Genome Sequence of Oxalobacter formigenes Strain OXCC13.

The lack of Oxalobacter formigenes colonization in the human gut is generally acknowledged as a risk factor for kidney stone formation since this microorganism can play an important role in oxalate homeostasis. Here, we present the genome sequence of OXCC13, a human strain isolated from an individual residing in Germany.

GENOME ANNOUNCEMENT

Oxalobacter formigenes, an anaerobe with substrate specificity for oxalate, was isolated in 1985 and a new genus and species were established (1). This microorganism can play an important role in oxalate homeostasis, and the absence of this gut commensal is considered a risk factor in the formation of calcium oxalate kidney stones (2). The genomic sequence of O. formigenes strain OXCC13, determined by the Broad Institute Genome Sequencing Platform (RefSeq NZ_ACDQ00000000.1), is currently available. The present study was undertaken to determine the complete genome sequence of the OXCC13 strain, which has been archived in the Hatch laboratory since 2011 and is notated here as OXCC13MH.

A genomic DNA library was constructed following the protocol provided by Pacific Biosciences (Menlo Park, CA). Briefly, genomic DNA was sheared to an average fragment length of 20 kb by use of the SAGE ELF (Sage Science, Beverly, MA), end repaired, and then blunt-end ligated with single-molecule real-time (SMRT) bell oligonucleotide adaptors to construct a DNA fragment library for sequencing on the Pacific Biosciences RSII instrument. A single SMRT cell produced a total of 1.18 Gb in 71,943 polymerase reads having an N50 of 18.1 kb and a subread N50 of 11.5 kb.

The OxCC13MH genome was assembled from long PacBio sequencing reads using HGAP version 3 (3). The OxCC13M.H. genome was deposited in GenBank (accession number CP019430) and annotated using RAST (http://rast.nmpdr.org) (4–6). The complete OxCC13MH genome contains a single contig of 2,433,653 bp and has an average GC content of 49.6%. A total of 2,599 genes were annotated by RAST, including 47 tRNAs, 6 ribosomal RNAs, and 2,499 predicted coding sequences (CDS). RAST annotation assigned 1,060 (43%) of the 2,499 OxCC13 CDS as members of 269 categorized subsystems. Subsystems are defined as sets of functional roles implementing specific biological process or structures (7). In general, subsystems are considered biological pathways. The most abundant subsystem classifications included 202 genes involved in protein metabolism; 169 involved in metabolism of cofactors, vitamins, prosthetic groups, and pigments; 205 involved in amino acid and derivative metabolism; and 108 involved in carbohydrate metabolism. A total of 1,439 CDS (57%) were not assigned to specific subsystems.

The complete, annotated OxCC13MH genome was compared to O. formigenes CC13 (NCBI RefSeq NZ_ACDQ00000000.1). The OxCC13MH genome was assembled as a single closed circular sequence of 2,433,653 bp. The public OxCC13 draft sequence (RefSeq NZ_ACDQ00000000.1) contains 9 scaffolds with a total length of 2,436,766 bp. The largest scaffold (NCBI accession number GG658170.1) is 2,424,267 bp. At the protein level, 2,447 of 2,499 (98%) OxCC13MH CDS have greater than 99% amino acid identity with CDS identified in OxCC13. MUMmer (https://sourceforge.net/projects/mummer/) alignment of OxCC13MH with OxCC13 showed the genome sequences to be collinear, with a collective total of approximately 4.5 kb of structural variation, mostly in the form of small deletions, tandem expansions, and a small repeat contraction. Besides the small structural variations, at the nucleotide level, there is less than 0.03% difference between genomes. The overall homology between OxCC13MH and OxCC13 suggests, as expected, that both genome sequences are derived from the same genomic source DNA.

Accession number(s).

This genome sequencing project was deposited in GenBank under accession number CP019430.