Workshop on microbiome analysis at CCMAR
Date of publication: Dec 15, 2022

Peter Kuperus and Gerard Muyzer from the University of Amsterdam (UvA) visited the Center of Marine Sciences (CCMAR) to give a hands-on workshop on microbiome analysis of marine organisms. The 16S rRNA genes of the microbiomes of different organisms and environments (i.e., seagrasses, green and brown algae, seawater and sediments) were PCR-amplified with different primer sets and subsequently sequenced on a Nanopore MinION device. Comparative analysis of the microbial communities obtained with the different primer sets showed different compositions due to the different primer specificities. In addition, the genomes of two isolated bacteria were sequenced and analyzed with bioinformatic tools; sequence reads were trimmed with NanoFilt, assembled with the software program Flye, and further analyzed in KBase.

Participants of the workshop on microbiome analysis. Peter explains and demonstrates the Nanopore sequencing. Aschwin analysed the results.

In addition to the use of state-of-the-art sequencing methods, ‘good-old’ microbiological techniques such as dilution shake tubes and pour plates were practiced for isolating microaerophilic and anaerobic bacteria from seagrasses and seaweeds. The genomes of selected isolates will be sequenced, and their phylogeny and potential physiology determined by comparative sequence analysis. Selected bacterial isolates will be used as probiotics in the RESTORESEAS project for the restoration of seagrasses and seaweeds.

PhD students Julia van Duijnhoven and Katrin Walter collecting seagrass samples for bacterial cultivation.

Written by Gerard Muijzer, University of Amsterdam