Methane metabolism bioinformatics pipeline

BaseClear has developed a state-of-the-art, in-house methane metabolism pipeline to assist researchers in identifying taxa, genes and enzymes that influence methane production in livestock. The pipeline is tailored towards profiling the relative abundance of species and proteins associated with methane production in the rumen metagenome. Furthermore, it provides an ideal tool for animal feeding trials to study the effects of interventions in ruminants.

This bioinformatics pipeline is an advanced and robust instrument to examine the impact of feeding interventions, to develop novel feed additives and to assess whether in-farm management strategies reduce methane production. Our dedicated microbiome database includes rumen methanogens and eukaryotes. Thus, we can integrate functional and taxonomic analyses with trial metadata and provide robust insights into the activities of the microbial community involved in methane production. Improving the sustainability of livestock production is our priority, and we can support you in engineering  the microbiome.

The Methane Metabolism Bioinformatics Pipeline: – Enabling Feed Additives and Management Practices to Reduce Methane Emissions

The role of the microbiome on methane production is central in the development of the methane metabolism pipeline. The flexibility of this pipeline allows for:

  • Identifying taxa, genes and enzymes influencing methane production.
  • Elucidating relationships across bacteria, archaea and fungi present in the ecosystem.
  • Assessing the efficacy of a supplement following a feed trial.
  • Profiling the relative abundance of both species and proteins present in the rumen microbiome.
  • Establishing associations between functional and taxonomic abundance, and trial metadata, using powerful statistical tools.
  • Delivering custom analysis and reporting to the client.

Our pipeline pinpoints protein sequences of interest, which are used to construct a database of over 16,000 gene marker sequences in total. Shotgun metagenome analysis of the rumen or gut contents is run in parallel, so the abundance of genes of interest is quantified, and the relative abundance of each member of the microbial community is calculated. Relationships between the trial metadata and both taxonomic and functional profiles are computed, and an association analysis is performed to find relationships between taxonomic and functional abundances. Finally, tables and visualisations are produced following client specifications.

BaseClear solutions

BaseClear provides the metagenomics sequencing and advanced bioinformatics to elucidate how the animal gut microbiome influences methane output, nitrogen utilization and feed efficiency. Harnessing this knowledge will support microbiome interventions and further changes in management practices, feed additives and genetic selection. With our expertise in study design and microbiome sampling and sequencing, we can support you from study conception to reporting and together we can contribute to a healthier and sustainable world.

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BaseClear Microbiology services

Meet Emma Hernandez-Sanabria!

With an international career spanning five countries, working in academia and for industry, Dr. Emma Hernandez-Sanabria brings a wide range of experience into her position as Product Manager in Animal Health and Performance. She combines knowledge about the microbiome of production animals with strong teamwork and mentoring skills to assist animal nutrition clients. Emma works in close collaboration with product managers and other stakeholders to develop products related to the microbiome of livestock. Microbial technologies offer distinctive opportunities for sustainable agriculture and livestock production. She explains: “The European Union has a major role to play in addressing global food and nutrition security. My experience in host-microbe interactions and with horticultural crops can support innovation to improve and safeguard animal health and welfare, thus promoting sustainability.”

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