Methane metabolism & antimicrobial screening

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.


Antibiotic resistance gene screening

BaseClear offers a state-of-the-art antibiotic resistance gene screening service based on complete genomics analysis. Our method is much more efficient than the classical screening methods. With our unique antibiotic resistance gene screening service we use highly curated databases. This service is part of our complete package for genomics-based Microbial Strain Assessment.

The use of antibiotics during the last decade has led to antibiotic resistance among microorganisms, which is a growing public health concern on a global scale. The mechanisms that enable bacteria to become resistant to antibiotics are quite diverse, but the genetic basis for the antibiotic resistance can be either intrinsic, through naturally occurring antibiotic resistance genes, or acquired through transfer of genetic material (e.g. plasmids) from other bacteria in the environment.

Screening for novel antibiotic resistance genes

To minimize the risk of spreading antibiotic resistance, EFSA advises to use the least resistant organism whenever possible and that the organisms used in animal feed or used as probiotics should not add to the existent pool of antimicrobial resistance genes that are already present in the environment. Screening microorganisms for antibiotic resistance can be very laborious and time consuming. BaseClear offers a new type of antibiotic resistance gene screening based on complete genome sequencing, which is much more efficient than the classical screening methods. Using unique bioinformatics tools that are developed by our bioinformatics team, we can determine which antibiotic resistance genes are present in the microbial genome. This genome screening method can dramatically reduce the number of disk diffusion tests required.

BaseClear can provide you with information about the location of the antibiotic resistance gene (chromosome or plasmid), identification of novel antibiotic resistance genes, as well as identification of mobile genetic elements that may promote transfer of genomic regions coding for the antibiotic resistance to other organisms. Knowledge of (novel) antibiotic resistance genes helps you to understand how antibiotics function and how bacteria fight them.


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