Rumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains Bareket Dassa 1 , Ilya Borovok 2 , Vered Ruimy-Israeli 1 , Raphael Lamed 2 , Harry J. Flint 3 , Sylvia H. Duncan 3 , Bernard Henrissat 4 , Pedro Coutinho 4 , Mark Morrison 5,6 , Pascale Mosoni 7 , Carl J. Yeoman 8 , Bryan A. White 9,10 , Edward A. Bayer 1 * 1 Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel, 2 Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel, 3 Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom, 4 Architecture et Fonction des Macromolecules Biologiques, Aix-Marseille University and Centre National de la Recherche Scientifique (CNRS), Marseille, France, 5 University of Queensland Diamantina Institute, Woolloongabba, Queensland, Australia, 6 Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America, 7 The French National Institute for Agricultural Research (INRA), UR454 Unite ´ de Microbiologie, Saint-Gene ` s-Champanelle, France, 8 Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America, 9 The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America, 10 Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America Abstract Background: A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels. Methodology/Principal Findings: Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin- and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37). Conclusions/Significance: Our comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass. Citation: Dassa B, Borovok I, Ruimy-Israeli V, Lamed R, Flint HJ, et al. (2014) Rumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains. PLoS ONE 9(7): e99221. doi:10.1371/journal.pone.0099221 Editor: Mickae ¨ l Desvaux, INRA Clermont-Ferrand Research Center, France Received February 9, 2014; Accepted May 12, 2014; Published July 3, 2014 Copyright: ß 2014 Dassa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The research described in this communication was supported by a grant (No. 24/11) issued to RL by The Sidney E. Frank Foundation through the Israel Science Foundation (ISF) and by a grant (No. 1349/13) to EAB also from the ISF (http://www.isf.org.il/english/). This research was also supported by the establishment of an Israeli Center of Research Excellence (I-CORE Center No. 152/11, EAB) managed by the ISF, grants from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel (http://www.bsf.org.il/BSFPublic/Default.aspx), by the Weizmann Institute of Science Alternative Energy Research Initiative (AERI) and the Helmsley Foundation (http://helmsleytrust.org/), a project (FiberFuel) funded through the ERA-NET Scheme of the 7th EU Framework Programme European Union Contract (within the framework of the Third ERA-IB Call). A grant to EAB and RL from the Israel Ministry of Science (http://most.gov.il/ english/Pages/default.aspx) is gratefully acknowledged. The North American Consortium for Genomics of Rumen Bacteria Consortium was supported by the Initiative for Future Agriculture and Food Systems, Grant no. 2000-52100-9618 and Grant No 2001-52100-11330, from the USDA Cooperative State Research, Education, and Extension Service’s National Research Initiative Competitive Grants Program (http://www.csrees.usda.gov/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors wish to declare that BAW, a PLOS ONE editor, was involved in the work performed. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials. * Email: ed.bayer@weizmann.ac.il Introduction The bovine rumen hosts a wide range of strictly anaerobic and some facultatively anaerobic microorganisms [1–5]. The rumen microbiota is highly diverse, including both prokaryotic and eukaryotic anaerobes, that maintains a mutualistic relationship with its host [6]. On the one hand, the rumen flora is dynamic and known to adapt to changes in the host diet and age [7,8]. On the other, the rumen microbiota produces large quantities of short- chain fatty acids that are absorbed across the rumen wall and used as energy sources by the host [9]. Fermentation of plant material by rumen fiber-degrading microorganisms in the rumen typically provides 70% of the energy obtained from the diet [10]. Herbivore health and productivity are greatly affected by the composition PLOS ONE | www.plosone.org 1 July 2014 | Volume 9 | Issue 7 | e99221