20946531, Environ Microbiol. 2011 Feb;13(2):518-28. doi: 10.1111/j.1462-2920.2010.02355.x. Epub 2010 Oct 15.

Characterization method

microarray,growth assay,gene deletion mutant and growth assay

Genomic accession number


Nucelotide position range







Enterococcus faecium/1352

Degradation or Biosynthesis


Cluster number


Gene name

Gene position

Gene type

Found by CGCFinder?

gtfA 1 - 1461 (-) CAZyme: GH13|GH13_18 Yes
- 1458 - 2441 (-) CAZyme: GH13_31|GH13 Yes
- 2522 - 2677 (-) other Yes
- 2738 - 4921 (-) CAZyme: GH36 Yes
- 4961 - 5791 (-) TC: gnl|TC-DB|Q00751|3.A.1.1.28 Yes
- 5803 - 6675 (-) TC: gnl|TC-DB|Q00750|3.A.1.1.28 Yes
- 6685 - 7944 (-) TC: gnl|TC-DB|Q00749|3.A.1.1.28 Yes
- 8093 - 9403 (-) CAZyme: GH4 Yes
- 9435 - 10259 (-) TC: gnl|TC-DB|Q93J92|3.A.1.1.36 Yes
- 11254 - 12363 (-) TC: gnl|TC-DB|Q9WZR7|3.A.1.1.40 Yes
- 12657 - 13682 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0044558 No




20946531, Environ Microbiol. 2011 Feb;13(2):518-28. doi: 10.1111/j.1462-2920.2010.02355.x. Epub 2010 Oct 15.


A genetic element present on megaplasmids allows Enterococcus faecium to use raffinose as carbon source.


Zhang X, Vrijenhoek JE, Bonten MJ, Willems RJ, van Schaik W


Enterococcus faecium is a commensal of the gastrointestinal tract of humans and animals. Since the 1990s, it has also emerged as a nosocomial pathogen. Little is known about carbon metabolism of E. faecium even though the ability to utilize different sugars could be an important factor in adapting to different ecological niches. In this study we identify an E. faecium gene cluster that is responsible for the metabolism of the alpha-galactoside sugar raffinose. Phenotypic testing of seven E. faecium isolates of which the genomes were previously sequenced showed that one isolate (strain E980) could grow on raffinose. Genome analysis identified a gene cluster containing two genes encoding alpha-galactosidases (termed agaA and agaB) that was uniquely present in E980. The agaA and agaB genes were significantly more frequently found in strains that are phylogenetically related to E980 and were more prevalent in surveillance isolates from hospital and community sources than in isolates from clinical infections. Disruption of the alpha-galactosidase gene agaB, but not of agaA, disabled growth on raffinose in strain E980. In all strains agaA and agaB are carried on megaplasmids that are between 150 and 300 kb in size. Filter-mating experiments showed that the megaplasmid of E980 can be transferred to a plasmidless recipient which then gains the ability to grow on raffinose. The observation that raffinose utilization by E. faecium is a trait carried by megaplasmids indicates that these megaplasmids can have important roles in shaping the competitive fitness of E. faecium in the environment, for example by expanding the metabolic repertoire of this organism.