Draft Genome Sequence of Clostridium scatologenes ATCC 25775, a Chemolithoautotrophic Acetogenic Bacterium Producing 3-Methylindole and 4-Methylphenol.

Clostridium scatologenes ATCC 25775 is a strictly anaerobic and chemolithoautotrophic acetogenic bacterium that converts syngas into multi-carbon compounds such as acetate, indole, 3-methylindole, and 4-methylphenol. Here we report the draft genome sequence of C. scatologenes ATCC 25775 (7.3 Mbp) to elucidate its metabolic pathway for syngas fermentation.

GENOME ANNOUNCEMENT

Carbon monoxide (CO), carbon dioxide (CO2), and hydrogen (H2) are main components in syngas, which are key precursors for the sustainable production of value-added chemicals through microbial metabolism known as syngas fermentation (1, 2). Compared to thermo-chemical processes like Fischer-Tropsch synthesis, the usage of acetogenic bacteria (acetogens) during syngas fermentation has important advantages for the production of various industrial commodities. These include higher catalytic specificity, lower energy costs, greater resistance to catalyst poisoning, and independence of the CO/H2 ratio (3). As one of the syngas-utilizing acetogens, Clostridium scatologenes ATCC 25775 oxidizes hydrogen to grow chemolithoautotrophically and fix CO2 or CO into acetate as the main end product under anaerobic conditions (4). The bacterium also produces malodorous chemicals such as 3-methylindole and 4-methylphenol, which are widely used and intermediates the production of other chemicals such as antioxidants and fixatives (4, 5). Despite the metabolic capabilities of C. scatologenes as a chemical producer from syngas, lack of genetic information limits strain engineering to design the production host for the useful chemicals. To understand its physiological and metabolic properties, we obtained the draft genome sequence of the acetogen.

For the isolation of its genomic DNA, C. scatologenes were grown under anaerobic conditions using the medium reported previously (6). Genomic DNA was isolated using a Wizard Genomic DNA purification kit (Promega) and fragmented using Covaris S220 (Covaris, Inc.). The Illumina paired-end library was prepared using a TruSeq kit (Illumina, Inc.) and sequenced using a MiSeq v2 instrument with the 250 bp paired-end read recipe. The collected reads were trimmed with the default parameters using CLC Genomics Workbench (CLC bio). A total of 1,118,842,164 bases in 7,455,788 reads were then assembled using Velvet (version 1/2/08) (7), resulting in 174 contigs, the largest of which is 472,553 bp. With the assembled genome, rRNAs and tRNAs were predicted using RNAmmer 1.2 and tRNAscan-SE 1.21, respectively (8, 9) and annotation was performed using Rapid Annotation using Subsystem Technology (10).

The draft genome sequence of C. scatologenes is 7,353,834 bases, comprising 6,842 predicted open reading frames, 118 tRNA genes, and 13 rRNA genes. It shows a G+C content of 30.2%, consistent with a previous report (31 mol% by nuclease digest) (11). 16S rRNA gene sequence analysis shows that C. scatologenes is closely related to C. carboxidivorans (99.9%) and C. drakei (99.8%) (11, 12). However, the genome of C. scatologenes is larger than that of C. carboxidivorans (5.63 Mbp, accession number ACVI01000000) and C. drakei (5.64 Mbp, accession number JIBU00000000). As expected, C. scatologenes uses the Wood-Ljungdahl pathway for fixing CO2 to organic carbon via acetyl-CoA. C. scatologenes has tryptophan 2-monooxigenase (EC 1.13.12.3) and aliphatic amidase (EC 3.5.1.4), indicating that it contains a metabolic pathway from tryptophan to 3-methylindole via indoleacetic acid (4). The draft genome sequence of C. scatologenes will provide genetic information for the understanding of its metabolic capabilities for syngas fermentation.

Nucleotide sequence accession number.

The draft genome sequence of C. scatologenes has been deposited at the DDBJ/EMBL/GenBank database under the accession no. JIDX00000000. The version described in this paper is the first version.