Research

Founded in 2019, the Becket Lab studies the spread of antibiotic resistance in coastal microbiomes. Blending microbial genomics and ecology, the lab examines the effects of anthropogenic input and stormwater on the spread of antibiotic resistance genes along the southern California coast.

The lab is located within California State University San Marcos, a primarily undergraduate institution. Therefore, the sample isolation, processing, next-generation sequencing, and bioinformatics pipelines are all performed by outstanding CSUSM undergraduate students.

Ongoing Projects

Effects of rainstorm runoff on coastal microbial communities and antibiotic resistomes

Rainstorm runoff results in the flushing of urban and agricultural buildup into our coastal ecosystems, resulting in the known "72-hour rule" where fecal indicator bacterial counts are high in coastal waters for three days following rainstorms. In addition to bacteria, antibiotic waste and antibiotic resistance genes are also part of these runoffs. Through a combination of chromatin capture assays and next-generation sequencing approaches, the Becket lab seeks to quantify the changes to coastal microbiome and resistome profiles year-round and surrounding rainstorms.

Effects of antibiotic exposure and climate change conditions on horizontal gene transfer in coastal microbiomes

Microbial antibiotic resistance (AR) is easily spread between microbial community members, as genes that encode antibiotic resistance can be transferred between microbes through horizontal gene transfer (HGT). Exposure to antibiotics has been shown to induce the exchange of genetic material through HGT. Coastal environments are particularly at risk, as anthropogenic inputs such as sewage, aquaculture/agricultural contaminants, and climate change conditions can influence the spread of antibiotic resistance genes. Thus, we seek to explore the mobility of the AR genes in coastal microbial populations in response to common antibiotics seen in agricultural and urban waste through a combination of enrichment assays and genomic approaches. Becket lab undergraduates are trained in start-to-finish next-generation sequencing assays and are performing all parts of the workflow.

NIH R15 project summary towards these goals: https://reporter.nih.gov/project-details/10203465

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