Ecological Metagenomics

Ecological Metagenomics was a course that Dr. Dinsdale developed in 2010, which leveraged two new areas of science: metagenomics, which is the analysis of multiple genomes collected from a community of microbes; and next-generation DNA sequencing, which enables the sequencing of DNA rapidly and reliably. Undergraduate students in the class have sequenced samples from the California coastline, including the kelp forest environment, and rocky shores. To continue the integrative theme, students obtain the microbial samples and thus obtain experience of field research. The students have sequenced a range of microbial communities, including individual microbes cultured from inside the kelp fronds, the community of microbes from the seawater surrounding the kelp forest and the genome from the sea lion, an organism that hunts in the kelp forest. They sequenced the genome of the California sea lion in 2010 and have conducted various analyses on the genome (Edwards et. al., 2013). The variety of organisms allowed students to investigate a range of topics, from evolution, microbiology, genetics and the interaction of microbial communities to the health of ecosystems. Dr. Dinsdale was awarded a NSF Training Undergraduate Engineering and Sciences (TUES) grant for this.

Students use the latest technology. Conducting a successful sequencing run using these instruments is not a trivial task. Dr. Dinsdale started the course using then state-of-the-art 454 pyrosequencing, and have since updated the class to enable the students to use the rapidly developing sequencing technologies, including Ion Torrent, Illumina, and Nanopore. The processes are all different, and therefore students learn about the advantages and disadvantages of each sequencer and how to annotate the various sets of data.
Once sequenced the students use a range of bioinformatic tools. First they check the quality of the sequeces using FastQC or Prinseq. Second they annotate the sequences using Kracken, MG-RAST and discuss the benefits or drawbacks of each tool. On some occasions the students assemble the sequences using SPAdes and compare the resulting sequences with NCBI. Several of the students have annotated the mitochondria of the host species. From the annotated sequences, the students compare and contrast the taxonomy and functions of each of the metagenomes and graph the data in excel and conduct statistics in STAMP.

Assessments have shown that students have gained important scientific skills and many have received jobs in the biotechnology industry.

Research questions: Tide pool microbiomes


The first class in 2010.