Expanding the cultivable human archaeome:Methanobrevibacter intestinisp. nov. and strainMethanobrevibacter smithii “GRAZ-2”from human feces

Abstract

Two mesophilic, hydrogenotrophic methanogens, WWM1085 and M. smithii GRAZ-2 were isolated from human fecal samples. WWM1085 was isolated from an individual in the USA, and represents a novel species with in the genus Methanobrevibacter. M. smithii GRAZ-2 (= DSM 116045) was retrieved from fecal samples of a European, healthy female and represents a novel strain within this genus. Both Methanobrevibacter representatives form non-flagellated, short rods with variable morphologies and the capacity to form filaments. Both isolates showed the typical fluorescence of F420 and methane production. Compared to M. smithii GRAZ-2, WWM1085 did not accumulate formate when grown on H2 and CO2. The optimal growth conditions were at 37C, and pH 7. Full genome sequencing revealed a genomic difference of WWM1085 to the type strain of M. smithii PS (type strain; DSM 861), with 93.55% ANI and major differences in the sequence of its mcrA gene (3.3% difference in nucleotide sequence). Differences in the 16S rRNA gene were very minor and thus distinction based on this sequence might not be possible. M. smithii GRAZ-2 was identified as a novel strain within the Methanobrevibacter genus (ANI 99.04 % to M. smithii PS). Due to the major differences of WWM1085 and M. smithii type strain PS in phenotypic, genomic and metabolic features, we propose M. intestini sp. nov. as a novel species with WWM1085 as the type strain (DSM 116060T = CECT 30992).

Proteomic and Metabolomic Profiling of Archaeal Extracellular Vesicles from the Human Gut

“…The human gut derived strains Methanobrevibacter smithii ALI (DSM 2375), and Methanosphaera stadtmanae (DSM 3091, type strain) were obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ) GmbH, Braunschweig, Germany. Candidatus M. intestini WWM1085 (DSM 116060) was obtained from the Department of Microbiology, University of Illinois, USA, where it was isolated from a stool sample of a healthy woman 24 . In the following, we will use the abbreviation “M.…”

“…M. smithii GRAZ-2 (DSM 116045) was isolated in 2018 at the Medical University of Graz, Graz, Austria, from a stool sample of a healthy woman 24 . Instead of opting for the Methanobrevibacter smithii type strain (PS, DSM 861), our choice was M. smithii ALI, as it sourced from a human fecal sample and not from sewage water.…”

“…For the cultivation of all methanogens standard methanogenium medium (MS) with some modifications as previously described 24 . For vesicle production, aliquots of 250 ml media in 1000 ml infusion bottles were sealed, pressurized with H 2 /CO 2 (4:1) and autoclaved.…”