Recently, rate at which microorganisms are developing resistance to antibiotics is of increase. It will be very necessary to research for new antimicrobial origins.
First is sample collection; Hospitals and patient samples are the best place to start as the antibiotic resistance may be already characterized or generally guessable according to the common antibiotics used at the hospital or clinic.
Second is isolation. I recommend selection on antibiotic selection with concentrations below the MIC before restreaking onto normal effective antibiotic selection levels to verify the presence of a resistance gene.
Or you could just isolate straight onto antibiotic selection with normal antibiotic concentrations.
PCR verification of resistance genes to antibiotic of choice should also be done.
If I understand your question very well, you are asking for the best way to isolate microorganisms with good antagonistic properties. It is true that there is high rate of antibiotic resistance with a dearth of novel antibiotics discovery. To counter this, scientists are gradually turning to alternative sources. In fact, I am currently working on the isolation and characterization of bacteriocin-producing LAB from different sources in Nigeria. Using MRS agar, you can isolate LAB from diary sources, animal wastes and vegetables, and test for their bacteriocin activity on test pathogens. You can also isolate Pichia, Saccharomyces and other yeasts, and test for their myocin-producing ability. My regards
Due to high resistance to antibiotics,many efforts are done.In my group of research we are working on novel work on modification of plant proteins of legume seeds or egg yolk.We increase the methyl groups in the protein to increase its phobocity.Some papers are pblished in this respect such as:
Abdel Shafi etal.(2016).Antibacterial activity of methylated egg white proteins against pathogenic G + and G- bacteria matching antibiotics. SpringerPlus,5:983
Osman Etal (2016).Soybeag glycinin basic subunit inhibits methicillin resistant-vancomycin intermediate Staph aureus (MRSA-VISA. Intern. Journal of Applied Research in Natural Products.9(2):17-26.