Draft Genome Sequence of a Human-Associated Isolate of Methanobrevibacter arboriphilicus , the Lowest-G+C-Content Archaeon

Abstract

We report the draft genome sequence of Methanobrevibacter arboriphilicus strain ANOR1, isolated from the human gut. Its 2.21-Mb genome exhibits a 25.46% G+C content, the lowest value among archaea. The genome of M. arboriphilicus contains a total of 2,111 open reading frames and three clusters of regularly interspaced short palindromic repeat (CRISPR) loci with associated Cas proteins.

Culture of previously uncultured members of the human gut microbiota by culturomics

“…The culture of methanogenic archaea is a fastidious process, and the necessary equipment for this purpose is expensive and reserved for specialized laboratories. With this technique, we isolated seven methanogenic archaea through culturomic studies as previously described [25][26][27] . In addition, we propose here an affordable alternative that does not require specific equipment 17 .…”

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

“…Methanomassiliicoccus intestinalis' ( Borrel et al 2013 ), as well as human gut-derived MAGs of Methanomassiliicoccales Mx02, Mx03, Mx06 and additional Ca. M. intestinalis' ( Borrel et al 2017 ), and the human isolate Methanobrevibacter arboriphilus ANOR1 ( Khelaifia et al 2014b ) to complete the dataset. Those genomes were assigned a genome accession number (GUT_GENOME286998 to GUT_GENOME287004), as given in Supplementary Table 1.…”

“…P-values were corrected for multi hypothesis testing using the false discovery rate (FDR). Table 1 for details Zeller et al 2014 ;Nielsen et al 2014 ;Franzosa et al 2014 ;Gevers et al 2014 ;Youngster et al 2014 ;Khelaifia et al 2014b ;Bäckhed et al 2015 ;Cleary et al 2015 ;Zeevi et al 2015 ;Zhang et al 2015 ;Feng et al 2015 ;Sankaranarayanan et al 2015 ;Rampelli et al 2015 ;Vogtmann et al 2016 ;Liu et al 2016 ;Pehrsson et al 2016 ;Palleja et al 2016 ;Vincent et al 2016 ;Schirmer et al 2016 ;Vatanen et al 2016 ;Xie et al 2016 ;Borrel et al 2017 ;Asnicar et al 2017 ;Smits et al 2017 ;Wen et al 2017 ;Yu et al 2017 ;Gu et al 2017 ;He et al 2017 ;Bedarf et al 2017 ;Costea et al 2017 ;Lloyd-Price et al 2017 ;Loomba et al 2017 ;Petersen et al 2017 ;Wu et al 2017 ;Ye et al 2018 ;Mehta et al 2018 ;Pasolli et al 2019 Software and Algorithms…”

“…Based on taxonomic classification resolved at the species level, most species identified in the human gut are indeed host associated (reviewed in Bang and Schmitz 2018 ;Moissl-Eichinger et al 2018 ;Borrel et al 2020 ). More specifically, based on the information on their respective biomes, the archaeal genomes of this study can be classified into three groups: i) exclusively found in the human gut, ii) host (human, animal, plant)-associated and iii) widespread in the environment, with the first two groups representing the majority (reviewed in Bang ( Cui et al 2006 ), M. arboriphilus ( Zeikus and Henning 1975 ;Khelaifia et al 2014b) and M. luminyensis ( Dridi et al 2012 ;Borrel et al 2017 ), which are widespread in various kinds of environments. It should be noted that for certain clades only a limited number of genomes is currently available, and thus their host/environmental tropism remains to be precisely determined (e.g.…”

Metagenomics for Bacteriology

“…91,[109][110][111][112] In the upcoming years, we need to expand our understanding of the role of archaea in the human microbiomes, as their transcripts are overabundant compared with their cell relative abundance. Limited information is emerging about humanarchaeal associations and the role of these organisms in human physiology.…”