ORIGINAL ARTICLE An analysis of the ruminal bacterial microbiota in West African Dwarf sheep fed grass- and tree-based diets L.A. Omoniyi 1 *, K.A. Jewell 2 *, O.A. Isah 1 , A.P. Neumann 2 , C.F.I. Onwuka 1 , O.M. Onagbesan 3 and G. Suen 2 1 Department of Animal Nutrition, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria 2 Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA 3 Department of Animal Physiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria Keywords agriculture, bioinformatics, diversity, intestinal microbiology. Correspondence Garret Suen, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA. E-mail: gsuen@wisc.edu. *Contributed equally to this work. 2013/2035: received 7 October 2013, revised 10 December 2013 and accepted 10 January 2014 doi:10.1111/jam.12450 Abstract Aims: To measure the impact of supplementing a forage diet with tree-based browse on the ruminal bacterial communities of Nigerian West African Dwarf (WAD) sheep. Methods and Results: Fifteen WAD sheep were fed a control diet of forage (Panicum maximum), with 12 animals shifted in groups of three to one of four browse-supplemented diets (Albizia saman, Bridelia micrantha, Ficus sur, or Gmelina arborea). These browse plants were shown in a concurrent but separate study to be reasonably nutritious (based on chemical composition and fibre constituents) and nontoxic (based on tannin, phytate, saponin, alkaloid and oxalate levels). Rumen liquids and solids for DNA extraction were collected via intubation from two animals in each group before and after dietary shift. Bacterial 16S rRNA gene regions V6-V8 were sequenced by 454 pyrosequencing. All communities were highly diverse and dominated by the phyla Firmicutes, Bacteroidetes, Tenericutes, Actinobacteria and Proteobacteria. All communities shared members of the genera Butryivibrio, Prevotella and Ruminococcus. Our analysis defined a core sets of bacteria shared by all animals, forage-fed animals and browse-fed animals. Community structure shifted dramatically in animals fed A. saman or G. arborea. Conclusions: The impact of tree-based browse on the ruminal bacterial community of Nigerian WAD sheep varies by browse species, likely due to differences in browse composition. Significance and Impact of the Study: Our study describes the first neotropical small ruminant bacterial microbiome and supports diet supplementation with specific tree-based browse for WAD sheep. Introduction There is an ever-increasing need to understand agricul- tural practices, especially for subsistence farmers in equa- torial Africa. The West African Dwarf (WAD) sheep (Ovis aries, Djallonk e) is an important meat animal reared on family farms (Adesehinwa et al. 2004) from Senegal to Botswana and number in the millions of animals per country (Shaw et al. 2006). WAD sheep are highly adaptable to a broad range of environments, can live on crop by-products without grain supplementation (Anele et al. 2010), are trypanotolerant (Geerts et al. 2009), have rapid growth (Sowande and Sobola 2007) and are rich in genetic variation (Akinyemi and Salako 2010). Many African farmers use tree-based browse as feed supplements, as these feed sources require no culti- vation. Moreover, during the dry season, tree leaves and branches are potentially more nutritious than grasses (D’Mello and Fraser 1981; Aletor and Omodara 1994) and with measurably higher crude protein (Odedire and Babayemi 2008; Omoniyi et al. 2013). Previous work sug- gests that certain trees are acceptable feed substitutes with Journal of Applied Microbiology © 2014 The Society for Applied Microbiology 1 Journal of Applied Microbiology ISSN 1364-5072