15 February 2021

The Earth Hologenome Initiative

Earth Hologenome Initiative

The Center of Evolutionary Hologenomics has launched the Earth Hologenome Initiative (EHI, www.earthhologenome.org) led by Associate Professor Antton Alberdi. The Initiative aims to foster collaborative projects and optimise the use of biological resources and the data generated using the ‘hologenomic approach’. One project already emerging from EHI is the Squirrel Hologenomics project.

EHI kit box

What is the Squirrel Hologenomics project about?

Squirrel Hologenomics is a global collaborative effort to generate paired genomic and metagenomic population-level databases of Eurasian red squirrels (Sciurus vulgaris) and American Eastern grey squirrels (Sciurus carolinensis). The aim is to study the relationships between ecological niche properties, their genomic features and their intestinal microbiomes across their entire geographical distributions, including regions with species overlap after the introduction of grey squirrels. By sampling across environmental gradients such as climate and urbanisation we aim to elucidate the impact of host-microbiota interactions on ecological and evolutionary processes including adaptation to novel environments. We will also use this hologenomic approach to gain novel understanding on the interspecific competition between the two species resulting in the decline of native red squirrels, while obtaining high-quality population genomics insights of both species. 

Squirrel Hologenomics logo

Why is a project like this important?

Most animals on Earth live in association with microorganisms and are continuously interacting, with significant bi-directional effects on both hosts and microorganisms. A ‘hologenomic’ approach jointly analyses the interconnection between the host and microbial metagenomes, and their combined functions. Squirrel Hologenomics utilizes this approach and enables a novel opportunity to provide fundamental insight to explore broader implications of the microbiome in the context of ecological and evolutionary processes, as well as applied aspects related to disease ecology, conservation and invasive species management. 

How can the initiative aid other researchers?

Launched in 2020, the Earth Hologenome Initiative is a collaborative interdisciplinary network and open science initiative that aims to encompass projects with diverse study designs and goals around common sample collection and preservation, data generation and data management criteria to pioneer an open biological sample biobank and database. So please get in touch if you are working on projects of relevance to the EHI.

What is the impact of this initiative on the scientific community?

The hologenomic approach and standardised methods developed by EHI will be applicable across multiple fields. The aim is to be collaborative, not competitive, and create an interdisciplinary network of field biologists, (meta)genomicists, microbiologists and data scientists interested in Open Science to generate a global, standardised dataset.

Generating comparable hologenomic datasets requires standardised procedures, which must be affordable and open access to allow for low-income countries/research groups to participate in the Initiative and ensure an unbiased global sampling effort. Open access procedures will also ensure the Initiative is long-lasting and maximises the potential of the samples being collected and the hologenomic data being generated. 

In the short research talk below postdoc Aoife Leonard explains the Earth Hologenome Initiative as well as the Squirrel Hologenomics Project in more detail.



Postdoc Aoife Leonard 

Associate Professor Antton Alberdi

Outreach responsible Christina Noer