Partial Treponema spp. as candidate probiotics for rumen methane mitigation revealed by a module-based activity index

Area of Science:

• Microbiology
• Environmental Science
• Animal Science

Background:

• Methane emissions from ruminants are a significant greenhouse gas source, primarily driven by methanogenic archaea in the rumen.
• Current methods often use metagenomic (MG) data to estimate methanogenic potential, but this may not accurately reflect in-situ activity.

Purpose of the Study:

• To investigate the discrepancy between microbial abundance and transcriptional activity in bovine rumen methanogenesis.
• To identify microbial taxa and pathways associated with methane production in the rumen.

Main Methods:

• Analysis of paired metagenomic (MG) and meta-transcriptomic (MT) datasets from 48 bovine rumen samples.
• Development of a Methanogenesis Pathway Expression Activity Index (MPEAI) using KEGG modules.
• Application of Random Forest modeling to link microbial taxa to MPEAI.

Main Results:

• Metagenomic and meta-transcriptomic profiles showed significant incongruence in microbial composition and archaeal activity.
• Methanogenesis pathway modules were transcriptionally hyperactive despite suppressed archaeal abundance.
• Treponema species were negatively correlated with methanogenesis pathway activity.

Conclusions:

• Rumen methanogenesis is regulated by functional pathway activity, not solely by archaeal abundance.
• Treponema species show potential as probiotics for methane mitigation due to their negative association with methanogenesis.
• Bacterial-archaeal interactions play a crucial role in regulating rumen methane production.