- Find a research or journal article where researchers cultivate 2 or more microbial strains. What technology are they utilizing? How scalable is this approach to more than 2 strains? How do they address issues related to requiring multiple media?
- “Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean” Jaeho Song, Hyun-Myung Oh, Jang-Cheon Cho. FEMS Microbiology Letters, Volume 295, Issue 2, June 2009, Pages 141–147.
This is an interesting article from 2009, in which multiple strains of the SAR11 clade of Alphaproteobacteria were cultured in order to gain a thorough understanding of their role in the marine environment. “The successful culturing of SAR11 cells was credited to the use of a high-throughput culturing (HTC) method based on dilution-to-extinction culturing (Connon & Giovannoni, 2002), using pristine seawater as an incubation medium.” Dillution-to-extinction culturing is "diluting a microbial sample into sterilized seawater such that each well of a 96-well plate contains, on average, a single cell". Additional specifics of the protocol used: “In the current study, we applied the dilution-to-extinction culture method in the East Sea of Korea, using a conventional polystyrene plate. The inoculated multi-well plates were incubated at 10 °C for a prolonged period of up to 24 weeks. Consequently, 18 axenic cultures belonging to the SAR11 clade were isolated among 37 isolated strains. We suggest that long-term incubation at low temperatures may prove useful for the cultivation of new variants of the SAR11 clade”
- Propose a technology for culturing 2 or more strains. How might you innovate in this area given the paper you reviewed?
- A big challenge in microbial culturing is creating media that mirror very specific conditions. When culturing numerous microbial strains, it is time-inefficient and complicated to manually iterate through different media conditions. Therefore, an algorithm could be devised to generate variations of media parameters, and a technology could be created to automatically create these small differences in media. This way, many different variants could be tested with less room for error and more precise decision making.
- One of the great challenges in microbiology currently is culturing “unculturable” microbes. Propose a methodology for how you might explore this significant space of uncultured microbes.
- The best method to identify the presence of unculturable microbes in a sample is to utilize whole genome sequencing. The culturable strains will be identified, and any other DNA that is present can be attributed to unculturable strains. Single-cell sequencing is useful to eliminate repeats and reduce confusion. A technique that has been implemented is called Multiple Displacement Amplification (MDA) and can amplify the genetic material without having to culture the cell itself.Drawing from the Song paper above, “One of the reasons for this success is considered to be the application of culture conditions that mimic closely the chemical composition of aquatic environments.”