Global climate change is a major environmental concern, primarily driven by the significant increase in CO2 emissions due to the burning of fossil fuels, which accounts for 77% of CO2 emissions worldwide. Conventional plastics manufacturing relies heavily on crude oil and natural gas, contributing to climate change and environmental pollution. The production of plastic polymers has increased dramatically, from 2 million tons in 1950 to approximately 381 million tons in 2015, with an estimated total plastic waste accumulation of about 25,000 million tons. This underscores the urgent need to develop biodegradable, compostable, and environmentally friendly substitutes for conventional plastics to ensure future economic and ecological security.

Bioplastics, such as polyhydroxyalkanoates (PHAs), present a promising strategy to address the global fossil fuel crisis. Despite their potential, bioplastics currently account for only 1% of annual plastic production. PHAs are biopolyesters produced by bacteria under unfavorable growth conditions and can be synthesized from eco-friendly feedstocks without depleting natural resources. They decompose into non-contaminant substances via composting after use, making them ideal for sustainable applications in industrial and medical fields. However, to make PHAs competitive with fossil-fuel-derived plastics, it is crucial to develop high-yield, cost-effective production processes.

One effective method for PHA biosynthesis involves using mixed microbial cultures (MMCs). However, optimizing the PHA production process using waste streams, such as those from the cheese making industry, remains challenging due to high salt content and organic matter affecting microbial communities.

Project objective

The primary objective of this internship project is to analyze the shifts in size and structure of bacterial communities in two MMCs involved in PHA production using protein rich waste from the diary industry as a substrate. This will be achieved through metagenomic sequencing using Oxford Nanopore technology and subsequent bioinformatics analysis.

Project description

  1. Literature Review and Theoretical Background:
    • Conduct a comprehensive review of existing research on PHA production, MMCs, and the use of industrial waste streams as substrates.
    • Understand the biochemical pathways involved in PHA biosynthesis and the impact of environmental factors on microbial community dynamics.
  2. Metagenomic Sequencing and Bioinformatics Analysis:
    • Extraction of high quality DNA according to the need of sequencing
    • Perform metagenomic sequencing using Oxford nanopore technology to analyze the shifts in bacterial community size and structure in a time course.
    • Apply bioinformatics tools to interpret sequencing data, focusing on successional patterns of key PHA-biosynthesizing genera.
  3. Data Collection and Analysis:
    • Use existing and novel bioinformatic tools to define the bacterial species in MMA,
    • Integrate data on PHA production yields, bacterial community dynamics, and operational variables.
    • Use statistical tools to identify trends and correlations between microbial community structure, PHA yields, and cultivation conditions.
  4. Comparative Analysis and Reporting:
    • Compare the performance of different MMCs in terms of PHA production efficiency and microbial community resilience.
    • Document experimental procedures, results, and analyses in a detailed project report.

Expected outcomes

  • Enhanced understanding of the microbial community dynamics in PHA-accumulating MMCs via megagenomics (16s is also possible).
  • Comprehensive project report with recommendations for industrial application and future research.

Skills and Competencies Gained

  • Hands-on experience with nanopore sequencing and bioinformatics in metagenomics
  • Knowledge of metagenomic sequencing, bioinformatics, and microbial community analysis.
  • Experience in data analysis, reporting, and project management.


This internship project will span 20-30 weeks, with a structured timeline for literature review, experimental work, data analysis, and reporting. The start of the project will be from 2nd September 2024.

Mentorship and Guidance

The intern will be supervised by experienced researchers and professionals in biotechnology and bioinformatics (MNEXT Smart Fermentation, Bazante Sanders and Tim Verschuren), with regular progress reviews and support to ensure the successful completion of project objectives.

For more info or to submit your application, contact Jasper Meijer (

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