Candidate in the Spotlight: THU

A couple posts ago I introduced you to many of our potential candidates for sequencing. As it turns out, the organism that I will be sequencing is THU (more about the name here), an organism that was already in the pilot project stage and one that is a very strong candidate for sequencing.

 What do we look for in a candidate organism?

Since the goal of this project is to add useful genomes to the reference genome database, it is important that we choose organisms that have not been sequenced before and are relatively abundant without being too common. Genomes of organisms that are very common can be reconstructed from metagenomic samples so it is less important that we sequence their genomes. On the other hand, organisms that are very rare may not be characteristic of the built environment ecosystem at all.  Although rare organisms of the built environment will be interesting to sequence in the future, they are not our priority right now.

The case of THU

THU is from the Leucobacter clade and is a close relative of a strain known as Leucobacter chironomi MM2LB.

BLAST-generated 16s tree of THU (THU highlighted in yellow)

Leucobacter is a group within the microbacteriacae family and is characterized by the presence of 2,4-diaminobutyric acid in peptidoglycan. Leucobacter have been found in many different environments including soil, chromium-contaminated wastewater, nematodes guts, potato leaves and eggs of a midge known as Chironomidae. Some of the clade are chromium-resistant and have been found in chromium-rich environments.1

The organisms THU is most closely related to have been associated with a variety of human-related activities and built environments in the past (i.e. activated sludge and industrial wastewater). Many other organisms from Leucobacter have also been found in built environments (fuel tanks, duck barns and biogas systems)2.  However, although present in these environments, Leucobacter is generally not overly prevalent2.

Although there are no completed or permanent draft genomes in the GOLD database, we did find a draft genome for one species of Leucobacter (Leucobacter chromiiresistens), through a GoogleScholar search.3 To our knowledge no other genomes have been published for the group.

Because of Leucobacter’s association with the built environment, its level of abundance in these environments, and the lack of many published genomes, we’ve concluded that THU is a strong candidate organism.

Edit 5/14/12:

A note about naming:

“THU” is a three letter code that we originally used to designate our organisms. The first letter designates the environment from which the organisms was isolated (in this case a residential toilet), the second designates the specific organism identifier (organism “number” H from the toilet samples) and the third number designates the number of lab generations (in this case, unknown).

It is important to note that our naming system evolved as we learned what information was most relevant to our work. Many of the later isolates do not follow the same code as THU (we left off the generation number, for example, in many of the later samples because we discovered it was not important to keep track of for our purposes).

References:

1. Halpern, Malka, Shaked, Tamar, Pukall, Rudiger et al. (2009). Leucobacter chironomi sp. nov., a chromate-resistant bacterium isolated from a chironomid egg mass. International Journal of Systematic and Evolutionary Microbiology, 665–670. http://ijsb.sgmjournals.org/content/59/4/665.full#cited-by

2. http://www.sciencedirect.com/science/article/pii/S0048969706001197

3. http://scholar.google.com/scholar?q=leucobacter+genome&hl=en&btnG=Search&as_sdt=1%2C5&as_sdtp=on

Author: Hannah Holland-Moritz

Hannah Holland-Moritz is a graduate student working in Noah Fierer’s lab. She graduated from UC Davis in June 2014 with a major in Biochemistry and Molecular Biology and minor in Bioinformatics and most recently spend a gap year working in Jonathan Eisen’s lab on the microbiome of seagrasses. Interested in Evolution, Ecology, Bioinformatics and all things microbial, she plans to pursue a career in research.

2 thoughts on “Candidate in the Spotlight: THU”

  1. Thanks for the tree and good to see more detail about this bug.

    Some comments/questions

    1. What does THU stand for? Was that in the previous post? If so, it would be good to include a link to the previous post or re-explain what it stands for …

    2. It would be useful to include references to some statements like “is generally not prevalent” and “found in build environments” and to the Google Search results of the draft genome project

    Like

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