Bacterial isolation and genome sequencing in the modern age

University

Goals

The goal of this project is to combine the two general topics – DNA sequencing and culturing by having undergraduates isolate, culture, and sequence the genomes of bacteria that are found in the various ecosystems under study in the Eisen lab.

Issues

The last decade has seen an explosion in the study of, and appreciation of, microbes and their functions and diversity. A major factor contributing to this explosion has been the exponential decreases in the cost of DNA sequencing. This has led in particular to a great expansion in the study of entire communities of microbes (i.e., microbiomes) via sequencing of DNA isolated directly from environmental samples. Although such sequencing-driven studies have been transformative to many areas – from agriculture or medicine to ecosystem science – they are insufficient for obtaining a full understanding of communities of microbes. There is in particular a great need for continued efforts to grow (i.e., culture) microbes from particular environments and to study those cultured microbes in controlled settings in the laboratory

Tools and Methods

Microbial colony isolation

Replicating microbial colonies in the lab

chemical grafting

DNA isolation

Genome sequencing

Correlating genomic data with environmental parameters

Designing rational models for microbiome-environment realtionships

Desired Majors

Microbiology

Biochemistry

Computer Science

Chemistry

Prep

Students interested in study of DNAs of microbial colonies and their correlation to the environment. Background and understanding of microbiology, DNA expression and quantitification, genome sequencing with softwared models.