Soil, Streptomyces, and the Microbes That Changed Medicine

This week’s post is a little different from my usual entries, where I typically discuss a very specific clinical case in infectious diseases. This time, it is more of a reflection on how microorganisms have shaped medicine over the last century—and how a single family of organisms has, quite literally, changed the world.

Let me introduce the Actinomycetales, and more specifically, Streptomyces spp.

Before jumping into the microbiology, it’s worth taking a step back and looking at the historical background that frames this post. Since moving to the U.S., I’ve heard many people comment on how “dirty” New Jersey is. And I have to admit that, judging the land next to New York City alone, that impression may not be entirely unfair.

But I would argue that New Jersey soil changed medicine forever.

How? The answer lies in the history of soil bacteriology, a field that was largely studied in New Jersey.

From Germ Theory to the Ground Beneath Our Feet

By the late 1800s, microbiology was a thriving discipline. Louis Pasteur in France and Robert Koch in Germany had established the germ theory of infectious disease, and medical bacteriologists had clear objectives: identify pathogenic bacteria and bring the diseases they caused under control.

By comparison, soil bacteriology was fragmented, unfashionable, and seemed to offer little practical benefit.

That perception changed dramatically in the 20th century, when Selman Waksman made a pivotal discovery: organisms found in soil—the actinomycetes—were nature’s most prolific producers of antibiotics. One of these compounds, streptomycin, would soon prove capable of curing one of the most feared diseases of all times: tuberculosis, caused by the tubercle bacillus identified by Robert Koch in 1882.

From that moment on, actinomycetes became central players in applied microbiology—not only in the antibiotic industry, but in modern medicine itself.

What Are Actinomycetes? A Taxonomic Journey

The story of actinomycetes begins in the 19th century, when these organisms puzzled microbiologists because they did not fit neatly into existing categories.

The name Actinomyces dates back to 1877, when it was applied to a microbe responsible for “lumpy jaw” in cattle. The microbiologist Carl Otto Harz observed structures resembling fungal hyphae—long, filamentous forms—and coined the term Actinomyces, meaning “ray fungus.”

Around the same time, Armauer Hansen discovered Mycobacterium leprae, and Robert Koch described Mycobacterium tuberculosis. All of these organisms belonged to what we now recognize as the broader group of actinomycetes.

It was Ferdinand Cohn, however, who first described what we now know as Streptomyces. He noted organisms with elongated, branching cells reminiscent of fungi, though on a much smaller scale. With such diversity in morphology and clinical behavior, classification became necessary.

That task ultimately fell to Waksman, who proposed that the ability to form branching cells was the defining feature of actinomycetes. Based on the degree of branching and oxygen requirements, he and his collaborators divided them into several groups:

• Mycobacterium, which primarily grow as rod-like cells but occasionally form branches

• Actinomyces, anaerobes with branching filaments

• Nocardia, similar organisms that require oxygen

• Micromonospora, producing single spores on stalks

• And finally, Streptomyces, which form dense mats of branching hyphae that produce chains of spores

Streptomyces would become the focus of Waksman’s work—and the subject of this post.

Streptomycin and the Birth of the Antibiotic Era

The discovery of streptomycin was driven by a heuristic approach to medicine. At Rutgers University, Waksman and his team systematically screened soil organisms to find compounds capable of killing bacteria that penicillin could not—particularly gram-negative organisms and mycobacteria.

They tested bacteria, fungi, and actinomycetes by growing each candidate organism on nutrient agar and streaking pathogens at right angles. Antibiotic activity was evident when pathogen growth was inhibited by diffusible substances produced by the soil organism.

It quickly became clear that actinomycetes were extraordinarily productive.

The breakthrough came in 1943, when graduate student Albert Schatz identified an antibiotic produced by Streptomyces griseus. Not only did streptomycin kill gram-negative pathogens—it was also effective against Mycobacterium tuberculosis.

The first scientific report appeared in January 1944. Later that year, TB specialists William Feldman and Corwin Hinshaw at the Mayo Clinic demonstrated its efficacy in guinea pigs. Human trials followed rapidly, and by 1946, the U.S. National Research Council reported results from the first 1,000 TB patients treated with streptomycin.

The verdict was unmistakable: streptomycin could treat tuberculosis.

From New Jersey Soil to the World

This discovery launched a new era in antibiotic research and transformed soil bacteriology into one of the most important fields in microbiology. Streptomyces species became foundational to modern medicine.

A few notable examples include:

• Bleomycin — Streptomyces verticillus (soil, coal mine)

• Amphotericin B — S. nodosus (soil, Orinoco River, Venezuela)

• Chloramphenicol — S. venezuelae (soil and compost, Venezuela)

• Clavulanic acid — S. clavuligerus (South American soil, unknown country)

• Clindamycin / Lincomycin — S. lincolnensis (Lincoln, Nebraska)

• Daptomycin — S. roseosporus (Mount Ararat, Turkey)

• Erythromycin — S. erythraeus (soil, Philippines)

• Fosfomycin — S. fradiae (Mount Montgó, Spain)

• Ivermectin — S. avermitilis (Japanese golf course)

• Kanamycin — S. kanamyceticus (Nagano, Japan)

• Neomycin — S. fradiae and S. albogriseus (soil)

• Nystatin — S. noursei (garden soil)

• Rapamycin — S. hygroscopicus (Easter Island soil)

• Streptomycin — S. griseus (Rutgers Farm, New Jersey)

• Tetracycline — S. aureofaciens and S. rimosus (Missouri grassland)

• Vancomycin — S. orientalis (now Amycolatopsis orientalis; Borneo soil)

A Final Thought

Today, it is hard to imagine medicine without vancomycin, clindamycin, amphotericin B, tetracyclines, and so many other compounds derived from Streptomyces. In short, it is hard to imagine our daily practice without them.

So maybe the next time you go for a hike and look down at the soil beneath your feet, you’ll remember just how much it has done for all of us.

Musical Coda

Next time you start amphotericin, think of the Orinoco River quietly flowing by!