Methanobrevibacter smithii strain U29 whole genome sequence delineates M. smithii intermediate cell variants

Methanobrevibacter smithii (M. smithii), the predominant methanogen in the human digestive tract, plays a key role in methane production. Despite its importance, the genomic diversity of M. smithii is poorly characterised, especially in extra-digestive sites such as the urinary and respiratory tracts, and the blood. Understanding this diversity would help unravel its potential role in human health and diseases.

We report the genome of M. smithii strain U29, isolated from urine, expanding the known diversity of the species. The M. smithii U29 genome (scaffold level; 1̵822‒124-bp, 1745 protein-coding sequences) lacks Candidatus Nanopusillus sequences, unlike digestive tract strains. Comparative analysis has revealed a high similarity (99.86% ANI) with the reference M. smithii strain ATCC 35,061, although U29 contains 71 unique coding sequences including 12/71 (13 200-bp; 69% of the total extra-material size) with demonstrated Siphoviridae viral ancestry. Accordingly, M. smithii U29 has been identified as an intermediate M. smithii cell variant, exhibiting genomic traits potentially conferring adaptability to the urinary tract.

This study enhances our understanding of M. smithii genomic diversity and highlights the presence of viral sequences in the urinary tract M. smithii strain U29. These findings open up a hypothesis that viral integration may play a role in M. smithii mucosae colonisation and dynamics, underscoring the need for further investigations into the mechanisms underlying its tissue translocation and potential health implications.