Draft Genome Sequence of the Cellulolytic, Mesophilic, Anaerobic Bacterium Clostridium termitidis Strain CT1112 (DSM 5398)

Abstract

Here, we report the draft genome sequence of Clostridium termitidis strain CT1112 (DSM 5398), a mesophilic, cellulolytic bacterium that can utilize a variety of sugars, as well as pure cellulose, as a sole carbon source; it also synthesizes fermentation end products with potential industrial applications.

GENOME ANNOUNCEMENT

Clostridium termitidis strain CT1112 (DSM 5398) is a Gram-positive, mesophilic, anaerobic, cellulolytic bacterium isolated from the gut of the wood-feeding termite Nasutitermes lujae (1). Based on its 16S rRNA, C. termitidis belongs to Clostridium cluster III (2). It can utilize a wide variety of substrates, such as cellulose, cellobiose, glucose, fructose, and many other sugar monomers, as a sole carbon source, and it produces hydrogen (H₂), carbon dioxide (CO₂), acetate, formate, lactate, and ethanol as major fermentation end products (1, 3).

The genome of C. termitidis CT1112 was sequenced by the Genome Québec/McGill University platform using a Roche/454s GS-FLX Titanium sequencer by a whole-genome shotgun strategy, which obtained 303,437 reads. A 454 standard flowgram format (.sff) read file was assembled using Newbler v2.3. The final draft genome assembly has approximately 17-fold coverage and contains 78 contigs (>800 bp in length), with a total size of 6,415,858 bp, an N₅₀ contig length of 146,289 nucleotides, and a mean G+C content of 41.18%. The draft genome sequence was automatically annotated using IMG-ER, an online system developed by the U.S. Department of Energy Joint Genome Institute (JGI) (http://www.jgi.doe.gov/). The IMG-ER annotation was processed by a JGI-developed Gene Prediction Improvement Pipeline (GenePRIMP) (4) and was further subjected to manual curation using Artemis (5). The draft genome sequence of C. termitidis is estimated to have a total of 5,389 genes, including 5,302 protein-coding genes, 55 tRNAs, and 7 rRNAs.

The C. termitidis genome is larger than those of other mesophilic and thermophilic cellulolytic Clostridium spp., such as Clostridium cellulolyticum H10 (4,068,724 bp), Clostridium cellulovorans 743B (5,262,222 bp), Clostridium phytofermentans ISDg (4,847,594 bp), Clostridium thermocellum ATCC 27405 (3,843,301 bp), and C. thermocellum DSM 1313 (3,561,619 bp). The G+C content of C. termitidis is higher (41.18%) than those of other cellulolytic Clostridium species (31.21% to 39.15%), as is the number of predicted genes (5,389).

C. termitidis protein-coding genes were verified using other cellulolytic Clostridium species as reference organisms. Amino acid sequences for each gene product were retrieved from the JGI genome portal (http://genome.jgi-psf.org/) (6) and the NCBI database (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi), and sequence alignments against C. termitidis genes were performed. The corresponding gene loci and enzymes for each pathway were identified by percent amino acid sequence identity and were based on a conserved domain of proteins (7). In this manner, the key enzymes involved in C. termitidis core metabolism, as well as the major cellulosomal components and glycoside hydrolases, were identified. C. termitidis has potential as an industrial microorganism for the production of biofuels and/or other value-added products through direct cellulose fermentation via consolidated bioprocessing.

Nucleotide sequence accession numbers.

The genome sequence of C. termitidis strain CT1112 (DSM 5398) has been deposited at DDBJ/EMBL/GenBank under the accession no. AORV00000000. The version described in this paper is the first version, accession no. AORV01000000.