Are we feeding potentially pathogenic microorganisms during curing?

Inactivating potential pathogens during composting is a two step process. The first step is the thermophilic or temperature kill process that kills most potentially pathogenic microorganisms. The second step is removal of readily available energy compounds for potentially pathogenic organisms. We are well aware that some potential pathogens survive the thermophilic stage either because they are in cooler zones in the composting material or they are able to enter a VBNC state (viable but not culturable). We normally assume that during the curing process, aerobic microbes that decompose the more resistant carbon compounds flourish and outcompete the potentially pathogenic microbes that thrive on readily available energy compounds.

Is it possible that in some of our curing processes, we may actually be feeding and culturing potentially pathogenic microbes? Can thermotolerant anaerobic microbes such Clostridia decompose cellulose and other more resistant carbon compounds and produce readily available carbon compounds to feed potential pathogenic bacteria?

Presence of Clostridia in Finished Composts

Anaerobic microorganisms such as Clostridia survive the composting process (Bohnel and Lube 2000, Jones and Martin 2003, Cornell Waste Management Institute 2004). While testing 94 marketable composts in the US, 70% of the composts contained measurable Clostridia and 20% contained > 1000 CFU/g. (Brinton et al. 2009).

If oxygen limiting conditions persist during composting and curing, Clostridia produce odorous substances that persist (acetic, butyric and valeric acids) (Partanen et al. 2010, Sundberg et al. 2013, Yu 2014).

Volatile Fatty Acid Production in Composts

Clostridia are anaerobic bacteria that decompose cellulose and other organic materials, producing short chain organic acids such as acetic and butyric acids. Butyric acid production is well known with animal feed storage (silage), where Clostridia flourish if the grass silage is not properly processed.

In a study of over 700 finished composts from throughout the US, Brinton (1998) measured > 500 ppm volatile fatty acids in 95% of the composts. Volatile fatty acids including acetic, propionic and butyric acids are excellent and easily degradable carbon sources for aerobic bacteria during the composting process.

Presence of E. coli in Finished Composts

In the study of 94 marketable composts in the US, Brinton et al. (2009) found that more than 50% of composts contained quantifiable fecal coliform bacteria, and that the fecal coliform counts were closely related to the measured E. coli. Many other research reports have discussed potential pathogen regrowth or its persistence during the composting  and curing process despite high temperatures.

Many of the potentially pathogenic organisms are known as facultative anaerobic bacteria. This means that they would prefer to use oxygen as an electron acceptor, but  are able to use other electron acceptors if oxygen is not available.

Are the Anaerobic Bacteria Feeding the Fecal coliform and E. Coli?

If our curing process occurs on large piles, where little to no oxygen is present, could Clostridia and other anaerobic bacteria continue to produce readily available carbon in the form of volatile fatty acids in anaerobic microsites, which then allow potential pathogenic microorganisms to thrive by consuming these volatile fatty acids in the presence of oxygen?

It may help understand some of the “frustration” over the “persistence” of fecal coliform during the compost process, leading some of us to suggest “false positives”.

Perhaps we need to focus on maintaining an aerobic environment to limit the ability of Clostridia and other obligate anaerobic bacteria to thrive, rather than simply focusing on keeping the temperatures high, particularly given that both Clostridia and many of the potential pathogenic organisms are thermotolerant?

In the next blog, we will address potential pathogen kill at lower temperatures during compost curing.


Bohnel, H., and K. Lube 2000. Clostridium botulinum and bio-compost. A contribution to the analysis of potential health hazards caused by bio-waste recycling. J. Vet. Med. B Infect. Dis. Vet. Public Health: 47: 785-795

Brinton, W. F. 1998. Volatile organic acids in compost: Production and Odorant Aspects. Compost Science and Utilization 6: 75-82.

Cornell Waste Management Institute. 2004. Hygienic implications of small-scale composting in New York State: Final Report of the Cold Compost Project.

Jones, P., and M. Martin. 2003. A review of the literature on the occurrence and survival of pathogens of animals and humans in green compost. WRAP (Waste and Resources Action Programme, UK.

Partanen, P., J. Hultman, L. Paulin, P Auvinend and M. Romantschuk. 2010. Bacterial diversity at different stages of the composting process. BMC Microbiology 2010 10: 94

Sundberg, C., D. Yu, I. Franke-Whittle, S. Kauppi, S. Smars, H. Insam, M. Romantshcuk and H. Jonsson. 2013. Effects of pH and microbial composition on odour in food waste composting. Waste Management 33: 204-211.

Yu, D. 2014. Microbial community profiling of biodegradable municipal solid waste treatments – aerobic composting and anaerobic digestion. PhD thesis. Faculty of Biological and Environmental Sciences, University of Helsinki, Finland.

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