APPLIED MICROBIAL AND CELL PHYSIOLOGY Effect of dietary monensin on the bacterial population structure of dairy cattle colonic contents Jeffery A. McGarvey & Scott W. Hamilton & Edward J. DePeters & Frank M. Mitloehner Received: 23 June 2009 / Revised: 25 August 2009 / Accepted: 26 August 2009 / Published online: 26 September 2009 # US Government 2009 Abstract To determine the effect of monensin, a carboxylic polyether ionophore antibiotic, on the bacterial population structure of dairy cattle colonic contents, we fed six lactating Holstein cows a diet containing monensin (600 mg day -1 ) or an identical diet without monensin. Fresh waste samples were taken directly from the animals once a month for 3 months and assayed for their bacterial population structure via 16S rRNA gene sequence analysis. In total 6,912 16S rRNA genes were examined, comprising 345 and 315 operational taxonomic units (OTUs) from the monensin fed and control animals, respectively. Coverage estimates of the OTUs identified were 87.6% for the monensin fed and 88.3% for the control colonic content derived library. Despite this high level of coverage, no significant difference was found between the libraries down to the genus level. Thus we concluded that although monensin is believed to increase milk production in dairy cattle by altering the bacterial population structure within the bovine gastrointes- tinal tract, we were unable to identify any significant difference in the bacterial population structure of the colonic contents of monensin fed vs. the control dairy cattle, down to the genus level. Keywords Dairy cattle waste . Monensin . 16S rRNA Introduction California is the largest dairy-producing state in the USA, with approximately 1.8 million lactating cattle that produce approximately 20% of the US milk supply (Agricultural Statistics Board 2007). California dairy production has increased every year since 1985, and along with this growth, new challenges have emerged, including the environmental impacts associated with the emission of volatile organic compounds and greenhouse gasses from the animals and their waste, the high cost of animal feed, the reduced availability of suitable farmland for dairy production, and the release of pathogenic bacteria into the environment. Feeding monensin, a carboxylic polyether ionophore antibiotic (Haney and Hoehn 1968), to dairy cattle has the potential to alleviate some of these problems. For example, monensin has been shown to increase the feed efficiency in cattle (Russell and Strobel 1989), reducing the amount of feed needed to produce a given quantity of milk. Monensin has also been reported to increase the amount of milk produced per cow (Sauer et al. 1998; Gallardo et al. 2005), allowing greater milk production without the need for additional farmland. Monensin is also believed to reduce methane emissions. Although monensin has little or no direct effect on methanogenic archaea (Russell and Houlihan 2003), it is believed to inhibit methanogenesis by reducing the levels of Gram-positive bacteria in the rumen (Russell and Strobel 1989; Haney and Hoehn 1968; Westley et al. 1973) that produce the vast majority of the methano- genic substrates (e.g., hydrogen and acetate; Russell and Strobel 1989). Monensin is also believed to increase animal performance by reducing the levels of amino-acid- fermenting bacteria in the rumen that wastefully convert ruminal protein to ammonia, which is subsequently excreted as urea (Richerdson et al. 1976; Russell and Martin 1984). J. A. McGarvey (*) Plant Mycotoxin Research Unit, Agricultural Research Service, U. S. Dept. of Agriculture, 800 Buchanan St., Albany, CA 94710, USA e-mail: Jeffery.mcgarvey@ars.usda.gov S. W. Hamilton : E. J. DePeters : F. M. Mitloehner Department of Animal Science, University of California, Davis, CA, USA Appl Microbiol Biotechnol (2010) 85:1947–1952 DOI 10.1007/s00253-009-2229-8