Archive for November, 2012

There have been some major developments in urine separation at the source. The image on the left is a urine diverting toilet. The urine is directed into a storage tank  on site and transported to fields to be spread as a fertilizer – much like how liquid animal manure is utilized. Urine contains higher concentrations of macronutrients nutrients (nitrogen, phosphate and potassium) by mass than faeces and urine is sterile from a healthy person (Höglund 2001). Treating urine and faeces separately decreases the required sterilization storage period and maintains the level of nitrogen in the urine by limiting evaporation.  There are legitimate concerns about the safety for the people handling the waste and those consuming the crops grown from the excrement. To decrease this risk some institutes are focusing on just the use of human urine as a fertilizer. A healthy person will excrete sterile urine, while the same person can still excrete potentially harmful pathogens in their faeces. Still, the use of the human urine as a fertilizer has risks due to cross-contamination from the faeces. The study by Dr. Hoglund concluded that the use of human urine as a fertilizer in temperate climates is low risk (Höglund 2001).


The following table has recommended storage periods for urine depending on the crop to be fertilizer  and temperature.



Calculations were based on statistics in Sweden where the procedure of collection, transportation, and application of urine is mechanized (Höglund 2001) and in a country with few cases of mortality from to diarrhoeal diseases.

My question is: is human urine safe to use as a fertilizer in a developing country, such as India, with higher diarrheal outbreaks?

People’s health is potentially at risk for the six stages in the process of using the urine as a fertilizer (see the figure bellow): collection, storage, transportation, application, harvest and consumption. There is a risk of accidental ingestion of urine (urine-oral pathway of transmission) during the first four stages. And there is risk of harmful pathogens present on crops during the last two stages.


For my project, I did my own rough Quantitative Microbial Risk Assessment (QMRA) to assess the risk of using human urine as fertilizer for spinach in Northern India. The QMRA is used to calculate the potential disease burden from exposure to pathogens at each stage and is based on several wide-range factors, such as the distribution and the occurrence of indicator pathogens (Howard, Pedley et al. 2006). This method is not yet widely used in developing countries due to limited available data and its complexity (Howard, Pedley et al. 2006). MatLab was used to model the QMRA and the acceptable disease burden was set to the recommend < 10-3 (Höglund, Stenstrom et al. 2002).  I don’t want bore you with all the details so below is summary of the information I used.

Pathogen excreted in urine

The urine of a healthy individual is sterile in the bladder (Höglund 2001), but from an unhealthy person microorganisms can be transmitted to the environment and potentially cause infectious diseases. There are four commonly known pathogens excreted in urine: Leptospira interrogans, Salmonella typhi, Salmonella paratyphi and Schistosoma haematobium (Feachem, Bradley et al. 1983). Leptospira is a higher risk for sewage and farm workers in developing countries and is deemed an occupational hazard (Höglund 2001). The occurrence of infection is low and urine-oral transmission is not a key route (Feachem, Bradley et al. 1983). The S. typhi and S. paratyphi are more prevalent in developing countries with 16 million reported cases per year, but the probability of urine-oral transmission is low to that of faecal-oral transmission (Feachem, Bradley et al. 1983). For Schistosoma, the eggs are excreted in the urine and are then dependent on snails to continue their life cycle; thus again urine-oral transmission is low risk.

There are other examples of pathogens being excreted in urine, such as E. Coli (cause of more than 80% of urinary tract infections), Mycobacterium tuberculosis, Mycobacterium bovis and Microsporidia (protozoa implicated in HIV-positive individuals), but there is little evidence of urine-oral transmission (Höglund 2001).  Venereal diseases caused by pathogens have in some cases been reported to be excreted in urine but their potential survival outside of the body is low (Feachem, Bradley et al. 1983).

Pathogens excreted in faeces

The pathogens from faeces are the principal concern of microbial activity when setting safety standards (WHO 2011). Examples of parasites with the ability to cause disease in humans and are transmitted in human faeces  are Campylobacter, Salmonella, Giardia, Yersinia, Shigella, Balantidum coli and helminths ( Fasciola, Fasiolopsis, Echinococcus) – the list goes on, but the typical route of transmission is food-oral and soil-oral (Höglund 2001; WHO 2011). Helminths have higher rates of infection in developing countries, causing morbidity and mortality (Höglund 2001). The viruses excreted by faeces are estimated to cause 80% of the gastrointestinal infections in humans in the United States (Höglund 2001). One of the most commonly identified viral pathogens is the rotavirus which can be transmitted in waterborne outbreaks (Höglund 2001). Their reported cases are typically underestimated as not everyone goes to the hospital each time they are sick, and the aetiological agent is also typically not known (Höglund 2001). Some diseases are zoonoses making them difficult to track and control, but also increasing the complexity of transmission to humans (Höglund 2001). It should be noted that human faeces do not always contain harmful pathogens, but for a risk assessment their presence should be assumed.

Survival of Microorganisms

After excretion, the enteric pathogens decline due to death or loss of reproductive ability (viability), but their process of life and death is complex and difficult to approximate (Höglund 2001). For urine separated at the source, the main factors affecting the pathogens survival are temperature, pH and ammonia (Höglund 2001). After a few days, the stored human urine pH rises to 9.0, creating a noxious environment for pathogens, increasing decay rate sterilizing of the urine over time (Höglund 2001). The survival of the pathogens once the urine is applied as a fertilizer is assumed to be marginal (Höglund 2001). The risk of pathogens contaminating a water source downstream was also assumed to be low risk due to the high dilution from the rain fall (Höglund 2001).

QMRA Results for use of human urine as a fertilizer for spinach in Northern India*

The disease burden will change depending on the local conditions (temperature, mortality rates, disease outbreaks, etc.) and it is impossible to have exact data for every variable, but what this roughly calculated QMRA was able to demonstrate how important the risks are when using human urine as a fertilizer in countries with greater overall risks of diseases from cross-contamination of faeces. Knowing such facts should impact how organizations promote and manage the projects.

The acceptable disease burden was set to the recommended < 10-3 (Höglund, Stenstrom et al. 2002). For the worse-case scenario (low decay rates), the disease burden for each indicator was high above the set target = not safe. For the better-case scenario (typical decay rates), the disease burden was < 10-3 except for the rotavirus, which was above the target.

Based my assumptions from literature, the QMRA demonstrates that human urine as a fertilizer for SPINACH would be a high risk in developing countries. FOR OTHER CROPS, such as rice, THE RISK WOULD BE MUCH LOWER. The high risks could be decreased with proper communication and management, personal protective equipment (PPE, such as wearing a mask while collecting the urine) and with the use of better designed models which decrease people’s interaction with the urine. 

*These results are based on the frequency of diarrhea in India and for fertilizing spinach. The risk would be very different crops used to feed animals or crops where the edible parts are higher off the ground or are cooked before consumption. If you are interested in the methodology, let me know.


Feachem, R., D. Bradley, et al. (1983). Sanitation and disease – health aspects of excreta and wastewater management. Chichester, UK, John Wiley and Sons.

Höglund, C. (2001). Evaluation of microbial health risks associated with the reuse of source-separated human urine. Department of Biotechnology. Stockholm, Royal Institute of Technology. Doctoral.

WHO (2011). Evaluating household water treatment options: Health-based targets and microbiological performance specifications. Geneva, Switzerland, World Health Organization.



Concerns such as heavy metals, pharmaceuticals and personal care products (PPCPs) and pathogens potentially contaminating our food has risen some legitimate questions about the safety of using human urine as fertilizer. The next two blogs will be focused on  summarizing the current scientific-literature on associated risked with using humane urine as a fertilizer. Today’s blogs focuses on heavy metals and pharmaceuticals and personal care products and next Monday’s will be on pathogens. The use biosolids (the sludge or remaining solids from waster water treatment plants) will be addressed in a later blog.

Heavy metals and pharmaceuticals and personal care products (PPCPs)

The use of human excrement as fertilizer is a debated subject as people are skeptical of the presences of heavy metals and organic pollutants (Tidaker, Mattsson et al. 2005). For this reason human excrement are not allowed on organic farms in Europe (Tidaker, Mattsson et al. 2005) and in Canada (Martin 2009). Heavy metals enter the body predominantly through food consumption, with some uptake through the skin and lungs, and concentrations vary greatly (Jonsson, Stintzing et al. 2004; Ronteltap, Maurer et al. 2007). Some studies claim human urine does not have hazardous chemical compounds and heavy metals (Ganrot, Dave et al. 2006). Others state that heavy metals in human urine are lower than most chemical fertilizers (Kirchmann and Pettersson 1995; Jönsson, Stenström et al. 1997; Jonsson, Stintzing et al. 2004; Ronteltap, Maurer et al. 2007). There are concerns about the accumulation of heavy metals in the soil over time (Ronteltap, Maurer et al. 2007). Sludge from waste water treatment plants will contain various other compounds from industries and runoff from storm pipes. Urine separation at the source eliminates such contamination. By manipulating the pH, metals that are present could be precipitated out of solution before application to the fields. Table 8 lists some heavy metals concentrations present in human bodies – human urine has the lowest concentrations compared to human faeces and cattle manure (Jonsson, Stintzing et al. 2004).

Table 3 – Concentration of heavy metals (copper, zinc, chromium, nickel, lead and cadmium) in urine, faeces and farmyard manure from organic cattle farms in Sweden in mg/kg wet mass (Jonsson, Stintzing et al. 2004)


Zinc Chromium Nickel Lead


Urine (mg/kg)


30 7 5 1 0
Faeces (mg/kg)


65000 122 450 122


Manure (mg/kg)

5220 26640 684 630 184


Throughout evolution mammals have been excreting in terrestrial environments and as all mammals produce hormones, vegetation and microbes are adapted to degrading the naturally produced human hormones (Jonsson, Stintzing et al. 2004). Unused pharmaceuticals’ active ingredients are excreted in the urine, average 64% from a screening assay of 212 pharmaceuticals,  and in the feces, average 35% (Jonsson, Stintzing et al. 2004; Lienert, Bürki et al. 2007). The numbers vary greatly, for example radioactive  ingredients do not degrade and 94% is excreted in the urine, while other pharmaceuticals may excrete 6% of their active ingredients through the urine (Lienert, Bürki et al. 2007). Pharmaceuticals have different biodegradation rates in soils: ibuprofen degrades to non-detectible levels in soils and plants after three months, while 53% of the original Carbamazepine present in urine was detected in soil samples three months after application (Winker, Clemens et al. 2010). Interestingly,  consumption of pharmaceuticals is concentrated in developed countries: 15% of the world’s population in rich countries consumes 90% of total medicines (WHO 2012). As developing countries consume on average per capita fewer pharmaceutical products a year (WHO 2012), human urine could be used without concern of pharmaceutical products, but should be monitored as consumption habits may change.

Overall, you can see there is still limited knowledge on how heavy metals and PPCPs present in the urine could be up-taken by plants, diffused into the hydrological system (into the groundwater and/or into the surface water as run off) and into the soils (Lienert, Bürki et al. 2007; Ronteltap, Maurer et al. 2007; Winker, Clemens et al. 2010). The mobility would be influenced by the compounds molecular weight (Winker, Clemens et al. 2010), pH and presences of organic molecules (Ronteltap, Maurer et al. 2007). There is limited published data on the potential risks of consuming plants with PPCPs. Currently there are no set thresholds as to what values of pharmaceutical should be let into the environment through fertilizer application (Ronteltap, Maurer et al. 2007).

More research is required to gain a better understanding of the risks. We have to also look at what is going into our waters as presently most waste water treatments plants are not able to effectively remove PPCPs from the effluent. So the question is: are PPCPs degraded faster on land (exposed to UV) than in our waters? Much more to come on this subject. Thanks for reading and asking hard questions!


Ganrot, Z., G. Dave, et al. (2006). “Recovery of N and P from human urine by freezing, struvite precipitation and adsorption to zeolite and active carbon.” Bioresource Technology 98: 3112-3121.

Jönsson, H., T.-A. Stenström, et al. (1997). “Source separated urine-nutrient and heavy metal content, water saving and faecal contamination.” Water science and technology 35(9): 145-152.

Jonsson, H., A. R. Stintzing, et al. (2004). Guidelines on the Use of Urine and Faeces in Crop Production. EcoSanRes Publication Series. Stockholm, Stockholm Environment Institute. Report 2004-2.

Kirchmann, H. and S. Pettersson (1995). “Human urine – Chemical composition and fertilizer use efficiency.” Fertilizer Research 40: 149-154.

Lienert, J., T. Bürki, et al. (2007). “Reducing micropollutants with source control: substance flow analysis of 212 pharmaceuticals in faeces and urine.” Water science and technology 56(5): 87-96.

Martin, H. (2009). “Introduction to Organic Farming.” Fact Sheet. Retrieved September 19 2012, from

Ronteltap, M., M. Maurer, et al. (2007). “The behaviour of pharmaceuticals and heavy metals during struvite precipitation in urine.” Water Research 41(9): 1859-1868.

Tidaker, P., B. Mattsson, et al. (2005). “Environmental impact of wheat production using human urine and mineral fertilisers – a scenario study.” Journal of Cleaner Production 15(2007): 52-62.

WHO (2012). Chapter 4. World pharmaceutical sales and consumption. The World Medicines Situation, World Health Organization.

Winker, M., J. Clemens, et al. (2010). “Ryegrass uptake of carbamazepine and ibuprofen applied by urine fertilization.” Science of The Total Environment 408(8): 1902-1908.

What is ideal?

Posted: November 5, 2012 in Uncategorized

What is an ideal poop?

This is call the Bristol Stool Chart and was developed by K. W. Heaton and S. J. Lewis at the University of Bristol to aid in assessing intestinal transit rate. This chart is used in the medical field to monitor change in intestinal function. Ideal poohs are types 3 and 4.

Have good pooh.

First published in 1997: Heaton, K W & Lewis, S J 1997, ‘Stool form scale as a useful guide to intestinal transit time’. Scandinavian Journal of Gastroenterology, vol.32, no.9, pp.920 – 924