Title Genomic Characterization of Novel Bacteria with Plastic Degradation Potential
Advisor Assist. Prof. Dr. Luis Miguel Rodriguez Rojas, Department of Microbiology and Digital Science Center (DiSC)
Number of students 1
Language English


Bioprospection of microbial aggregates is a promising avenue for the reduction of the global environmental impact of plastics. Two of the most important metabolic processes to achieve this aim are microbial plastic degradation and synthesis of bioplastics. The laboratory of Dr. Diego Jiménez (Universidad de Los Andes, Colombia) has sampled lignocellulose-rich mangrove soils heavily impacted by plastics contamination, and selected a consortium with reduced diversity by successive transfers in minimum media only amended with PET as their carbon source. A collection of high-quality genomes from this consortium was obtained by long-read metagenomic sequencing. The successful candidate will lead the efforts on characterizing these genomes with an emphasis on their taxonomic description and metabolic annotation. The latter will focus on the identification of enzymes and metabolic pathways potentially associated to plastic degradation and/or bioplastic synthesis.


  • Training on environmental genomics fundamental concepts and basic computational techniques
  • Training on the use of High-Performance Computing (HPC) to access the services of the LEO clusters
  • Taxonomic description of the microorganisms presented here following the guidelines of the SeqCode (Code of Nomenclature of Prokaryotes Described from Sequence Data)
  • Functional annotation of genes associated to plastic-degradation in the genome collection
  • Targeted metabolic reconstruction for pathways relevant to plastic degradation and/or bioplastic synthesis
  • Presentation of results orally and in a written report

Theoretical skills

Foundations on microbiology and molecular biology are highly desirable. Additionally, knowledge on distributed systems and High-Performance Computing is appreciated but not required. Interest in environmental genomics is required, but no previous knowledge necessary.

Practical skills

HPC Scheduler Systems and Basic knowledge on Bash is preferred, but not required.

Additional information

The student will remotely interact with the Jimenez Laboratory at the Universidad de Los Andes (Colombia) at least once, and a presentation of their results is highly encouraged.