Swabs to Genomes: Week 8 (Genome Annotation and pathways)

(this blog post was written by group #4 as a writing assignment)

Our goal for this week’s lesson was to double check that the genome we sequenced is, in fact, the organism we are interested in. After uploading our sequences up to RAST last week, we found out the results and were able to look at the genome of our bacteria as a whole. We could explore the functions many of their genes had and what pathways those genes were related to. Using the RAST server we were also able to compare functional genes that were shared between different species. This means we were able to compare our bugs (which were mostly Vibrio sp) with similar bugs such as Vibrio cholera. This was especially interesting for our group as cholera is very prominent in place where clean water is scarce.

To verify our organisms we found the full-length 16S sequence from the assembly in RAST, we made sure the length of the sequence was long enough (at least 1000bp) to identify the bacteria, and used BLAST to verify the sequences. Next, we used RAST to explore the various features of our bacteria like metabolism, virulence, stress response, and motility just to name a few. Once an interesting gene or pathway of the bacteria was found, we were able to compare those with characteristics in relation to other species. Once we explored the genome for a bit we came up with mock experiments that we thought would be exciting to perform with the bacteria we had found! Here, we were given an opportunity to choose one of the characteristics of our bacteria, make a hypothesis, and design an experiment that we could use to test the hypothesis in the wet lab.

As the class is coming to an end, (only 2 weeks left!) we began working on our Genome Announcements to get ready for our big reveal! We were each told to work over the weekend and come up with a genome announcement as to what our bacterial species could be and in the following week, we will try to come up with a consensus genome announcement as a class. So stay tuned!

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David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter