with removal of two cryptic plasmids pMUT1 and pMUT2.
Escherichia coli EPEC DNA Standard LBGF-0125-GF75 Escherichia DNA Standard DNA standard for quantitative research, assay development, verification, validation, and QC.
Escherichia coli DNA Standard LBGF-0125-GF77 Escherichia DNA Standard DNA standard for quantitative research, assay development, verification, validation, and QC.
Escherichia coli ETEC DNA Standard LBGF-0125-GF79 Escherichia DNA Standard DNA standard for quantitative research, assay development, verification, validation, and QC.
Escherichia coli EIEC DNA Standard LBGF-0125-GF88 Escherichia DNA Standard DNA standard for quantitative research, assay development, verification, validation, and QC.
Escherichia coli EHEC DNA Standard LBGF-0125-GF137 Escherichia DNA Standard DNA standard for quantitative research, assay development, verification, validation, and QC.
Escherichia coli EHEC DNA Standard LBGF-0125-GF145 Escherichia DNA Standard DNA standard for quantitative research, assay development, verification, validation, and QC.
Inactivated Escherichia coli LBGF-0125-GF160 Inactivated Escherichia Escherichia coli has been inactivated.
Inactivated Escherichia coli EIEC LBGF-0125-GF161 Inactivated Escherichia Escherichia coli EIEC has been inactivated.
Inactivated Escherichia coli EAEC LBGF-0125-GF162 Inactivated Escherichia Escherichia coli EAEC has been inactivated.
Inactivated Escherichia coli ETEC LBGF-0125-GF163 Inactivated Escherichia Escherichia coli ETEC has been inactivated.
Inactivated Escherichia coli EHEC O157:H7 LBGF-0125-GF194 Inactivated Escherichia Escherichia coli EHEC O157:H7 has been inactivated.
Inactivated Escherichia coli EPEC LBGF-0125-GF210 Inactivated Escherichia Escherichia coli EPEC has been inactivated.
Inactivated Escherichia coli phage T7 LBGF-0125-GF217 Inactivated Phage Escherichia coli phage T7 has been inactivated.
Inactivated Escherichia coli bacteriophage PhiX174 LBGF-0125-GF218 Inactivated Phage Escherichia coli bacteriophage PhiX174 has been inactivated.
Inactivated Escherichia coli bacteriophage Qbeta LBGF-0125-GF219 Inactivated Phage Escherichia coli bacteriophage Qbeta has been inactivated.
Inactivated Escherichia coli bacteriophage T1 LBGF-0125-GF220 Inactivated Phage Escherichia coli bacteriophage T1 has been inactivated.
Inactivated Escherichia coli bacteriophage T4 LBGF-0125-GF221 Inactivated Phage Escherichia coli bacteriophage T4 has been inactivated.
Inactivated Escherichia coli bacteriophage MS2 LBGF-0125-GF222 Inactivated Phage Escherichia coli bacteriophage MS2 has been inactivated.

FAQs

Creative Biolabs employs CRISPR/Cas9, recombineering, and modular plasmid systems to enable precise genome editing, pathway reconstruction, and promoter tuning for E. coli strains, including Nissle 1917 and other research-relevant backgrounds.

Yes. We conduct long-term passaging, copy number tracking, expression quantification, and WGS validation to evaluate genetic and phenotypic stability of engineered E. coli constructs under diverse growth and process conditions.

We apply epithelial, immune cell, and organoid-based co-culture models to examine E. coli adhesion, colonization, and host response markers, producing quantitative datasets that reflect real biological relevance.

Clients receive authenticated E. coli strains, validated plasmid constructs, comprehensive data packages, and summarized experimental reports detailing workflow parameters, verification results, and performance metrics for reproducibility and internal review.

References

  1. Massip, Clémence, and Eric Oswald. "Siderophore-microcins in Escherichia coli: determinants of digestive colonization, the first step toward virulence." Frontiers in cellular and infection microbiology 10 (2020): 381. https://doi.org/10.3389/fcimb.2020.00381
  2. Hare, Patricia J., Hanna E. Englander, and Wendy WK Mok. "Probiotic Escherichia coli Nissle 1917 inhibits bacterial persisters that survive fluoroquinolone treatment." Journal of applied microbiology 132.6 (2022): 4020-4032. https://doi.org/10.1111/jam.15541
  3. Sonnenborn, Ulrich. "Escherichia coli strain Nissle 1917—from bench to bedside and back: history of a special Escherichia coli strain with probiotic properties." FEMS microbiology letters 363.19 (2016): fnw212. https://doi.org/10.1093/femsle/fnw212
  4. Scheel, Ryan A., et al. "Optimizing a fed-batch high-density fermentation process for medium chain-length poly (3-hydroxyalkanoates) in Escherichia coli." Frontiers in bioengineering and biotechnology 9 (2021): 618259. https://doi.org/10.3389/fbioe.2021.618259
  5. Kafle, Saroj Raj, Rhudith B. Cabulong, and Beom Soo Kim. "A novel pH-stat fed-batch strategy to boost the production of nicotinamide mononucleotide by high cell density fermentation." Chemical Engineering Science 296 (2024): 120240. https://doi.org/10.1016/j.ces.2024.120240
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