Bacterial isolation and genome sequencing in the modern age

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 Involved or Addressed

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

Methods and Technologies

  • 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

Academic Majors of Interest

  • Microbiology
  • Biochemistry
  • Computer Science
  • Chemistry

Preferred Interests and Preparation

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.

Team Advisors

Sponsor(s)

NSF