3.2 Pre-lab - Microbial Genomes

3.2.1 Purpose

Impress all the information that is freely available about well studied (and not so well studied) bacterial species. Start with E. coli as one of the best and longest studied before going into recently discovered bacteria (with less information).

3.2.2 Learning Objectives

  1. GenBank – Explore sequence database of all publicly available DNA sequences
  2. Sequence Browser – Observe genome organization using graphical representation
  3. Bacterial database BV-BRC - Explore bacterial genes and their function
  4. Taxonomy Browser – Identify relationships between taxa
  5. Lifemap - Tree of Live viewer to visualize relationships between taxa

3.2.3 Activity 1 – GenBank

Image test

3.2.3.1 Activity 1 - Part I

Estimated time: 5 min

3.2.3.2 Instructions

Navigate to GenBank https://www.ncbi.nlm.nih.gov/genbank and enter ‘E. coli strain K-12’ in the search bar (which should default to Nucleotide). This will give you a list of almost 300,000 E. coli sequences. Go down the list and click on the entry that corresponds to the complete genome of the substrain MG1655, which should be on page 1! Click on the selection and answer the following questions.

3.2.3.3 Questions

1. What is the size of this E. coli genome in bp and Kbp?

2. Is the E. coli genome linear or circular?

3. What is the ACCESSION number?

3.2.3.4 Activity 1 - Part II

Estimated time: 5 min

3.2.3.5 Instructions

Back in GenBank https://www.ncbi.nlm.nih.gov/genbank, under the Nucleotide search tab, instead of typing ‘E. coli strain K-12’, type in the ACCESSION number you found (NZ_CP169634).

3.2.3.6 Questions

1. How many records do you observe after an ACCESSION number entry?

2. What can you conclude about what is the ACCESSION number?

3.2.4 Activity 2 – Genomes, genes, and other databases

3.2.4.1 Activity 2 - Part I

Estimated time: 5 min

3.2.4.2 Instructions

After entering your accession number, the on the right of the page, under Related Information, click on Assembly link to explore genome assembly information.

3.2.4.3 Questions

1. How many chromosomes does E. coli have?

2. What is the genome coverage of this sequenced genome?

3. How many genes were annotated for this genome?

3.2.4.4 Activity 2 - Part II

Estimated time: 10 min

3.2.4.5 Instructions

Go back and on the top of the page and click on Graphics to explore genome browser.

  1. Hover along one of many green vertical sticks.
  • You can also zoom into a smaller and smaller genomic region for higher resolution.
  1. Hover along one of many red vertical sticks.
  • You can also zoom into a smaller and smaller genomic region for higher resolution.

3.2.4.6 Questions

1. What do the ‘green sticks’ represent?

2. What do the ‘red sticks’ represent?

3. Record 5 genes you found present in E. coli.
Gene 1
Gene 2
Gene 3
Gene 4
Gene 5

3.2.4.7 Activity 2 - Part III

Estimated time: 10 min

3.2.4.8 Instructions

To learn more about the genes of interest and their function scientists often use specialized databases. One such bacterial database is BV-BRC https://www.bv-brc.org. Use BV-BRC to find information about some of the E. coli genes. If there are 0 results then indicate No results found.

For the 3 genes below, and one gene of your choice from activity above, in the BV-BRC Search space,

  1. From a dropdown menu select “Pathways”.

  2. Type in the gene name and click enter. This will result in a lot of entries for different organisms.

  3. To retrieve information specifically for E. coli (Escherichia coli), in the Keyword space type “Escherichia”.

  4. Check one of the boxes corresponding to E. coli strains and enter below which E. coli strain (Genome Name) you selected. If no E. coli entry is present, select and record another bacterial Genome Name to learn about your gene’s function.

3.2.4.9 Questions

1. Record Genome Name associated with the following genes.
Gene ID Genome Name
Gene 1: ampC Escherichia coli 07798
Gene 2: mgtA
Gene 3: cdd
Gene 4: Your gene

2. For the 3 genes from the activity above, record gene Product.
Gene ID Gene Product
Gene 1: ampC Beta-lactamase
Gene 2:
Gene 3:

3. For the 3 genes from the activity above, record Pathway Name (relates to function).
Gene ID Pathway Name
Gene 1: ampC beta-Lactam resistance
Gene 2:
Gene 3:

Note, For some well characterized genes you can additionally obtain more detailed information about the gene/protein function.

  • To do so, from the ‘green’ menu on the right, select FEATURE option, to learn from the Special Properties section about a special property of your gene.

3.2.5 Activity 3 - Taxonomy and tree of life

Estimated time: 30 min

3.2.5.1 Activity 3 - Part I

3.2.5.2 Instructions

  1. Back in NCBI enter the E. coli accession number again. Under Related Information on the right, click on Taxonomy and then on the provided link for the E. coli.

  2. Find Lineage information. Full Lineage information contains 7 core taxonomy ranks: Kingdom, Phylum, Class, Order, Family, Genus and Species, plus any additional classification ranks. To just get the 7 core lineage names, click on Lineage link for the abbreviated Lineage, or, simply hover over lineage names.

3.2.5.3 Questions

1. Record 7 core taxonomy ranks below.
Kingdom:
Phylum:
Class:
Order:
Family:
Genus:
Species:

3.2.5.4 Activity 3 - Part II

3.2.5.5 Instructions

  1. As with the BV-BRC database above, we can use another database called Lifemap to visually explore the E. coli in the context of the tree of life. Go to https://lifemap-ncbi.univ-lyon1.fr, type E. coli and click species tab.

  2. On the tree map, the yellow tag will indicate E. coli. Use plus and minus tabs to zoom in and out and visualize E. coli relative to other organisms on the map.

3.2.5.6 Questions

1. How many Domains of life are there?.

2. Zoom into and find nodes for the E. coli Genus, Family, Order, Class and Phylum. Do they match what you found in the NCBI Taxonomy Browser for Lineage?.

3. What are some other members of the Genus (Escherichia) to which E. coli belongs?.

4. What are some other members of the Family (Enterobacteriaceae) to which E. coli belongs?.

5. What are some other members of the Order (Enterobacterales) to which E. coli belongs?.

6. What are some other members of the Class (Gammaproteobacteria) to which E. coli belongs?.

7. What are some other members of the Phylum (Pseudomonadota) to which E. coli belongs?.

3.2.6 Grading Criteria

  • Download as Microsoft Word (.docx) and upload on Canvas.

3.2.7 Footnotes

Resources

  • Google Doc

Contributions and Affiliations

  • Valeriya Gaysinskaya, Johns Hopkins University
  • Frederick Tan, Johns Hopkins University

Last Revised: June 2025

All materials CC-BY unless noted otherwise.