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Applied and Environmental Microbiology, May 2009, p. 2841-2849, Vol. 75, No. 9
0099-2240/09/$08.00+0     doi:10.1128/AEM.02698-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Genomic Analysis of "Elusimicrobium minutum," the First Cultivated Representative of the Phylum "Elusimicrobia" (Formerly Termite Group 1) ^,

D. P. R. Herlemann,¹ O. Geissinger,¹ W. Ikeda-Ohtsubo,¹ V. Kunin,² H. Sun,² A. Lapidus,² P. Hugenholtz,² and A. Brune^1*

Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse, 35043 Marburg, Germany,¹ U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, California 94598-1698²

Received 25 November 2008/ Accepted 26 February 2009

Organisms of the candidate phylum termite group 1 (TG1) are regularly encountered in termite hindguts but are present also in many other habitats. Here, we report the complete genome sequence (1.64 Mbp) of "Elusimicrobium minutum" strain Pei191^T, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut, and we discuss the findings in light of physiological data. E. minutum has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading to the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60 pilE-like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, nonribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of "Elusimicrobia" (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.

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* Corresponding author. Mailing address: Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse, 35043 Marburg, Germany. Phone: 49 6421 178701. Fax: 49 6421 178709. E-mail: brune{at}mpi-marburg.mpg.de

Published ahead of print on 6 March 2009.

Supplemental material for this article may be found at http://aem.asm.org/.

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Applied and Environmental Microbiology, May 2009, p. 2841-2849, Vol. 75, No. 9
0099-2240/09/$08.00+0     doi:10.1128/AEM.02698-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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