Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2023

Genomic and transcriptomic analyses of Methanosphaera spp. reveal evidence of host-adaptation (#165)

Harley McRae 1 , James Volmer 1 2 , Yang Lu 3 , Phillip Pope 4 , Rochelle Soo 3 , Paul Evans 3 , Mark Morrison 1 5
  1. Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
  2. Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD, Australia
  3. School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD, Australia
  4. Norwegian University of Life Sciences, As, Norway
  5. Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia

Gut methanogens typically use H2 via interspecies hydrogen transfer to support methanogenesis and growth. However, recent studies suggest members of the genus Methanosphaera are exceptional in their phylogenetic bifurcation according to genome size, and the capacity of at least some species to utilise ethanol for methanol reduction to methane. Here, we use a unique collection of Methanosphaera spp. from human, marsupial and ruminant hosts to undertake comparative genomic and transcriptomic analyses of their methylotrophic growth.

 

Methanosphaera stadtmanae DSMZ 3091T (human) as well as three newly isolated strains from human (PA5), macropodid (WGK6) and bovine (BMS) were cultured using rumen fluid based medium containing 250 mM methanol and a headspace gas mixture of H2:CO2. In parallel, strain WGK6 was also cultured using the basal medium supplemented with both methanol and ethanol without added H2 gas. Each strain was cultured three times and the biomass collected for RNA extraction, clean-up, and cDNA library construction for short-read sequencing.

 

The four Methanosphaera genomes possess a substantial amount of genetic homology and synteny, emphasising their shared metabolic functions. However, the bovine genome is considerably larger than the others, with the additional content largely encoding microbial “dark matter”. Principal Component Analysis of the RNA-seq data suggests there is a basis for the host-specific separation of the transcriptomic profiles, including differentiation of the human and non-human isolates based on expression of cobalamin biosynthesis genes. Interestingly, expression of the V-ATPase genes is reduced in strain WGK6 (macropodid) in response to ethanol- rather than H2-fueled methanogenesis. All the genomes contain a substantial amount of coding sequences (~40-55%) that are deemed “unassigned” or “uncharacterised” via KEGG-based orthology but still comprise a substantial amount of the transcriptional activity (~20-30% of total reads). Collectively, our findings show the genus Methanosphaera is comprised of strains with varying genomic complexity, and their transcriptomic profiles are substantially different and reflective of their host specificity, with a considerable contribution of genetic dark matter to their growth.