Methods for isolating bacteria
View Patent ↗The present invention relates to compositions and methods to identify novel bacteria and metabolites derived therefrom. More specifically, the invention describes a novel method to isolate bacteria producing metabolites of interest from environmental samples. Particularly, the invention discloses a method to select rare antibiotic producing bacteria. The invention can be used from any sample and allows the isolation of bacteria having e.g., pharmaceutical or agrochemical interest.
1. A method to identify or isolate from a sample a bacterium producing a pharmaceutical compound, the method comprising:
a) providing a sample comprising uncharacterized and uncultivated bacteria;
b) subjecting the sample to a repeated sequential irradiation treatment that is sufficient to reduce by at least 2 log the bacterial titer in a culture of E. coli , said treatment comprising at least 2 sequential irradiations at intervals of between 1 and 8 hours;
c) identifying or isolating a living or growing bacterium having the ability to either reassemble its genome or to resist DNA damage, from said treated sample; and
d) selecting a bacterium of step e) which produces the pharmaceutical compound.
2. The method of claim 1 , wherein the sample is an environmental sample.
3. The method of claim 1 , wherein said treatment comprises repeated irradiations selected from UV-, gamma- and/or X ray-irradiation(s), either alone or in combination.
4. The method of claim 1 , wherein the treatment comprises subjecting the sample to 2 to 5 UV treatments of between 0.5 and 400 mJ/cm 2 carried out at an interval of between 1 and 8 hours.
5. The method of claim 1 , further comprising a step of selecting a Deinococcus bacterium.
6. The method of claim 1 , wherein step b) is performed in a solid culture medium.
7. The method of claim 1 , wherein, in step c), colonies are identified or isolated.
8. The method of claim 1 , wherein steps c) and d) are performed sequentially, in any order, or simultaneously.
9. The method of claim 1 , wherein step d) comprises exposing identified or isolated bacteria of step c) to one or several indicator cells and selecting a bacterium which affects the viability, growth, metabolism, mobility, RNA expression, protein expression, protein secretion or virus production of at least one of said indicator cells.
10. The method of claim 1 , wherein the method comprises a further step of isolating or purifying said pharmaceutical compound.
11. A method of producing a pharmaceutical compound selected from an antibiotic or bacteriostatic or anti-fungal or anti-parasitic or anti-viral or anti-metabolite or chemotherapeutic agent or a cytokine-activity compound or cell growth factor, the method comprising identifying or isolating a pharmaceutical compound-producing bacterium according to the method of claim 1 and producing said pharmaceutical compound.
12. A method of producing a recombinant host cell, the method comprising identifying or isolating a bacterium according to the method of claim 1 , and cloning one or several genes from said bacterium in another host cell to produce a recombinant host cell.
13. The method of claim 1 , wherein the repeated sequential irradiation treatment comprises three UV treatments of 4 mJ/cm 2 carried out at an interval of 4 hours.
14. The method of claim 1 , wherein the pharmaceutical compound is selected from antibiotics, bacteriostatic compounds, anti-metabolite, chemotherapeutic compounds, anti-parasitic agents, anti-fungal agents, anti-viral compounds, cytokine-activity compounds or cell-growth factors.
15. The method of claim 14 , wherein said pharmaceutical compound is an antibiotic.
16. The method of claim 15 , wherein said antibiotic inhibits the growth of Staphylococcus aureus.
17. The method of claim 15 , wherein said antibiotic inhibits the growth of Candida tropicalis.
18. The method of claim 15 , wherein said antibiotic inhibits the growth of Escherichia coli.
19. The method of claim 15 , wherein said antibiotic inhibits the growth of Streptococcus pneumoniae.
20. The method of claim 15 , wherein said antibiotic inhibits the growth of Pseudomonas aeruginosa.