Ibrahim Al'Abri

Works (8)

Updated: August 30th, 2025 05:03

2025 article

Inducible genome-wide mutagenesis for improvement of pDNA production by E. coli

Li, Z., Sun, G., Al’Abri, I., Zhou, Y., & Crook, N. (2025, August 13). Microbial Cell Factories, Vol. 24.

By: Z. Li n, G. Sun n, I. Al’Abri n, Y. Zhou  n & N. Crook* 

author keywords: Plasmid DNA; <italic>Escherichia coli</italic>; Strain engineering; Genome mutagenesis
topics (OpenAlex): Bacteriophages and microbial interactions; CRISPR and Genetic Engineering; Bacterial Genetics and Biotechnology
Sources: Web Of Science, NC State University Libraries
Added: August 25, 2025

2023 article

Improving therapeutic protein secretion in the probiotic yeast Saccharomyces boulardii using a multifactorial engineering approach

Durmusoglu, D., Al’Abri, I., Li, Z., Williams, T. I., Collins, L. B., Martínez, J. L., & Crook, N. (2023, June 7). Microbial Cell Factories, Vol. 22.

By: D. Durmusoglu n, I. Al’Abri n, Z. Li n, T. Williams n , L. Collins n , J. Martínez *, N. Crook n 

Contributors: D. Durmusoglu n, I. Al’Abri n, Z. Li n, T. Williams n , L. Collins n , J. Martínez *, N. Crook n 

MeSH headings : Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces boulardii / genetics; Saccharomyces boulardii / metabolism; Saccharomyces / genetics; Saccharomyces / metabolism; Probiotics / metabolism; Endopeptidases / metabolism
topics (OpenAlex): Fungal and yeast genetics research; Bacterial Genetics and Biotechnology; Microbial Inactivation Methods; Transgenic Plants and Applications; Microbial Metabolic Engineering and Bioproduction
TL;DR: A quadruple protease-deficient Sb strain is constructed that produces 5045 mg/L secretory NPA, an improvement of tenfold over wild-type Sb and highlights the ability of proteomics to highlight under-explored mediators of this process. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: June 19, 2023

2022 article

A Novel Method of Inducible Directed Evolution to Evolve Complex Phenotypes

Al'Abri, I., Li, Z., Haller, D., & Crook, N. (2022, January 1). BIO-PROTOCOL, Vol. 12.

By: I. Al'Abri n, Z. Li n, D. Haller n & N. Crook n 

author keywords: Directed Evolution; Inducible Systems; Complex Phenotypes; Pathways; Gene Clusters; P1 Phage; Mutagenesis
topics (OpenAlex): Genomics and Phylogenetic Studies; CRISPR and Genetic Engineering; Bacteriophages and microbial interactions
TL;DR: A new directed evolution method (Inducible Directed Evolution, IDE) is developed that combines the specificity and throughput of recent continuous directed evolution methods with the ease of ALE, which enables long DNA sequences to be mutated in a high throughput manner via a simple series of incubation steps. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: June 12, 2023

2022 article

Carotenoids and Their Health Benefits as Derived via Their Interactions with Gut Microbiota

Eroglu, A., Al’Abri, I. S., Kopec, R. E., Crook, N., & Bohn, T. (2022, December 16). Advances in Nutrition, Vol. 14, pp. 238–255.

By: A. Eroglu n , I. Al’Abri n, R. Kopec *, N. Crook n  & T. Bohn *

author keywords: Carotenes; xanthophylls; digestion; carotenoid metabolites; gut bacteria; microbiome; mucosal layer; inflammation; oxidative stress; bactericidal effects; Bifidobacterium spp; Akkermansia spp
MeSH headings : Humans; Carotenoids / pharmacology; Carotenoids / metabolism; Gastrointestinal Microbiome; Colon / metabolism; Prebiotics; Dietary Supplements
topics (OpenAlex): Antioxidant Activity and Oxidative Stress; Biochemical Analysis and Sensing Techniques; Nutritional Studies and Diet
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3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 11, 2023

2022 article

Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts

Jensen, E. D., Deichmann, M., Ma, X., Vilandt, R. U., Schiesaro, G., Rojek, M. B., … Jensen, M. K. (2022, October 19). Nature Communications, Vol. 10.

By: E. Jensen *, M. Deichmann *, X. Ma *, R. Vilandt*, G. Schiesaro *, M. Rojek*, B. Lengger *, L. Eliasson* ...

MeSH headings : Saccharomyces cerevisiae / metabolism; Reproduction / genetics; Receptors, G-Protein-Coupled / metabolism; Pheromones / metabolism; Receptors, Cell Surface / metabolism; Cell Differentiation; Cell Communication; Probiotics; Ligands
topics (OpenAlex): Fungal and yeast genetics research; Plant Reproductive Biology; Yeasts and Rust Fungi Studies
TL;DR: This work reports transcriptome profiles following mating pathway activation in native and hGPCR-signaling yeast, and uses a model-guided approach to correlate gene expression to morphological changes, and devise a ligand-free screening strategy for hGpcR compatibility with the yeast mating pathway and enable hG PCR-Signaling in the probiotic yeast Saccharomyces boulardii. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: October 31, 2022

2022 article

Inducible directed evolution of complex phenotypes in bacteria

Al’Abri, I. S., Haller, D. J., Li, Z., & Crook, N. (2022, February 1). Nucleic Acids Research, Vol. 2.

By: I. Al’Abri n, D. Haller n, Z. Li n & N. Crook n 

MeSH headings : Bacteria / genetics; Bacteria / metabolism; Bacteria / virology; Bacteriophages / genetics; Directed Molecular Evolution / methods; Mutagenesis; Phenotype; Plasmids / genetics
topics (OpenAlex): CRISPR and Genetic Engineering; Bacteriophages and microbial interactions; Polyamine Metabolism and Applications
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: February 13, 2022

2021 article

In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii

Durmusoglu, D., Al’Abri, I. S., Collins, S. P., Cheng, J., Eroglu, A., Beisel, C. L., & Crook, N. (2021, April 12). ACS Synthetic Biology, Vol. 10, pp. 1039–1052.

By: D. Durmusoglu n, I. Al’Abri n, S. Collins n, J. Cheng n, A. Eroglu n , C. Beisel n, N. Crook n 

author keywords: Saccharomyces boulardii; probiotic engineering; metabolic engineering; colonization profile; in situ production; beta-carotene
MeSH headings : Animals; Antineoplastic Agents / metabolism; CRISPR-Cas Systems; Feces / chemistry; Female; Gastrointestinal Microbiome; Gastrointestinal Tract / metabolism; Gastrointestinal Tract / microbiology; Gene Editing / methods; Gene Expression; Indoles / metabolism; Male; Metabolic Engineering / methods; Mice; Mice, Inbred C57BL; Microorganisms, Genetically-Modified; Multigene Family; Plasmids / genetics; Probiotics / metabolism; Promoter Regions, Genetic; Provitamins / biosynthesis; Saccharomyces boulardii / genetics; Saccharomyces boulardii / metabolism; Saccharomyces cerevisiae / genetics; beta Carotene / biosynthesis
topics (OpenAlex): Microbial Metabolism and Applications; Probiotics and Fermented Foods; CRISPR and Genetic Engineering
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 6, 2021

2021 article

What E. coli knows about your 1-year-old infant: Antibiotic use, lifestyle, birth mode, and siblings

Al’Abri, I. S., Durmusoglu, D., & Crook, N. (2021, June 1). Cell Host & Microbe, Vol. 6.

By: I. Al’Abri n, D. Durmusoglu n & N. Crook n 

MeSH headings : Anti-Bacterial Agents / pharmacology; Asthma; Child; Environmental Exposure; Escherichia coli; Gastrointestinal Microbiome; Humans; Infant; Life Style; Siblings
topics (OpenAlex): Pharmaceutical studies and practices; Neuroendocrine regulation and behavior; Antibiotic Use and Resistance
TL;DR: The causes, spread, and dynamics of ARGs and their relationship with asthma-associated microbiota in Danish children are studied and the relationship between asthma and the gut microbiota is studied. (via Semantic Scholar)
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11. Sustainable Cities and Communities (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: June 28, 2021

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