Skip to content

Does anaerobic digestion reduce antibiotics or antibiotic resistance in manure?

September 10, 2015

Anaerobic digestion of animal manures reduces the amount of antibiotics and antibiotic resistant organisms but does not eliminate them. Research indicates that potential pathogens in manure can be reduced by more than 99% by anaerobic digestion, but the important point to note is that the level of potential pathogens likely remains above the safe level. We need to understand the primary objective of anaerobic digestion is not to sterilize the manure:

“Digesters are designed to produce methane, not inactivate pathogens.” (Borchardt et al. 2013)

“As long as anaerobic digestion has been considered an attractive method to promote a clean fuel from renewable feed stocks, such as animal manure, to develop a well-established technology, the optimization of anaerobic digestion processes requires effective operative control and possible correlation with reduction of pathogens” (Holm-Nielsen et al. 2009)

On-Farm Digestion Dramatically Reduces Potential Pathogens in Manure

On-farm anaerobic digestion reduces potential pathogens in the manure by over 90% in most cases. Wright et al. (2001) reported that fecal coliforms in manure on a farm in upstate New York decreased from 3.8 million to 3,400 CFU/g. Fecal coliform counts in digestate from two other farm digesters had reduced to just over 10,000 CFU/g. Harrison et al. (2005) reported that potential pathogen reduction was greater than 98% following anaerobic digestion in most cases, but that anaerobic digestion of dairy manure would not remove all biosecurity hazard. In Ontario, Crolla (2010) reported 70-95% pathogen reduction during anaerobic digestion on two dairy farms. For example, E. coli counts reduced from 1-6 million to approximately 30,000 CFU/100 mL. Pandey and Soupir (2011) reported that potential pathogens during anaerobic digestion of dairy manure in Iowa were destroyed in less than 4 days at thermophilic temperatures (52.5 C), but required 40 days at 37 C, and more than 60 days at 25 C.

Crolla et al. (2011) measured E.coli and Salmonella in drainage water following application of either raw or digested dairy cattle manure. They measured a log higher bacteria count following application of raw or digested manure compared with the control (no manure), but observed no differences between manure treatments.

Antibiotic Degradation

Degradation of antibiotics are enhanced through both higher temperatures and more biological activity (Masse et al. 2014). In this review of the research, they noted that with anaerobic digestion, thermophilic digestion was more likely to degrade antibiotics faster than mesophilic digestion. They concluded that:

“Generally, antibiotics are degraded during composting > anaerobic digestion > manure storage > soil” (Masse et al. 2014).

In recent research in China, seven antibiotics as well as antibiotic resistance genes were found in the effluent of anaerobic digestion of pig manure (Zhang et al. 2015).

Antibiotic Resistance

Mesophilic anaerobic digestion of dairy cattle manure resulted in lower potential pathogens in the manure, but the antimicrobial resistance persisted during the anaerobic digestion process (Resende et al. 2014). Others have found that thermophilic anaerobic digestion has dramatically reduced antimicrobial resistant organisms (Beneragama et. al. 2011). Ihara et al. (2013) reported that mesophilic anaerobic digestion of livestock manure reduced potential pathogens and antimicrobial resistance genes but a chemical oxidation process was required to reduce it further.

German researchers have found drug resistant E. coli in digested pig manure (von Salviati et al. 2015). Schauss et. al. (2014) reported the presence of ESBL-producing E. coli in output samples of six German biogas plants. They found that the numbers were 2-4 orders of magnitudes lower following mesophilic digestion, and in the same order of magnitude following thermophilic digestion. Wolters et al. (2015) found transferable antibiotic resistance in the output of 7 mesophilic anaerobic digesters. They concluded that:

“Since all plasmids conferred multiple antibiotic resistance and harbored integrons, they might contribute to the increasing problems caused by multi-resistant pathogens in clinical settings, nowadays threatening public health”


It appears that the risk of antibiotic resistance is reduced following anaerobic digestion of animal manures, and that the consensus is the the risks are not eliminated.

“The data point out the need of discussions to better address management of biodigesters and the implementation of sanitary and microbiological safe treatments of animal manures to avoid consequences to human, animal and environmental health.” (Resende et al. 2014)


Beneragama, N., M. Yusuke, T. Yamashiro, M. Iwasaki, L.S. Adekunle and K. Umetsu. 2011. The survival of cefazolin resistant bacteria in thermophilic co-digestion of dairy manure and waste milk. Journal of Agricultural Science and Technology A 1: 1181–1186.

Borchardt, M., S. Spencer, S. Borchardt, B. Larson and A. Ozkaynak. 2013. Inactivation of dairy manure borne pathogens by anaerobic digestion and bedding recovery units.

Crolla, A. 2010. Assessment of environmental impacts from on-farm manure digesters. Presentation at IEA Bioenergy Task 37. May 27, 2010.

Crolla, A., C. Kinsley, E. Pattey and A. Thiam. 2011. Environmental Impacts from Land Application of Digestate. Research Note. Ontario Rural Wastewater Center.

Harrison, J.H., D. Hancock, M. Gamroth, D. Davidson, J.L. Oaks, J. Evermann, and T. Nennich. 2005. Evaluation of the pathogen reduction from plug flow and continuous feed anaerobic digesters. Symposium – State of the Science Animal Manure and Waste Management. San Antonio, TX. Jan. 5-7.

Holm-Nielsen, J.B., T. Al Seadi and P. Oleskowicz-Popiel. 2009. The future of anaerobic digestion and biogas utilization. Bioresource Technology 100: 5478–5484

Daniel I. Massé, D.I., N. M. Cata Saady and Y. Gilbert. 2014. Potential of Biological Processes to Eliminate Antibiotics in Livestock Manure: An Overview. Animals 2014, 4, 146-163; doi:10.3390/ani4020146

Ihara, I., M. Yoshitake, K. Toyoda, M. Iwasaki and K. Umetsu. 2013. Risk reduction of antibiotic resistant bacterial by anaerobic digestion and electrochemical oxidation for manure application. Bio-Robotics, Volume # 1 | Part# 1.

Pandey, P.K. and M.L. Soupir. 2011. Escherichia coli inactivation kinetics in anaerobic digestion of dairy manure under moderate, mesophilic and thermophilic temperatures. AMB Express Volume 1.

Resende, J.A., V.L. Silva, T.L.R de Oliveira, S. de Oliveira Fortunato, J. da Costa Carneiro, M.H. Otenio and C.G.Diniz 2014. Prevalence and persistence of potentially pathogenic and antibiotic resistant bacteria during anaerobic digestion treatment of cattle manure. Bioresource Technology 153: 284–291.

Schauss, T., S.P. Glaeser, A. Gütschow, W. Dott and P. Kämpfer. 2014. Improved Detection of Extended Spectrum
Beta-Lactamase (ESBL)-Producing Escherichia coli in Input and Output Samples of German Biogas Plants by a Selective Pre-Enrichment Procedure. PLoS ONE 10(3): e0119791. doi:10.1371/journal.pone.0119791

von Salviati, C., H. Laube, B. Guerra, U. Roesler and A. Friese. 2015. Emission of ESBL/AmpC-producing Escherichia coli from pig fattening farms to surrounding areas. Veterinary Microbiology 175: 77-84.

Wolters, B., M. Kyselková, E. Krögerrecklenfort, R. Kreuzig and K. Small. 2015. Transferable antibiotic resistance plasmids from biogas plant digestates often belong to the IncP-1ε subgroup. Frontiers in Microbiology. January 21, 2015 doi: 10.3389/fmicb.2014.00765

Wright, P.E., S.F. Inglis, S.M. Stehman and J. Bonhotal. 2001. Reduction of selected pathogens in anaerobic digestion. 5th Annual NYSERDA Innovations in Agriculture Conference 1-11.

Zhang, S., J. Gu,  C. Wang,P. Wang, S. Jiao, Z. Li He and B. Han. 2015. Characterization of Antibiotics and Antibiotic Resistance Genes on an Ecological Farm System. Hindawi Publishing Corporation Journal of Chemistry Article ID 526143.



Leave a Comment

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: