Most antibiotics used in the clinic are derived from natural products made by bacteria and fungi that live in the soil. Actinomycete bacteria make around 60% of the total while all other bacteria account for 30% and all fungi only 10% of the known antibiotics. Although penicillin was the first natural product to be discovered, and is made by a fungus called Penicillium, this was quickly followed by the discovery of numerous antibiotics made by Streptomyces bacteria. These included streptomycin, which was the first effective antibiotic against tuberculosis. Streptomycin was discovered by Selman Waksman (and colleagues) who coined the term "antibiotic".
The discovery of penicillin and then streptomycin kick-started a Golden Age of antibiotic discovery and scientists collected soil from weird and wonderful locations all over the world to isolate new actinomycete bacteria and thus find new antibiotics. We know now that these were the "low hanging fruit" and by the 1980's scientists began to rediscover the same antibiotics over and over again and big pharmaceutical companies turned away from natural product discovery and tried to make synthetic antibiotics in the lab. The last natural product antibiotic to be introduced to the clinic was daptomycin, which is made by Streptomyces roseosporus and was discovered in 1987! Daptomycin is the treatment of last resort for people infected by MRSA.
15 years and billions of dollars later big Pharma eventually gave up on synthetic chemistry and focus is now returning to natural products as our best hope of developing new antibiotic treatments. New scientific advances, most importantly genome sequencing, and the discovery of actinomycetes in unusual places (including leafcutter ant nests and the marine environment) has renewed interest in natural products. It is has been estimated that there are more than 100,000 natural product antibiotics still waiting to be discovered, so now governments and industry need to invest money to allow scientists to find these compounds and develop new antibiotics for the clinic.