Rumen transfaunation between low- and high-methane-yielding dairy cows reveals asymmetric microbiome reconstitution patterns: a pilot study
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
Background
This study investigated rumen microbiome reconstitution and methane (CH 4 ) emissions following a complete exchange of rumen contents between low- and high-CH 4 -yielding Norwegian Red dairy cows. Twenty cows were screened for CH 4 yield, and two low and two high emitters were selected for rumen cannulation and content swap. Total rumen contents were swapped after complete evacuation and washing of both the rumen and omasum. Rumen samples were collected twice in weeks −1, 1, 3, and 7 for fermentation analysis, metagenomics, and metaproteomics, and at week 8 CH 4 production was measured.
Results
Prior to the swap, low and high emitters produced 21.2 ± 0.7 and 26.3 ± 1.4 g CH 4 /kg dry-matter intake (DMI), respectively. Eight weeks after swap, CH 4 yields were 12.7 ± 0.3 and 28.9 ± 0.3 g CH 4 /kg DMI, respectively, showing that the CH 4 phenotype of each cow was maintained. Analysis of metagenome-derived 16S rRNA gene sequences showed that low emitters gradually re-established their original microbial community, whereas high emitters retained donor-like microbiota. Metaproteomic mapping suggested higher expression of Prevotella-associated succinate–propionate pathway enzymes in low emitters at week 7, though these differences were modest.
Conclusion
These findings suggest that host factors influence CH 4 output and microbial reconstitution, with low emitters restoring their native microbiome while high emitters retained a donor-associated community yet continued to emit high CH 4 . Results should be interpreted with caution given the small sample size (n = 2 per phenotype) and require confirmation in larger studies.
Importance
Reducing enteric methane from cattle requires understanding whether the rumen microbiome or the host animal is the primary driver of methane output. We exchanged the entire rumen contents between low- and high-methane-yielding dairy cows and measured methane production alongside metagenomic and metaproteomic profiling over two months. Despite receiving each other’s microbiomes, each cow’s methane phenotype persisted—low emitters stayed low and high emitters stayed high. Microbiome reconstitution was asymmetric: low emitters restored their original microbial community, while high emitters retained the donor microbiota. Methanogen communities did not differ between phenotypes, pointing to host-level rather than microbial-level control of methane yield. These pilot findings suggest that breeding for favorable host traits may be essential for lasting methane reduction, and that microbiome transfer alone is unlikely to shift an animal’s methane phenotype. Larger studies are needed to confirm these observations.
