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

doi:10.1186/1471-2164-7-22

BMC Genomics
Volume 7

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Ricard G
McEwan NR
Dutilh BE
Jouany JP
Macheboeuf D
Mitsumori M
McIntosh FM
Michalowski T
Nagamine T
Nelson N
Newbold CJ
Nsabimana E
Takenaka A
Thomas NA
Ushida K
Hackstein JH
Huynen MA

on PubMed

Ricard G
McEwan NR
Dutilh BE
Jouany JP
Macheboeuf D
Mitsumori M
McIntosh FM
Michalowski T
Nagamine T
Nelson N
Newbold CJ
Nsabimana E
Takenaka A
Thomas NA
Ushida K
Hackstein JH
Huynen MA
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Research article

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

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

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

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

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

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

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

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

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

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

author email corresponding author email

BMC Genomics 2006, 7:22doi: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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