ENVIRONMENTAL MICROBIOLOGY Analysis of Rumen Methanogen Diversity in Water Buffaloes (Bubalus bubalis) Under Three Different Diets Raul Franzolin & Benoit St-Pierre & Korinne Northwood & André-Denis G. Wright Received: 18 August 2011 / Accepted: 2 January 2012 / Published online: 28 January 2012 # Springer Science+Business Media, LLC 2012 Abstract The water buffalo (Bubalus bubalis) is a prom- inent livestock species for the production of milk and meat in many countries. We investigated the diversity of rumen methanogens in Mediterranean water buffaloes maintained in Brazil under different diets: corn silage, grazing pasture, or sugar cane. A total of 467 clones were isolated from three methanogen 16S rRNA gene clone libraries that each represented a distinct feed type. The 467 clones were assigned to 19 species-level operational taxonomic units (OTUs). Four OTUs were represented in all three libraries, eight OTUs were library-specific, six OTUs were found in only the corn silage and pasture grazing libraries, and one OTU was shared only between pasture grazing and sugar cane libraries. We found that Methanobrevibacter-related sequences were the most abundant in the water buffaloes sampled for our analysis, in contrast to previously reported studies showing that Meth- anomicrobium mobile-like methanogens were the most abundant methanogens in water buffaloes of Murrah and Surti breeds sampled in India. Considering the worldwide distribution of water buffaloes and the likely wide variety of diets provided, our results combined with studies from other groups support that larger scope analyses of microbiomes for this livestock species would provide great insight into the contribution of geographical location, breed, and diet in determining the population structure of rumen microorganisms. Introduction With a global population of at least 170 million animals, the water buffalo (Bubalus bubalis) is an important ruminant species in many regions of the world, including Asia, North Africa, Southern Europe, and South America [5]. Compared to cattle, the water buffalo is more resistant to disease and parasites, and it has a higher adaptability to different ambi- ent and local conditions, which makes it a very suitable livestock choice in tropical regions [16]. Because of its body structure and resilience, the water buffalo is often consid- ered to be a better work animal and provides a cost-effective alternative to machinery, which is vital to small farmers and to the economy of many countries, especially in Asia [11, 15]. Productivity from the water buffalo is also more effi- cient, with its ability to grow faster than cattle on poor- quality roughage diets [17, 27], an advantage that can be used to promote sustainability by converting plant fiber by- Electronic supplementary material The online version of this article (doi:10.1007/s00248-012-0007-0) contains supplementary material, which is available to authorized users. R. Franzolin : B. St-Pierre : K. Northwood : A.-D. G. Wright (*) CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd, St. Lucia, QLD 4067, Australia e-mail: agwright@uvm.edu Present Address: R. Franzolin Departemento de Zootecnia, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de Sao Paulo, Sao Paulo, Brazil Present Address: K. Northwood Imperial College, Commonwealth Building, Du Cane Rd, Hammersmith W120NN, UK Present Address: B. St-Pierre : A.-D. G. Wright Department of Animal Science, The University of Vermont, 570 Main Street, Burlington, VT 05405, USA Microb Ecol (2012) 64:131–139 DOI 10.1007/s00248-012-0007-0