Case Studies

  • Atacama Desert

GreenGate wishes to showcase its extensive and specialized bioinformatic portfolio and is actively seeking partners and clients to  pilot its services. Working with us as part of a pilot project offers the unique opportunity to receive a high quality bioinformatic service. If you are interested in such a partnership we are happy to meet and discuss how to provide our bioinformatic expertise to your project in more detail.

Here we show one-page case studies to give you a nice overview of our expertise and possible projects.

Nanopore Genome Sequencing

  • Evaluation of Oxford Nanopore Technologies (ONT) base calling options
  • Careful execution of different computational steps from basecalling to binning of final genome.
  • Some steps of this workflow have a high influence on the size and quality of the final genome.
  • Read more …

Plastisphere

  • Isolation and Oxford Nanopore Sequencing of six different bacterial strain isolates from plastic polluted landfill soil
  • Reconstruction of metagenome assembled genomes (MAGs)
  • Taxonomic classification of recovered genomes
  • Functional annotation allowed the discovery of specific genes involved in polyethylene degradation (PE) degradation
  • Read more … 

Atacama Desert

  • Evaluation of extracellular and intracellular DNA fractions in soil and rock samples from different Atacama desert locations
  • 16S rRNA amplicon sequencing and reconstruction of microbial community patterns
  • Identification of highly adapted microbial species to investigate their response to extreme aridity and UV exposure, and gather important insights on microbial turnover in Mars like environments.
  • Read more … 

Biocide Resistance

  • Differential gene expression analysis  of Pseudomonas biofilms in response to sodium hypochlorite
  • RNA-seq and Transcriptome data analysis
  • Identification of significantly up- and down regulated genes
  • Reconstruction of potential resistance pathways
  • Read more …

Deep Biosphere

  • Reconstruction of Microbial distribution patterns across a 230m terrestrial subsurface drill core
  • Application of specifically adapted laboratory and bioinformatic workflows for low biomass environments
  • Amplicon and metagenomic based taxonomy analysis
  • MAG recovery and annotation allowed detection and characterization of CO2 utilizing methanogenic and chemolithotrophic microorganisms
  • Statistical evaluation provided insights into microbial co-occurrence patterns and bio-geo interactions.
  • Read more …

Methane-Cycling Microbiome in Permafrost

  • Taxonomic and functional profiling of methane cycling microbiomes in permafrost soil
  • Characterization of microbial diversity via 16S rRNA amplicon data analysis
  • Evaluation of active microbial populations by targeting microorganisms contributing to greenhouse gas (CH4 and CO2) production
  • Read more …

Oil and Gas Ecology

  • Investigation of microbial abundance and composition s patterns in oil and gas wells to identify the potential for bio-corrosion and well fouling
  • 16S rRNA and metagenomic sequencing to reconstruct microbial distribution and diversity
  • Assembly and annotation of metagenomic data to identify metabolic potential
  • Reconstruction and characterization of draft genomes provided insights into cellular processes in oil and gas environments.
  • Read more …