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Beneficial Soil Microbes: The Potential for New Antibiotic and Anticancer Agents

Updated on April 20, 2015

Copyright 2012 - Kris Heeter

Soil is believed to contain the most diverse population of bacteria of any ecosystem on earth. With the large diversity of soil types out there, the number of unique microbial niches is vast. Most soil microbe populations have never been studied.

With recent advances in DNA sequencing and molecular techniques, scientists can now start to study this rich diversity more.

New populations are being discovered and the underground world of microbes is proving to hold a previously unforeseen potential value to medical research.


How many species of bacteria are found in soil?

It has been estimated that of the number of species of bacteria per gram of soil could vary anywhere between 2,000 and 8.3 million.

To put it in a visual perspective: 1 gram is roughly equal to 1 small paper clip or pen cap.

That’s 2,000 to 8.3 million species living in the space of a paper clip or pen cap!

Up until recently, determining the number of microbial species in a soil sample was literally impossible and scientists could only provide estimates. Advances in DNA sequencing techniques is now allowing scientists to test these estimates.

The number of unique species may not be in the millions per gram of soil (the work is still very preliminary and the jury is still out) but the numbers coming out of recent studies are still pretty astounding. Try up to 52,000 on for size!


Related References

Society for General Microbiology. (2012). "Harmless soil-dwelling bacteria successfully kill cancer." ScienceDaily, 4 Sep. 2011.

Reddy et al. (2012)Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes.” Applied and Environmental Microbiology 78: 3744.

Gans et al. (2005). “Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil” Science Vol 309 1387-1390

Roesch et al. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. The ISME Journal (2007) 1, 283–290

Getting the good dirt for medical advances

In 2011, scientists found that the spores of the soil bacterium Clostridium was a promising cancer-fighting microbe. This bacterium was found to have the ability to grow within tumors and can be genetically engineered to activate a cancer drug.

In the laboratory, Clostridium has been shown to work in tumor cells because its spores will only grow within solid tumors that are oxygen deprived, (e.g., breast, brain and prostate tumors). Healthy tissues and cells are not affected by the bacterium because Clostridium cannot proliferate in these oxygen rich environments. Reports suggest this new advancement could be tested in cancer patients as early as 2013.

These results have opened the door to the notion that other bacteria in the soil may hold similar potential in medical advancements.

But how does one find a good needle (microbe) in the haystack (soil)?

While millions and probably billions of bacterial species live in the soil, they are difficult and often impossible to culture in a laboratory setting. Up until recently that has made exploring and classifying these microbes difficult. More modern DNA sequencing advances and molecular technology is allowing scientists to identify and study soil microbes at a level never before possible.

In an recent study, researchers from the Howard Hughes Medical Institute (HHMI) at Rockefeller University were able to directly extract DNA from soil microbes, amplify it and study it at a molecular level. Using this approach, this research team was able to create “libraries” of microbial DNA sequences which are now being tested for the potential to encode drug-like molecules, antibiotics and cancer-fighting molecules.

Discovering New Species

Scientists estimate that there are millions of new species (microbial, plant and animal) waiting to be be identified.

Each year, the number of new species identified are tabulated - the number discovered each year might surprise you - take a guess at:

How Many New Species Have Been Discovered in One Year?

Some marine biologist have speculated that up to 20 million new marine microbial species may still be waiting to be discovered.

The number of soil microbes waiting to be discovered is most likely in the millions as well!

Future of soil microbial studies in medical and cancer research

In the HHMI study mentioned above, soils from three similar ecological terrains in the U.S. Southwest were examined. While from an environmental standpoint, the areas are similar they are geographically distinct. Surprisingly each location has a very different microbial population. These findings suggest that soil microbial populations are far more diverse than originally thought.

This large diversity means that there is a greater possibility other microbes are out there that may prove useful in disease-fighting compounds.

Undoubtedly, identifying genetic material from newly identified soil bacteria for possible medical therapeutic reagents will continue and prove to be very interesting.


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    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @girishpuri - you've made a very interesting point. At the Genus level, yes, but from a species or at the even more variant level they are different (variations within a species).

      Clostridium is a good example - the species of Clostridium that is common in human gut flora is different than the species of Clostridium commonly found in soil. Just like some variants of E.coli can be deadly when ingested while other variants of E. coli happily live in humans. It all boils down to the genetic differences among species and variants within species!

    • girishpuri profile image

      Girish puri 5 years ago from NCR , INDIA

      This is very interesting that majority of these microbes , you mentioned are also useful for gut flora, in't it strange ?, useful share. thanks

    • RTalloni profile image

      RTalloni 5 years ago from the short journey

      We live in amazing times! So interesting--my husband thought so too.

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @bravewarrior - that's a great set of questions!

      I'm purely speculating here as this is not my focused field of study but from a biologist's broad perspective, I would hypothesize that the current damage we are doing to the soil through chemicals, etc., is definitely altering the microbial fauna. Perhaps killing off some species but also forcing the evolution and mutation of other species so that the species can survive in the damaged environment.

      Microbes can be pretty resilient and capable of adapting under selective pressure. The super strep strains are great examples. Microbes can still be found in some of the most harshest environments.

    • bravewarrior profile image

      Shauna L Bowling 5 years ago from Central Florida

      Kris, this is very interesting and promising. But I have to wonder, how is the damage we are doing to our earth affecting these microbes? What will we ingest if the proposed panaceas use matter from the earth as it is today? Will or can it bring on an onslaught of other maladies?

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @Sally's Trove - thanks for stopping by and adding to the discussion. I've heard that saying too or some version of it and always thought "yuck", but this all makes it seem perhaps not so bad!

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @SilverGenes - thanks for stopping by. I agree, it's pretty amazing what is being discovered these days. Makes you wonder what else is on the horizon waiting to be explored and discovered!

    • Sally's Trove profile image

      Sherri 5 years ago from Southeastern Pennsylvania

      My mother always said kids should eat a little's good for them. Nice how science is corroborating what folklore has told us forever. Very interesting article!

    • profile image

      SilverGenes 5 years ago

      Excellent article! And as Melis mentioned, it becomes even more important to clean up our act when it comes to farm chemicals. It's amazing what is being discovered and explored now.

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @Melis- yes, I agree! Soil becomes "dead" the more it is treated with chemicals.

      The use of chemicals can destroy beneficial bacteria - bacteria that is needed for the plant root systems, bacteria that is needed to help decompose organic matter (a process that returns nutrients to the soil), and bacteria that could hold promising medical breakthroughs.

    • Melis Ann profile image

      Melis Ann 5 years ago from Mom On A Health Hunt

      I'm sure just as there is beneficial bacteria to be discovered the opposite danger exists as we treat soil with chemicals. Thanks for SHARING this new perspective!

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @Angela - thanks for your question. This won't address the issue of top soil disappearing. I believe top soil can disappear by runnoff or depletion of nutrients.

      But the more microbes and organic material there is for the microbes to feed off of (and less chemicals), the healthier soil becomes.

    • Angela Brummer profile image

      Angela Brummer 5 years ago from Lincoln, Nebraska

      With this help with topsoil disappearing?

    • Brett.Tesol profile image

      Brett Caulton 5 years ago from Thailand

      Very interesting ... a cure for cancer would be a fantastic breakthrough, as sooooo many suffer from it nowadays.

      Shared, up and interesting.

    • Mhatter99 profile image

      Martin Kloess 5 years ago from San Francisco

      Thank you for this eye opening report

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @thebiologyofleah - I agree, it will be interesting to see how that research goes and if Clostridium will make it to and through clinical trials!

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @m0rd0r - thanks for that tip! I had not heard that before but that does make sense!

    • thebiologyofleah profile image

      thebiologyofleah 5 years ago from Massachusetts

      Great hub, another example of how bacteria is critical to the pharmaceutical world. It will be interesting to see how the work on Clostridium in cancer treatment goes.

    • m0rd0r profile image

      Stoill Barzakov 5 years ago from Sofia, Bulgaria

      The best way to know they are in the soil is by shoving your hands inside and pulling a handgful.

      If it smells like a mushroom - the germs are there.

      If it smells like feces - it is not.

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @kellyward - thanks for stopping by and sharing:)

    • profile image

      kelleyward 5 years ago

      What a useful Hub Kris! Thanks for sharing this one! Voted up and Shared. Take care, Kelley

    • Kris Heeter profile image

      Kris Heeter 5 years ago from Indiana

      @Shea - thanks for stopping by, I'm glad you found this interesting!

    • shea duane profile image

      shea duane 5 years ago from new jersey

      Really interesting information... as always. Another great hub.