Evolutionary metagenomics

Inference of microbial evolutionary processes from genetic heterogeneity present in metagenomes.

Microdiversity in soil bacteriophages (PhD student Thomas de Bruijn, with Hilje Doekes).

Virus discovery and evolution

Detection of viruses in plant and insect sequencing and estimation of their diversity and evolution.

Viruses <

Virus diversity and genome evolution in natural plant ecosystems (PhD student Dimitris Karapliafis, with Mark Zwart)

Virus discovery in insect genome sequencing (PhD student Laura Patiño Medina, with Astrid Bryon)

Microbial and phage pangenomes

Contribution of different evolutionary processes that shape pangenomes of bacteria and phages

Pangenomes <

Models for pangenome evolution (with Franz Baumdicker)

Function prediction in microbial pangenomes (PhD student Thijmen van der Loop, in collaboration with René Dirks, Daniel Probst, and Dick de Ridder)

Microbial communities

Communities <

Synthetic microbial communities for mitigating ammonia and greenhouse gases generated by fecal microbiota (in collaboration with Jun Liu)

Deciphering the role of the soil microbiome in intercropping (PhD student Joliese Teunissen, with Stefan Geisen)

Viral communities in fermented milk products (with Sijmen Schoustra and Anna Alekseeva)