After nearly ten weeks of learning our way around the lab, collecting samples, isolating organisms and sequencing their 16s ribosomal genes we are finally at the point where we are ready to choose our first candidate organisms for whole-genome sequencing!
- Choose candidate organisms
- Prepare a DNA library for each organism for Illumina sequencing
- Sequence and analyze genomes
Although we have a couple of pilot samples for which we are already preparing libraries, most of our organisms need to be screened for admittance into the elite group of “good candidate organisms.”
So who are these potential candidates?
Where were they found?
And perhaps most relevant to our project, have they been sequenced before?
AY4-Y: Brachybacterium (Isolation site: towel)
Available genomes: One completed genome, 3 incomplete (various institutes/projects). Actinobacteria. Nearest sequenced relative is Brachybacterium faecium DSM 4810. Completed genome, GC content 72%, total size 3.6 MB.
Interesting Background Information: B. faecium found in built environments including urban aerosols, floor dust, and poultry litter.
AKU: Curtobacterium flaccumfaciens (Isolation site: carpet)
Available genomes: No completed or in progress genomes; one other member of the genus is targeted by the DOE (from DSMZ).
Interesting Background Information: Known plant pathogen.
MAU: Bacillus Pumilus (Isolation site: library table)
Available genomes: Five incomplete genomes, one finished and published.
Interesting Background Information: Soil bacterium, some strains salt tolerant, but also found in metagenomic analysis of salmon guts.
MFU: Kocuria rosea (Isolation site: library table)
Available genomes: None, other members of Kocuria are being sequenced: one is completed and published (Kocuria rhizophila), one is in a permanent draft stage (Kocuria rhizophila, P7-4), three are targeted (K. marinus, K. palustris, and K. rhizophila).
Interesting Background Information: Soil bacterium, some samples isolated from chemically polluted soil and extreme environments such as spacecraft. Also found in indoor environments and deep-sea sediments.
MBU: Bacillus Simplex (Isolation site: library book)
Available genomes: Two incomplete genomes.
Interesting Background Information: Found in close association with corn and other plants, in marine sediment, as well as in “cloud water” collected from the Puy de Dome summit in France.
MCU: Micrococcus yunnanensis (BLAST also showed Micrococcus luteus as an equally possible result) (Isolation site: library book)
Available Genomes: None, but four other micrococcus species are in the database. One is targeted, one incomplete (Micrococcus luteus), one is in a permanent draft state (Micrococcus luteus) and one completed and published (Micrococcus luteus).
Interesting Background Information: Has been isolated from coral reef bacterial communities, endophytic bacterial communities and was used in a study for the application of bacteria in cement material.
MDU: Rhodococcus erythropolis (Isolation site: martial arts mats)
Available Genomes: Two incomplete, one complete and published, one permanent draft.
Interesting Background Information: Found in soil and bioremediation filters and in a potassium mine. R.Erythropolis was also found in a study of the effects of geochemistry on cave microbial communities.
MEU: Staphylococcus cohnii (Isolation site: martial arts mats)
Available Genomes: None, but many, many other Staphylococcus species are incomplete, targeted or published.
Interesting Background Information: Found in alkaline groundwater, marine samples, animal isolates and dairy products.
Pilot Samples in Library Prep
THU: Leucobacter (Isolation site: toilet):
Available Genomes: One completed genome, no In Progress or Targeted projects. Nearest sequenced relative is Leucobacter chromiiresistens. Draft genome, 29 scaffolds, GC content: 64%, total size 3.3 MB.
Interesting Background Information: Leucobacter species have been isolated from numerous outdoor and built environments (e.g. wastewater and barns). Actinobacteria. L. chromiiresistens is highly resistent to chromium.
TEU: Morganella morganii (Isolation site: toilet)
Availalbe Genomes: No completed or in progress genomes. Three targeted projects as part of the Human Microbiome Project.
Interesting Background Information: Gammaproteobacteria. BL2 pathogen (nosocomial in immune-compromised patients). Found in both the environment and as human-associated.
Perhaps the most interesting thing about all these organisms is their diversity. We collect samples from the environments we live in and interact with every day, it’s truly amazing the mixture of organisms that is literally right under our fingertips just waiting to be explored. We will take our next steps towards this exploration soon, we are hoping to choose and begin compiling libraries for our first set of candidate organisms within the next two weeks.