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. 2016 Nov 18;15:44–45. doi: 10.1016/j.nmni.2016.11.012

Draft genome sequence of a human-associated isolate of Haloferax alexandrinus strain Arc-hr, an extremely halophilic archaea

S Khelaifia 1,2,∗, A Caputo 1, F Djossou 3, D Raoult 1,2
PMCID: PMC5167240  PMID: 28018603

Abstract

We report the draft genome sequence of Haloferax alexandrinus strain Arc-hr (CSUR P798), isolated from the human gut of a 10-year-old Amazonian individual. Its 3 893 626 bp genome exhibits a 66.00% GC content. The genome of the strain Arc-hr contains 37 genes identified as ORFans, seven genes associated to halocin and 11 genes associated with polyketide synthases or nonribosomal peptide synthetases.

Keywords: Culturomics, genome sequence, genomics, Haloferax alexandrinus, halophilic archaea

Haloferax alexandrinus is an extremely halophilic archaea initially isolated from a solar saltern in Alexandria, Egypt. This Gram-negative halophilic archaea is highly pleomorphic, nonmotile and strictly aerobic, and it requires at least 10 g/L NaCl for growth [1]. Interestingly, DNA related to halophilic archaea from Halorubrum and Halobacterium genera was detected by PCR in colon mucous biopsy samples collected from patients with inflammatory bowel disease [2], but no isolate was made from any of these specimens. Recently we reported the first isolation of H. alexandrinus strain Arc-hr (Collection de Souches de l'Unité des Rickettsies (CSUR) P798) from a human stool specimen as part of a culturomics study of intestinal microflora of a 10-year-old Amazonian individual using media containing high salt concentrations [3]. H. alexandrinus strain Arc-hr is a Gram-negative archaeon, highly pleomorphic and strictly aerobic, with optimal growth observed at 37°C, pH 7.5 and 100 g/L NaCl. Sequencing the 16S ribosomal DNA confirmed the affiliation of the strain Arc-hr (GenBank accession no. HG931927) to the genus Haloferax and yielded a 99.9% sequence similarity with the reference H. alexandrinus JCM 10717T (GenBank accession no. NR_113438). Strain Arc-hr therefore represents the first H. alexandrinus isolate cultured from the human gut.

The complete genome of H. alexandrinus strain Arc-hr was sequenced on the MiSeq Technology (Illumina, San Diego, CA, USA) with the mate-pair strategy as previously described [4]. Open reading frames (ORFs) were predicted using Prodigal [5] with default parameters, but the predicted ORFs were excluded if they spanned a sequencing gap region (containing N) [6]. Noncoding genes and miscellaneous features were predicted using RNAmmer [7], ARAGORN [8], Rfam [9], PFAM [10] and Infernal [11]. Coding DNA sequences were predicted using Prodigal [5], and functional annotation was achieved using BLAST+ [6] and HMMER3 [12] against the UniProtKB database [13].

The genome the strain Arc-hr is 3 893 626 bp long with 66.00% GC content. It is composed of one scaffold (composed of five contigs); of the 3770 predicted genes, 3679 were protein-coding genes and 58 were RNAs (two genes are 5S rRNA, three genes are 16S rRNA, two genes are 23S rRNA and 51 genes are tRNA genes). A total of 2019 genes (65.38%) were assigned a putative function. The remaining genes were annotated as hypothetical proteins (924 genes, 29.92%). Moreover, the H. alexandrinus strain Arc-hr genome contains 37 genes identified as ORFans, seven genes associated to halocin and 11 genes associated with polyketide synthases or nonribosomal peptide synthetases.

Deposit in a culture collection

Strain Arc-hr was deposited in CSUR (WDCM 875) under number CSUR P974.

Nucleotide sequence accession number

The H. alexandrinus strain Arc-hr genome sequence has been deposited in European Molecular Biology Laboratory under the accession number CCDK010000001:CCDK010000010.

Acknowledgements

This study was funded by the Fondation Méditerranée Infection. We thank M. Lardière for English-language review.

Conflict of Interest

None declared.

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