Co-occurence analysis

Inference of microbial interactions from their co- occurrences

The use of network analysis to explore ecological communities has largely increased in popularity in the last few decades. In particular, it follows a significant accumulation of sequencing data of microbial composition obtained for hundreds of different environments. With this accumulation the target of research shifted from simply describing species diversity to the next step, which is to unravel how these ecological communities assemble in the first place. One of exploratory methods used with this aim is to build and analyze what is commonly known as species co-occurrence networks. These networks link species which have a pattern of co-existence, or avoidance of each other in a number of environmental samples. We have extensively reviewed the potential and the shortcomings of such analysis when applied to soil microbiome in two recent perspectives.

We use also apply co-occurrence analysis to reconstruct possible interactions of microorganisms in soil, with the aim to disentangle the drivers behind community assembly.


  • A critical perspective on interpreting amplicon sequencing data in soil ecological research Alteio, Lauren V., Séneca, Joana, Canarini, Alberto, Angel, Roey, Jansa, Jan, Guseva, Ksenia, Kaiser, Christina, Richter, Andreas, and Schmidt, Hannes Soil Biology and Biochemistry Sep 2021

  • From diversity to complexity: Microbial networks in soils Guseva, Ksenia, Darcy, Sean, Simon, Eva, Alteio, Lauren V., Montesinos-Navarro, Alicia, and Kaiser, Christina Soil Biology and Biochemistry Apr 2022