Analyses of Microbial Populations and Antibiotic Resistance Present in Stored Swine Manure from Underground Storage Pits


Why Study Antibiotic Resistance in Manure?

Antimicrobial compounds have been commonly used as feed additives for domestic animals to reduce infection and promote growth. Recent concerns have suggested such feeding practices may result in increased microbial resistance to antibiotics, which can have an impact on human health. As part of our research project we have been studying the commensal microbial populations present in stored swine manure and the swine GI tract. We have extended this work to include studies on the antibiotic resistance present in these populations.

What did we do?

Predominant microbial populations were identified by both pure culture isolations and direct 16S rDNA sequencing of total DNA from swine feces and stored manure samples. Antibiotic resistance was analyzed using similar pure culture isolation methods. Pure cultures were isolated following plating on anaerobic and aerobic media containing tetracycline, tylosin, or erythromycin. Polymerase chain reaction (PCR) analyses using primers based on a variety of antibiotic resistance genes was carries out with both pure culture isolates and total DNA from swine feces and stored manure.

What have we learned?

Results of pure culture isolation and direct 16S rDNA gene sequence analyses indicate that the bacterial populations of the swine GI tract (feces) and stored manure ecosystems are predominantly composed of anaerobic, low mole %G+C, Gram-positive bacteria, most of which represent novel genera and species. Results of antibiotic resistance gene PCR studies demonstrated the presence of a variety of tet (e.g., tetK, tetO) and erm (e.g., ermA, ermC) resistance gene classes in both anaerobic and aerobic pure cultures and total DNA from both swine feces and stored manure, as well as the identification of novel bacteria containing new resistance genes. Comparison of DNA sequences suggests that horizontal transfer of resistance genes between bacterial strains has also occurred. The data indicate that both the swine gastrointestinal (GI) tract and stored swine manure may serve as reservoirs of known and novel antibiotic resistant bacteria and resistan ce genes.

Future Plans

We are interested in developing methods to reduce antibiotic resistance in the swine GI tract and stored manure, and to determine if antibiotic resistance genes present in these ecosystems can be transferred to bacteria that may affect human health (e.g., E. coli, Salmonella, Campylobacter).


Terence R. Whitehead, Research Microbiologist, USDA-ARS- National Center for Agricultural Utililzation Research, Peoria, IL 61604

Michael A. Cotta, USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL 61604

Additional information

Terence R. Whitehead, NCAUR, 1815 N. University St., Peoria, IL 61615 309-681-6272

USDA-ARS-NCAUR-Bioenergy Research Unit:

Cotta, M.A., Whitehead, T.R., and Zeltwanger, R.L. Isolation, Characterization, and Comparison of Bacteria from Swine Faeces and Manure Storage Pits. (2003) Env. Microbiol. 5:737-745.

Whittle, G., Whitehead, T.R., Hamburger, N., Shoemaker, N.B., Cotta, M.A., and Salyers, A.A. Identification of a new ribosomal protection type of tetracycline resistance gene, tet(36), from swine manure pits . (2003) Appl. Environ. Microbiol. 69:4151-4158.

Cotta, M.A., Whitehead, T.R., Falsen, E., Moore, E. and Lawson, P.A. Robinsonella peoriae gen.nov., sp. nov., isolated from a swine-manure storage pit and a human clinical source. (2009) Int. J. System. Evol. Microbiol. 59:150-155.

Whitehead, T.R. and Cotta, M.A. Stored Swine Manure and Swine Feces as Reservoirs of Antibiotic Resistance Genes. (2013) Lett. Appl. Microbiol. 56:264-267.

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