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Barrick Lab :: Research

See also: Previous Research Projects

Representative Publications

• Lariviere et al. (2023) Nature Protocols PMID: 36460809
• Leonard et al. (2020) Science PMID: 32001655
• Leonard et al. (2018) ACS Synthetic Biology PMID: 29608282

Aphids are plant pests and model systems for studying bacteria-insect symbioses. We have developed tools for engineering strains of Serratia symbiotica that colonize the aphid gut. We are now using these tools to unravel how these strains, which can be pathogenic to their hosts, are related to strains of S. symbiotica that live within insect cells, are inherited across aphid generations, and can benefit their aphid hosts. We have showed that cultured S. symbiotica strains are capable of maternal transmission within aphids, suggesting that they possess a latent capacity to evolve a long-term symbiotic relationship with their hosts. We are also exploring applications of these engineered bacteria related to pest control.

Current Researchers: Anthony VanDieren

Representative Publications

• Elston et al. (2023) PeerJ PMID: 36874963
• Elston et al. (2020) Applied and Environmental Microbiology PMID: 33277267
• Perreau et al. (2020) mBio PMID: 35012344

• Deatherage et al. (2018) Nucleic Acids Research PMID: 30137492
• Jack et al. (2015) ACS Synthetic Biology PMID:26096262
• Renda et al. (2014) Molecular Biosystems PMID:24556867

Dynamics of Microbial Genome Evolution

Accumulation of mutations in population Ara-1 of the LTEE over 20,000 generations of evolution

• Zhang et al. (2019) Nature Communications PMID: 31863068
• Deatherage et al. (2017) PNAS PMID: 28202733

• Deatherage and Barrick (2014) Methods Mol in Molecular Biology PMID:24838886
• Barrick and Lenski (2013) Nature Reviews Genetics. PMID:24166031

Evolution and Engineering of Naturally Transformable Bacteria

Insertion sequences (red) deleted in the transposon-free strain Acinetobacter baylyi ADP1-ISx

Naturally competent bacteria have expanded evolutionary potential because they can readily acquire new DNA from their environment. We are using experimental evolution of the model organism Acinetobacter baylyi ADP1 to understand how horizontally acquired genes and mobile genetic elements become domesticated after their incorporation into a new genome and the broader effects of gene acquisition on the rest of the genome. We are also studying the role of chemical specificity in determining the fate of acquired DNA as either nutrition or genetic information. These bacteria also provide an improved platform for studying microbial genome engineering due to the ease of reconstructing mutations and introducing new genes. We are investigating sources of genetic instability in ADP1 and engineering a clean genome version of this strain by deleting transposable elements and prophages. This will promote the use of ADP1 in synthetic biology by reducing rates of mutations that lead to inactivation of introduced genes. Further, we are using ADP1 as a platform to understand the limits to streamlining bacterial genomes and identifying adaptations to overcome the fitness costs of reduced genomes.

• Suárez et al. (2020) Nucleic Acids Research PMID:32232367
• Suárez et al. (2017) Applied and Environmental Microbiology PMID:28667117
• Renda et al. (2015) Journal of Bacteriology PMID:25512307

Evolution and Engineering of Bacteriophages

The rise of multiple drug resistant pathogenic bacteria has raised the question of available, robust alternatives to antibiotics for disease treatment. Our lab is exploring new techniques for modifying bacteriophages for use in phage therapy. Evolution, engineering, and expansion of bacteriophage genomes has the potential to diversify target diseases for treatment, perform diagnostics for proactive disease prevention, and improve the efficacy of existing applications. We are working to accomplish these advancements through computational simulations and non-standard amino acid integration. The introduction of non-standard amino acids into the repertoire of protein production also brings insights into evolutionary outcomes that may not be possible in existing natural environments. Learning about evolution enabled by non-standard amino acids can lead to applications beyond the scope of viruses. We collaborate with the Wilke lab to use their Pinetree software for simulating phage gene expression and evolution.

• Monk et al. (2017) ACS Synthetic Biology PMID: 27648665