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

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.

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.