SciChat is an outreach initiative started by the graduate students in the Department of Immunology that focuses on providing comprehensive science education to adults. This recurring segment focuses on answering seemingly trivial questions. In the most recent talk entitled, “Hygiene Hypothesis: Is eating dirt good for your immune system?”, a question arose from an audience member: What is found in dirt?


Aside from minerals and plants, dirt or soil constitutes a plethora of various macro- (mites, nematodes, arthropods, earthworms) and micro-organisms (bacteria, viruses, fungi, protozoa). The majority of these are microbes and a single gram of soil can contain over 10 billion bacterial cells and approximately 2,000 different species. Bacteria in the soil can be divided into gram-positive species, Proteobacteria, or those belonging to Cytophaga/Flavobacteria/Bacteroides group. Among these, one can find plant pathogens such as Phytophthora cinnamon, a cause of root rot in many fruit-bearing and non-fruit bearing trees. Some bacteria are important components of a plant’s microbiome, and are found associated with plant root systems. Nitrogen-fixing Rhizobia, for example, release mediators to suppress the plant immune system to promote symbiosis. Other microbes such as Pseudomonas, Burkholderia, Bacillus spp., Serratia and fungal Trichoderma or Penicillium all act to suppress growth of plant pathogens.

Some soil bacterial species could benefit humans, or at least for now, mice. A few years ago, a report came out attributing some mood-boosting qualities to Mycobacterium vaccae. In mice infected with this bacterium, the activated peripheral immune system turned on serotonergic pathways in the brain and resulted in a decrease in stress-related behavior. Perhaps eating dirt can be a much cheaper alternative to Prozac. Soil also contains some human and animal bacterial commensals and pathogens, which gain access to the soil through wastewater, manure and fertilizers. For example, a known human gut commensal Bacillus subtilis is quite abundant in the soil.

Interestingly, in many environments around the world, anti-bacterial viruses, or bacteriophages, outnumber bacteria 10 to 1, arguably making them the most numerous soil residents. Over the years, soil phages have garnered attention for two reasons: First, they could potentially be used as alternative antimicrobial treatments in humans, and this is now being tested in clinical trials. Secondly, bacteriophages can act as donors of genes encoding for Shiga toxins, a class of proteins that causes severe diarrhea and even kidney failure in some cases.

Clearly, the question of “What is found in dirt?” is more complex, exciting and potentially dangerous than imagined.



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S. T. Abedon. “Communication Among Phages, Bacteria, and Soil Environments”  from Biocommunication in Soil Microorganisms, Soil Biology 23,  G. Witzany (ed), Springer-Verlag Berlin Heidelberg (2011): 37-65

R. Armon.  “Soil Bacteria and Bacteriophages” from Biocommunication in Soil Microorganisms, Soil Biology 23,  G. Witzany (ed), Springer-Verlag Berlin Heidelberg (2011): 67-112

P.-A. Maron et al. “Soil microbial diversity: Methodological strategy, spatial overview and functional interest”.  C. R. Biologies (2011) 334: 403–411

C. Zamioudis and C. M. J. Pieterse. “Modulation of Host Immunity by Beneficial Microbes”.  MPMI (2012) 25: 139–150

K. J. Forsberg et al. “The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens”. Science (2012) 337: 1107

S. C. Van Wees et al.  “Plant immune responses triggered by beneficial microbes”.  Curr. Opin. Plant Biol. (2008): 443

M. Turner. “Phage on the rampage.  Antibiotic use may have driven the development of Europe’s deadly E. coli”.  Nature News June 9th, 2011

P. Garbeva et al. “Microbial diversity in the soil: selection of microbial populations by plant and soil type and implications for disease supressiveness”.  Annual Review of Phytopathology (2004) 42: 243-270

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Patrycja Thompson

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