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Bioengineering a live biotherapeutic product from bench to business

Bacteria can be engineered to metabolize inflammation by-products for the treatment of inflammation-mediated diseases. We created a spin-off company to translate bioengineered Escherichia coli Nissle into a live therapeutic product, navigating translational, regulatory and biotech mindset challenges. Here, I provide some generalizable insights into academic entrepreneurship.

Deanna L. Gibson
Comments & Opinion02 Oct 2025
Nature Reviews Bioengineering

P: 1-3
The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation

Leah D. D’Aloisio
Mamatha Ballal
Deanna L. Gibson
ResearchOpen Access03 Aug 2025
npj Biofilms and Microbiomes

Volume: 11, P: 1-18
GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19

An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

Erola Pairo-Castineira
Konrad Rawlik
J. Kenneth Baillie
ResearchOpen Access17 May 2023
Nature

Volume: 617, P: 764-768
Prophage-mediated defence against viral attack and viral counter-defence

Characterization of ten temperate mycobacteriophages reveals at least five distinct prophage-expressed viral defence systems that interfere with infection by either closely related or unrelated lytic and temperate phages.

Rebekah M. Dedrick
Deborah Jacobs-Sera
Graham F. Hatfull
Research09 Jan 2017
Nature Microbiology

Volume: 2, P: 1-13
Mapping the human genetic architecture of COVID-19

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

Mari E. K. Niemi
Juha Karjalainen
Chloe Donohue
ResearchOpen Access08 Jul 2021
Nature

Volume: 600, P: 472-477
Whole-genome sequencing reveals host factors underlying critical COVID-19

Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

Athanasios Kousathanas
Erola Pairo-Castineira
J. Kenneth Baillie
ResearchOpen Access07 Mar 2022
Nature

Volume: 607, P: 97-103
A galactose-based auto-expression system improves T7-inducible protein production in Escherichia coli

James Bosco
Emily Gagliano
Ekaterina Voronina
ResearchOpen Access15 Mar 2025
Scientific Reports

Volume: 15, P: 1-18
DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome

The RNA helicase DDX3X has a critical role in regulating both the induction of stress granules and the activation of the NLRP3 inflammasome in cells under stress conditions.

Parimal Samir
Sannula Kesavardhana
Thirumala-Devi Kanneganti
Research11 Sept 2019
Nature

Volume: 573, P: 590-594
Fish oil supplementation reduces maternal defensive inflammation and predicts a gut bacteriome with reduced immune priming capacity in infants

Candice Quin
Deanna M. Vollman
Deanna L. Gibson
Research12 May 2020
The ISME Journal

Volume: 14, P: 2090-2104
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen
Jai Ram Rideout
J. Gregory Caporaso
Amendments and Corrections09 Aug 2019
Nature Biotechnology

Volume: 37, P: 1091
A second update on mapping the human genetic architecture of COVID-19

Masahiro Kanai
Shea J. Andrews
Matthew Solomonson
ResearchOpen Access06 Sept 2023
Nature

Volume: 621, P: E7-E26
Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2

Garry Cutting and colleagues report a genome-wide association and linkage study for loci that affect lung disease severity in cystic fibrosis. They identify two loci that influence lung function in individuals with cystic fibrosis.

Fred A Wright
Lisa J Strug
Garry R Cutting
Research22 May 2011
Nature Genetics

Volume: 43, P: 539-546
Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice

Kirsty Brown
Artem Godovannyi
Deanna L Gibson
Research14 Aug 2015
The ISME Journal

Volume: 10, P: 321-332
Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19

Erola Pairo-Castineira
Konrad Rawlik
J. Kenneth Baillie
Amendments and CorrectionsOpen Access11 Jul 2023
Nature

Volume: 619, P: E61
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen
Jai Ram Rideout
J. Gregory Caporaso
Correspondence24 Jul 2019
Nature Biotechnology

Volume: 37, P: 852-857
Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison

C. Quin
M. Estaki
D. L. Gibson
ResearchOpen Access29 May 2018
Scientific Reports

Volume: 8, P: 1-16

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Bioengineering a live biotherapeutic product from bench to business

The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation

GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19

Prophage-mediated defence against viral attack and viral counter-defence

Mapping the human genetic architecture of COVID-19

Whole-genome sequencing reveals host factors underlying critical COVID-19

A galactose-based auto-expression system improves T7-inducible protein production in Escherichia coli

DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome

Fish oil supplementation reduces maternal defensive inflammation and predicts a gut bacteriome with reduced immune priming capacity in infants

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

A second update on mapping the human genetic architecture of COVID-19

Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice

Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison

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