Abstract
Arcobacter species are members of the family Campylobacteraceae and are considered emerging enteropathogens and potential zoonotic agents. Here, we report the draft genome sequences of two Arcobacter strains isolated from human feces in an effort to provide further genetic resources for understanding the pathogenic dynamics and diversity of this important genus.
GENOME ANNOUNCEMENT
The genus Arcobacter was proposed as a new genus in 1991 by Vandamme et al. (1). This genus currently consists of 18 species that have been isolated from humans and animals as well as water and food sources (2). The first strain in this genus, Arcobacter butzleri RM4018, was isolated from a human clinical sample, and its whole genome was sequenced (3). The strain was noted for its ability to grow and survive under diverse environmental conditions, with a large number of annotated proteins associated with respiration, signal transduction, and chemotaxis, as well as DNA repair and adaptation.
We isolated two Arcobacter strains (AF1028 and AF1078) from human feces. Based on multiple pairwise alignment of 16S rRNA gene sequences, the strains show 91.5 to 97.5% similarity to other Arcobacter species, including A. nitrofigilis, A. butzleri, A. skirrowii, A. cibarius, and A. cryaerophilus. To gain a better understanding of the genetic and pathogenic mechanisms of these pathogens, we sequenced their whole genomes.
Whole-genome sequencing of the two Arcobacter strains was performed using paired-end sequencing reads on an Illumina HiSeq 2500 with TrueSeq V3 chemistry at the National Research Council Canada (Saskatoon, Saskatchewan, Canada). The reads were 101 bp in length and were obtained from 300-bp inserts, with an average coverage of 590×. The quality of the reads was checked with the program FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). De novo assembly was performed using ABySS version 1.3.6 (4). We used SSPACE version 2.0 (5) to extend and merge the resulting scaffolds based on read-pair information and short overlaps to reduce the number of scaffolds. GapFiller version 1.11 (6) was used to close the gaps between the short scaffolds that are contained within the large scaffolds by replacing the unknown nucleotides (Ns) with true nucleotides based on read-pair information and short overlaps. Mauve Contig Mover version 2.3.1 (7) was applied to order the draft genomes of both strains by using the genomes of A. butzleri ED-1 (8) and A. cibarius LMG 21996 (9) as reference strains. Consistent with previous reports (8, 9), the genome G+C contents of these strains were relatively low (27%). The genome information for each strain is summarized in Table 1. Gene prediction and annotation were carried out using the RAST annotation server (10). The draft genomes of the two strains have similar, but not identical, numbers of protein-coding sequences. Strain AF1028 contains 2,353 predicted protein-coding sequences (encoding 1,666 functional, 269 proposed functional, and 418 hypothetical proteins), whereas strain AF1078 contains 2,445 predicted protein-coding sequences (encoding 1,671 functional, 277 proposed functional, and 497 hypothetical proteins). Similarly, strain AF1028 contains 64 predicted noncoding RNAs (51 tRNAs, 1 pseudo-tRNA, and 12 rRNAs consisting of 6 copies each of 16S rRNA and 23S rRNA genes), whereas strain AF1078 contains 68 predicted noncoding RNAs (53 tRNAs, 1 pseudo-tRNA, and 14 rRNAs consisting of 7 copies each of 16S rRNA and 23S rRNA genes).
TABLE 1.
Summary of information for the draft genome sequences of two strains of Arcobacter species
| Strain | Source | Accession no. | Genome size (bp) | N50 (bp) | No. of scaffolds (>300 bp) | G+C content (%) |
|---|---|---|---|---|---|---|
| Arcobacter sp. AF1028 | Human feces | JART00000000 | 2,414,790 | 148,259 | 46 | 27.24 |
| Arcobacter sp. AF1078 | Human feces | JARS00000000 | 2,496,885 | 127,252 | 53 | 27.18 |
Nucleotide sequence accession numbers.
The draft genome sequences of the Arcobacter strains AF1028 and AF1078 in this study have been deposited as whole-genome shotgun projects at DDBJ/EMBL/GenBank under the accession no. JART00000000 and JARS00000000, respectively. The version of each strain described in this paper is the first version, JART01000000 and JARS01000000, respectively.
ACKNOWLEDGMENTS
This research study was funded by the Canadian Safety and Security Program (CSSP) and Agriculture and Agri-Food Canada under Agri-Food pathogen detection and next-gen sequencing (project CRTI 09S-462RD) and Mycology and Bacteriology Biosystematics projects, respectively.
We thank Julie Chapados, Ekaterina Ponomareva, Jenni Whiteduck-Léveillée, and co-op students for their laboratory assistance.
Footnotes
Citation Adam Z, Whiteduck-Léveillée K, Cloutier M, Chen W, Lewis CT, Lévesque CA, Topp E, Lapen DR, Tambong JT, Talbot G, Khan IUH. 2014. Draft genome sequences of two Arcobacter strains isolated from human feces. Genome Announc. 2(2):e00113-14. doi:10.1128/genomeA.00113-14.
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