Understanding phenotypic variation of plants using the hologenomic framework within the The Plant Hologenome Group

The Group focuses on understanding phenotypic variation of plants using the hologenomic framework. Together, the genome and the microbiome shape the functioning of plants. Within The Plant Hologenome Group, we consider the two simultaneously using multi’omic methods. We believe this will shed new light into how plants function, with particular interests in drought-tolerance and pathogen resistance.




There is still so much unknown about why plants of the same species can vary so much (their phenotype or functioning). This can have huge implications. For example, if this is susceptibility to disease, it could lead to some populations or crop varieties being decimated by a pathogen while others are relatively unaffected.

We know that many differences in the plant phenotype lie within the genome, but similarly, there a number of processes linked to the microbes that associate with plants. However, the genome and microbiome are rarely considered together, and neither has the interaction between the two. In The Plant Holobiome Group, we are interested in how the genome and microbiome interact to shape plant phenotypes, which we believe will help us better understand plant phenotypic variation than traditional methods (i.e. considering them alone).

In order to achieve this goal, we characterise the genome and microbiome using high-throughput sequencing methods. We profile the phenotype using transcriptomics, metabolomics or as morphological traits (such as yield or shoot:root ratio). We then integrate the multiple ‘omic datasets (genomic, transcriptomic, microbiomic, metabolomic) into comprehensive syntheses of plant functioning.


Maize genome-microbiome project

Plantago major holobiome project

Currently, we work on model plants (Zea mays, [maize]) and non-model plants (Plantago major [broadleaf plantain], Cinchona calisaya [the fever tree]). These approaches are ambitious, and therefore we generally focus on singular correlations initially (genome-microbiome or microbiome-plant chemistry) before building complexity into our models.


Maldonado, Carla, et al. "Phylogeny predicts the quantity of antimalarial alkaloids within the iconic yellow Cinchona bark (Rubiaceae: Cinchona calisaya)." Frontiers in Plant Science 8 (2017): 391.

Barnes, Christopher J., et al. "Extreme rainfall affects assembly of the root‐associated fungal community." New Phytologist 220.4 (2018): 1172-1184.

Iwanycki Ahlstrand, Natalie, et al. "Untargeted metabolic profiling reveals geography as the strongest predictor of metabolic phenotypes of a cosmopolitan weed." Ecology and evolution 8.13 (2018): 6812-6826.


Aage V. Jensen naturfond logo

Aage V. Jensen Naturfond



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European Research Council


Video on how microbes can help crops survive climate change

Meet Associate Professor Christopher James Barnes and hear how he aims to use a hologenomic approach to make plants such as crops like barley and their microbes better at surviving drought and climate change.

christopher barnes

Group Leader

Christopher James Barnes

Assistant professor
Section for Geogenetics
Phone: +45 35 33 78 67


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Daria Zharikova Guest Researcher +4535334986 E-mail
Nikolaj Meisner Vendelbo Postdoc +4535332083 E-mail

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Louise Isager Ahl Post doc +45 35 33 59 75 E-mail

Dustin Matthew Wolkis

PhD Student E-mail
Michael Opgenorth PhD Student
Kristina Egholm Hansen MSc Student