Last week the first real novel antibiotic since the ’90 saw the light. The authors made the discovery by diluting a soil sample in agar and casting this in a matrix with tiny holes. Next this matrix chamber (called iChip) was sealed with a semi-permeable membrane and placed back in the soil. After a month colonies were picked and after co-culturing with S. aureus the authors found the new antibiotic. The compound, teixobactin is produced by a large biosynthetic gene cluster of the previously uncharacterized bacteria Eleftheria terrae. The new antibiotic is functional against S. aureus but also against M. tuberculosis and probably a whole range of other Gram positives. Back to the culturing, with the iChip the authors claim to show the growth recovery “approaches 50%, as compared to 1% of cells from soil that will grow on a nutrient Petri dish10.”
iChip in action (Photo: Slava Epstein / Northeastern University)
It is thus encouraging to see that by reconstituting the environmental cues (by placing the iChip back in the soil) a bigger fraction of the microorganisms is able to grow. This back-to-nature approach has a parallel with in vitro culturing techniques of eukaryotic cells where supplementing with fecal calf serum is used to reintroduces as many growth stimulating cues as possible. The question remains whether the limit of this method has been hit or if the recovery rate can be even further ramped up.
Another paper published last month in Applied and Environmental Microbiology ramped up growth in a different way. The authors systematically investigated the role of autoclaving phosphate buffer together (which is currently the practice in most labs) or separately with agar. It turns out that separately autoclaving the components is a difference of day and night with regard to the amount of cells that grow on the plates. Figure 3 in the paper shows about 8*107 CFU/g of soil when phosphate and agar were not autoclaved together compared to 3*107 CFU/g of soil when they were autoclaved together. In other words a ~2.5 fold increase in colony formation. In the conclusion the authors’ even report at 50-fold increase in CFU. The reason for this difference lies in the formation of hydrogen peroxide in the agar when it is autoclaved together with the phosphate buffer. The authors include a figure that indeed shows a correlation between an increase in H2O2 and phosphate buffer.
What can be learned from these two articles? First of all that it remains very challenging to culture a large fraction of the microbes out there and second the process is, after 100 years of cell culturing, still being improved.