Amazing Samples: Digging Up New Findings on Soil

Posted by Jaydeb Mukherjee on Jun 9, 2015 11:00:00 AM


Longitudinal studies don’t typically have strict guidelines on the types of samples to collect and analyze. In some cases, the collection may be straightforward and include samples like blood, saliva, urine, or hair. Biological samples in general are usually a given if you’re studying the long-term health of the participants.

But the more samples you collect, the more information you can reap, and if you have the processing power and storage capacity for more data, you may choose to expand your collection to a wider variety of sample types. Many studies collect a broad range of external samples for downstream analysis, including things like dust, air, or soil. After all, we aren’t like spherical chickens in a vacuum – humans (or other animals, e.g. golden retrievers) exist in an open system, constantly interacting with legion external stimuli, many of which we barely could imagine existed a mere 100 years ago.

Last time in our Amazing Samples blog series, we discussed some of the fun research on fungi. This time, let’s start showcasing some of these longitudinal wallflowers, starting with soil.

Soil-SmallSo, what’s the dirt?

No, I can’t believe I just said that, either.

But being serious, soil has long been recognized as having a relationship with human health. The basic idea that some soil is more fertile than others began with the agricultural revolution, and, despite the lack of technology to determine the components of soil, that was one of the factors behind the development of the river valley civilizations millennia ago. Additionally, many early civilizations across the world understood some principles of hygiene and the role dirt played in some sicknesses, even though little was known about how pathogens work. In fact, Hippocrates, lauded as the “Father of Western Medicine”, attributed the influence of soil on human health as a potential cause for disease.

The advent of germ theory was a huge boon to epidemiology over the past few centuries, and suddenly we could explain so many diseases as being caused by microorganisms (or viruses). However, as Einstein put it, “As our circle of knowledge expands, so does the circumference of darkness surrounding it.” Determining where diseases come from, and how exactly they make us sick, became a much more complicated subject, and rather than just settling for “some soil is bad” we suddenly realized that something hidden in the soil could cause infirmity. Things only got worse with the discovery of epigenetics; that some illnesses could be caused by any number of external stimuli modifying our genetic expression with a far more subtle hand than brute force mutation. Soil can affect us both through direct exposure and by indirectly affecting our food.

Helminthes and Other Pathogens

Most people in developed countries only rarely think about hookworms, and usually in relation to animals that spend a lot of time outdoors. According to the World Health Organization (WHO), though, helminthes like hookworms, whipworms, and roundworms affect over 880 million children alone, not to mention the cohabiting adults in those impoverished communities. In fact, the treatment and eventual eradication of soil-transmitted helminthiases has been one of WHO's larger projects, but between reliance on donations for the deworming tablets and the logistic nightmare of preventative chemotherapy on so much of the world’s soil, the progress will be slow. Even in 2013, much of the world still had a high proportion of infected children:

Image courtesy of World Health Organization

While the map shows that two years of treatment provided some benefit for certain areas of Latin America compared to the 2011 map, there is clearly still much improvement to be made.

Helminthes aren’t the only soil-borne pathogen to worry about, though – anything that causes gastrointestinal irregularity as a symptom is going to be faecally transmitted, which brings us to everyone’s favorite Escherichia coli. Certain produce recalls in the US have occurred based on E. coli contamination, due to the soil getting contaminated by the fertilizer or water. Additionally, research from the University of Minnesota 10 years ago discovered that strains of the bacteria can survive and integrate itself into soil’s microbiome, which has some interesting implications on the lasting effects of soil contamination.

And while it’s easy enough to say, “Okay, just be clean, wash your hands, and all that jazz,” things get harder when you take into account cultural acceptance of practices like…


For people that have only ever lived in suburban or urban settings, the practice of geophagia or gephagy might come as a surprise, and every once in a while the internet circulates poorly-sourced stories like this Chinese woman who eats dirt for health reasons. However, the practice is far from rare, both historically and in modern times, and practiced by many animals in addition to humans. There are various reasons why people continue the practice, ranging from tradition, to psychological comfort, to the debatable nutritive value, to experiencing a depressing pseudo-fullness during times of famine.

Unfortunately, there is a significant correlation between practice of geophagy and the occurance the afore-mentioned helminthes. Even in treating the soil, and providing deworming tablets, eradication is difficult when transmission is linked to a popular tradition with deep cultural roots.

Additionally, geophagy becomes more dangerous with increased pollutants in the soil, whether heavy metals or persistent environmental pollutants like dioxins. Compounding that problem is who tends to engage in the practice: children and pregnant women. Granted, children pretty much anywhere in the world are likely going to try a nibble of soil at some point during early childhood, out of sheer curiosity. However, the more worrisome is pregnant women, if only because any exposure they suffer is shared with their unborn children, who are extremely susceptible to epigenetic influences.

Let's move on to a more light-hearted subject regarding how soil is an amazing sample.

Diamonds are a Pandanus’ Best Friend

Kimberlite_Soil_ImageDiamonds are usually found in kimberlite pipes, spikes of soil leftover from ancient eruptions that brought material from the geological mantle up through the crust to the surface. The soil in these pipes is extremely mineral-rich, and accordingly makes delicious fertilizer for plants, but recent research has discovered a plant in northwestern Liberia that exclusively grows in kimberlite soil. Sure, not all kimberlite pipes have diamonds, but this discovery still has twofold implications: firstly, this will make diamond mining far more cost-effective and less destructive than other methods, which could help bring economic strength to the region; and secondly, being able to easily find that region’s kimberlite pipes will be a boon to geologists, who will value the information kimberlite soil could provide about the mantle conditions when the pipes formed 150 million years ago.

While soil’s role in human health has a long history, too much evidence is anecdotal, which is the fastest way to have it dismissed in legitimate scientific discussion. Regardless, there have been some important factors discovered that make soil samples a viable option to consider for any comprehensive longitudinal study, whether or not geophagia is popular in the regions studied. With substantial collaboration between biologists and geologists, who know what discoveries could lie ahead. If you're interested in learning more about why soil is an amazing sample, here is a fascinating read on The Past, Present, and Future of Soils and Human Health Studies.

Do you have challenges with standardizing sample and data collection? Do you struggle with how to save time and money when working with large amounts of data? The California Teachers Study (CTS), a prospective longitudinal study, is making use of mobile devices and cloud-based technology to dramatically cut the time and cost of managing the huge amounts of data that are the cornerstone of longitudinal studies. To learn more, download our eBook Next Generation Cohort Studies and Biobanking: How Cloud Technology is Accelerating Translational Research.


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