Abstract
By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the first known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characterization as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities. The 4,015,175 bp long genome exhibits a G + C% content of 65.36% and contains 3911 protein-coding and 64 predicted RNA genes. PCR-amplified 16S rRNA gene of strain Arc-HrT yielded a 99.2% sequence similarity with Haloferax prahovense, the phylogenetically closest validly published species in the Haloferax genus. The DDH was of 50.70 ± 5.2% with H. prahovense, 53.70 ± 2.69% with H. volcanii, 50.90 ± 2.64% with H. alexandrinus, 52.90 ± 2.67% with H. gibbonsii and 54.30 ± 2.70% with H. lucentense. The data herein represented confirm strain Arc-HrT as a unique species and consequently we propose its classification as representative of a novel species belonging to the genus Haloferax, as Haloferax massiliense sp. nov.
Highlights
As 16S rRNA gene sequence comparison has been proven to poorly discriminate Haloferax species, we sequenced the complete genome of strain Arc-HrT and a digital DNA–DNA hybridization was made with four of the closest Haloferax species
DNA sequences belonging to some halophilic archaea frequently present or abundant in extreme environments were detected by PCR in the human gastro-intestinal tract as well as some members of the Halobacteriaceae family (Oxley et al 2010)
Based on the characteristics reported here and the phylogenetic affiliation of strain Arc-HrT, we proposed the creation of Haloferax massiliense sp. nov., as a new species belonging to the Haloferax genus with strain Arc-HrT as its type strain
Summary
The human intestinal microbiota is a complex ecosystem consisting of a wide diversity including bacteria (Lagier et al 2012), archaea (Khelaifia et al 2013), and unicellular eukaryotes (Nam et al 2008). The culturomics concept, recently introduced in our laboratory to study the prokaryotes diversity in the human gut (Lagier et al 2012), allowed the isolation of a huge halophilic bacteria diversity including several new species (Lagier et al 2016). Among the diverse culture conditions and several culture media used by culturomics to isolate new prokaryotes, some conditions targeting extremophile organisms were used (Lagier et al 2016). Culture media containing high salt concentration are essentially used to select halophilic bacteria and archaea
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