Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut

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.

A comprehensive analysis of the global human gut archaeome from a thousand genome catalogue

“…1), which showed 100% ANI similarity to the type strain originally isolated from a Chinese lake (Cui et al 2006). Together with isolate Haloferax massiliensis , which was retrieved from human feces in 2018 (Khelaifia et al 2018), they represent the only two genomes affiliated to halophilic archaea available from the human GIT. This observation is in contrast to the previously reported high prevalence of Haloarchaea of Asian cohorts (Kim et al 2020).…”

Introducing clinical nanoarchaeaology: Isolation by co-culture of Nanopusillus massiliensis sp. nov.

“…This discovery was made possible after we developed nanoarchaea-oriented specific laboratory tools, capitalizing on the previous expertise that we have acquired over years in the clinical microbiology of archaea, methanogens and halophilic archaea ( Khelaifia et al., 2018 ), including their potential role in pathological situations in dysbiosis ( Grine et al., 2018 ), anaerobe abscesses ( Nkamga et al., 2018 ; Nkamga et al., 2016 ; Drancourt et al., 2017 ) and archaeamia ( Drancourt et al., 2020 ). Routinely available scanning electron microscopy was highly contributive to this work and discovery.…”

Going Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease

“…Among these, methanogenic members of the orders Methanosarcinales, Methanobacteriales, Methanococcales, Methanomicrobiales, and Methanopyrales were found to populate the human gut, along with the members of Desulfurococcales, Sulfolobales, Thermoproteales, Nitrososphaerales, and Halobacteriales orders, also detected in the human intestine (Gaci et al, 2014). A recent work, while confirming an increased prevalence of M. stadtmanae in the majority of human samples, failed to detect any nonmethanogenic archaeal lineages (Raymann et al, 2017), unless the Haloferax massiliensis and Haloferax assiliense, demonstrating that halophilic archaea can inhabit the human gut (Khelaifia and Raoult, 2016;Khelaifia et al, 2018).…”