Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment.
BACKGROUND
The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium).


RESULTS
A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates.


CONCLUSIONS
Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.
Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands. g.ricard@cmbi.ru.nl
Guénola
G
Ricard
Neil R
NR
McEwan
Bas E
BE
Dutilh
Jean-Pierre
JP
Jouany
Didier
D
Macheboeuf
Makoto
M
Mitsumori
Freda M
FM
McIntosh
Tadeusz
T
Michalowski
Takafumi
T
Nagamine
Nancy
N
Nelson
Charles J
CJ
Newbold
Eli
E
Nsabimana
Akio
A
Takenaka
Nadine A
NA
Thomas
Kazunari
K
Ushida
Johannes H P
JH
Hackstein
Martijn A
MA
Huynen
D000222:Adaptation, Physiological / Q000235:genetics; D000693:Anaerobiosis; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001421:Bacteria, Anaerobic; D050260:Carbohydrate Metabolism / Q000235:genetics; D016798:Ciliophora / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D020224:Expressed Sequence Tags / Q000737:chemistry; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D017125:Genes, Protozoan; D006026:Glycoside Hydrolases / Q000235:genetics; D010802:Phylogeny; D012418:Ruminants / Q000382:microbiology / Q000469:parasitology
D006026:Glycoside Hydrolases