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Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

Guénola Ricard1*, Neil R McEwan2, Bas E Dutilh1, Jean-Pierre Jouany3, Didier Macheboeuf3, Makoto Mitsumori4, Freda M McIntosh5, Tadeusz Michalowski6, Takafumi Nagamine7, Nancy Nelson5, Charles J Newbold7, Eli Nsabimana3, Akio Takenaka4, Nadine A Thomas5, Kazunari Ushida8, Johannes HP Hackstein9 and Martijn A Huynen1

Author Affiliations

1 Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands

2 Institute of Rural Sciences, University of Wales, Aberystwyth, SY23 3AL, UK

3 I.N.R.A., Station de Recherches sur la Nutrition des Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, France

4 National Institute of Livestock and Grassland Science, 2 Ikenodai, Kukizaki, Ibaraki, 305-0901, Japan

5 Rowett Research Institute, Aberdeen, AB21 9SB, UK

6 Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Jablonna, Warsaw, Poland

7 Rumen Microbiology Research Team, STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba 305-0854, Japan

8 Laboratory of Animal Science, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan

9 Department of Evolutionary Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands

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BMC Genomics 2006, 7:22 doi:10.1186/1471-2164-7-22

Published: 10 February 2006

Additional files

Additional File 1:

Distribution of the complete proteomes over the various taxa. Eukaryotic proteomes are: Plasmodium falciparum, Guillardia theta, Candida albicans, Encephalitozoon cuniculi, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Anopheles gambiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio (zebrafish), Fugu rubripes, Homo sapiens, Mus musculus, Rattus norvegicus, and Arabidopsis thaliana.

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Additional File 2:

Classification of the 148 HGT candidates. Annotation was given on the basis of the complete analysis (homology with known proteins, homology to proteins of a KOG/COG, PFAM domains and confirmed from the tree). CCD: Complex carbohydrates degradation, F: Fermentation, G: Glycolysis, PD: protein degradation, NM: Nitrogen metabolism. Composition of the Smith Waterman comparison results (Hit; E-value < 1·10–5) or second-smallest partition (SSP): B: only Bacteria; AB: Bacteria and Archaea; A: only Archaea.

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