Genome Sequence of the Neurotoxigenic Clostridium butyricum Strain 5521.

Clostridium strains from six phylogenetic groups, C. botulinum groups I to IV, C. baratii, and C. butyricum, display the capacity to produce botulinum neurotoxin. Here, we present the genome sequence of a C. butyricum isolate, the neurotoxigenic strain 5521, which encodes the type E botulinum neurotoxin.

GENOME ANNOUNCEMENT

Clostridium butyricum is a Gram-positive bacillus named for its capacity to produce butyric acid. C. butyricum strains are found in a variety of environments and are common human and animal gut commensals. However, some C. butyricum strains have been found to cause the paralytic condition botulism (1–4). These neurotoxigenic C. butyricum strains harbor an operon encoding the type E botulinum neurotoxin (BoNT/E) likely to have been horizontally acquired (5). Neurotoxigenic C. butyricum strains were originally identified as the cause of botulism in infants in Italy (1, 2) and have since been identified in other countries. Here, we present the genome sequence of a neurotoxigenic C. butyricum strain, 5521, isolated from a case of botulism. The genome sequence of C. butyricum 5521 was determined to 8-fold coverage using Sanger shotgun sequencing. The sequence reads were assembled and annotated as previously described (6). The sequence is organized into 123 scaffolds and includes 3,827 putative protein-coding genes and 259 predicted pseudogenes.

The predicted protein-coding potential of C. butyricum 5521 is similar to that of C. butyricum BL 5262 (5); tblastx 2.2.5+ searches demonstrated that >96% of the 4,086 genes or pseudogenes of C. butyricum 5521 are shared between these two strains (E value ≤ 1e-30). Of the clostridial species for which complete genome sequences are available, 16S rRNA analyses have suggested that C. butyricum is most closely related to group II Clostridium botulinum, Clostridium acetobutylicum, and Clostridium beijerinckii (3). tblastx comparisons indicate that 2,352, 1,809, and 2,568 genes or pseudogenes of C. butyricum 5521 have orthologs within the genomes of C. botulinum E3 strain Alaska E43 (5) (Genbank accession no CP001078), C. acetobutylicum ATCC 824 (7), and C. beijerinckii NCIMB 8052 (8), respectively.

A defining characteristic of C. butyricum strains is their production of butyric acid. The enzymes involved in butyric acid production from acetyl-coenzyme A (CoA) in C. butyricum 5521 are encoded primarily within two gene clusters, CBY_2919-20 and CBY_3041-45 (both on scaffold ABDT01000094 in the current assembly). However, acetyl-CoA acetyltransferase, CBY_1290, which mediates the first step in this pathway (9), is encoded elsewhere (scaffold ABDT01000114).

The gene encoding the BoNT/E toxin within C. butyricum 5521 is present in a gene cluster localized within the chromosomal rarA resolvase locus. This gene cluster is identical to that carried by the neurotoxigenic C. butyricum strain BL 5262, which is also localized within the rarA locus (5). A detailed analysis of this gene cluster demonstrated that it shows an organization that is highly similar or identical to that of the BoNT/E gene clusters carried by group II type E toxin-producing C. botulinum strains (5).

The genome sequence of C. butyricum 5521 will prove useful for comparative studies and for future investigations of type E botulism.

Nucleotide sequence accession numbers.

The draft genome sequence for C. butyricum 5521 has been added to the GenBank database under the accession no. ABDT00000000. The version described here is ABDT00000000.1.