Aims to understand how increasing temperatures and aridity are affecting population genomic features and microbial community properties of small mammals, by focusing on edge-of-range that are expected to be either expanding (in the north) or contracting (in the south) under climate change.
Coordinator: University of Exeter
Participants: University of Copenhagen
Funding: Natural Environment Research Council (NERC) & Carlsberg Foundation
Period: 2021-2024
Aims to generate population-level paired genomic and metagenomic data of paired marsupial and placental species with similar ecological characteristics, to understand the impact of animal-microbiota interactions in the evolution of ecological features of mammals.
Coordinator: University of Copenhagen
Participants: University of Adelaide, University of Tasmania, Universidad Austral de Chile, University of Pittsburgh
Funding: Carlsberg Foundation
Period: 2021-2024
Aims to study the relationships between ecological niche properties of the squirrels Sciurus vulgaris and Sciurus carolinensis, their genomic features, and their gut metagenomic characteristics, across their entire geographical distributions, including regions in which the species can be found in sympatry and allopatry.
Coordinator: University of Copenhagen
Participants: Duke University, CIBIO-InBIO, Bournemouth University, Leibniz Institute for Zoo and Wildlife Research in Berlin, University of Insubria, University of Wyoming, Mongolian Academy of Sciences
Funding: Carlsberg Foundation, Danish National Research Foundation (DNRF)
Period: 2021-2024
Aims to generate population-level paired genomic and metagenomic data of vertebrates across elevational gradients in various mountain ranges to understand the hologenomic underpinnings of adaptation to different climatic regimes.
Coordinators: University of Copenhagen, University of Lund, CNRS
Funding: Carlsberg Foundation
Period: 2021-2024
Aims to investigate whether metagenomic plasticity plays a role in invasions, i.e., whether invasive species may be able to quickly adapt to their new environment and oust native species thanks to a higher diversity and/or dynamism of their gut microbial community.
Coordinator: University of Copenhagen
Participants: University of Insubria
Funding: EU Marie Skłodowska-Curie Action
Period: 2023-2025
Aims at uncovering the hologenomic features of fire-bellied and yellow-bellied toads (Bombina bombina and B. variegata), their hybrids, and how their evolutionary pathways are affected by chytrid fungus, a highly deadly disease for amphibians.
Coordinator: University of Copenhagen
Participants: Croatian Institute for Biodiversity & Hungarian National History Museum
Funding: EU Marie Skłodowska-Curie Actions
Period: 2023-2025
Scavenging is an extreme dietary strategy that requires immune adaptations to cope with the diverse microorganisms that grow in animal carcases. Some years ago, New World vultures were shown to possess a specialised microbiome that was hypothesised could enable them to cope with such conditions. This project aims to address this question by not only studying genomic features of bacterial communities, but also their gene expression and the expression of host vultures.
Coordinator: University of Copenhagen
Participants: Smithsonian Museum of Natural History
Funding: Carlsberg Foundation
Period: 2023-2025
Understanding the extent to which the microbiome affects individual and population-level fitness and productivity in birds is becoming increasingly important for the recovery of endangered bird populations. This project aims to characterise the microbiome diversity within the threatened echo parakeet, an IUCN Red Listed species endemic to the island of Mauritius and which has been successfully restored by the Government of Mauritius’ National Parks and Conservation Service and the Mauritian Wildlife Foundation.
Coordinator: Durrell Institute of Conservation and Ecology (DICE), University of Kent
Participants: University of Copenhagen, National Parks and Conservation Service, Government of Mauritius
Mauritian Wildlife Foundation, Chester Zoo (UK)
Funding: Chester Zoo, UK
Period: 2023-2025
Aims to investigate the presence of consistent genomic and gut metagenomic signatures in lizard populations that are restricted to tiny islets. To do so, we test if gut microbiome diversity and composition is shaped by loss of host genetic diversity, long-term isolation, or the unique ecological challenges associated with persistence on small islets.
Coordinators: University of Lund, University of Copenhagen
Funding: Carlsberg foundation, ERC Starting Grant
Period: 2023-2025
Restored and newly created ponds are a critical resource to counteract amphibian population declines in areas with severe anthropic pressure. While many amphibian species are able to colonise and take advantage of such microhabitats, we don’t know whether and how microbiome features are affected. This project aims to ascertain whether newt microbiome features are correlated with host health and pond attributes.
Coordinators: University of Copenhagen
Participants: Aranzadi Science Society
Funding: Kutxa foundation
Period: 2023-2025
A growing number of studies have linked the microbiome with individual performance, but there remains a limited understanding of how microbiome functional traits may underlie specific life history strategies. For food caching species (species that store food for future use), the microbiome could be specialised to facilitate the long-term storage of food or buffer individuals from the deleterious effects of food storage. We aim to quantify functional traits of the gut and oral microbiome to understand how the microbiome may allow individuals to continue to rely on cached food despite rapid environmental change.
Coordinators: Bangor University
Participants: University of Copenhagen, University of Konstanz
Funding: NERC, Bangor University, Carlsberg foundation
Period: 2023-2025
Recent evidence suggests that loss of host-genetic diversity constrains microbiome diversity. These results point out to consider population genomics tools to understand the mechanism involved in host-microbiome interactions. However, host-genetics and the diversity of its associated microbiomes are usually considered independently. This project aims to rethink diversity from an holobiont perspective. We adopt the term signatures of holobiont diversity (SHD) and propose a methodological framework to explore links between relative Site Frequency Spectrum (rSFS: nucleotide diversity split by their relative frequency in the entire population) patterns across host-genome and gut microbiota diversity and richness indices
Coordinators: Institute of Agrifood Research and Technology (IRTA)
Participants: Centre for research in Agricultural Genomics (CRAG)
Funding: Contrat Ramon y Cajal
Period: 2023-2025
Aims to investigate early assembly of gut microbiota in the colour polymorphic Eleonora’s falcon, living in an edge population that is subject to strong climate-driven food instability. We also aim at understanding whether the microbiota community and rearrangements in response to environmental stress may function as a protective mechanism shielding individuals from the physiological effects of food limitation and, importantly, its interaction with heritable genetically determined coloration.
Coordinators: Estación Biológica de Doñana EBD-CSIC
Participants: Complutense University of Madrid
Funding: CNS2022-135873
Period: 2023-2025
Aims to understand the associations between gut microbiota of desert predators, in particular bats, and their scorpion prey.
Coordinators: Ben-Gurion University of the Negev
Participants: University of Copenhagen
Funding: Ecological Society
Period: 2023-2027
Aims to generate population level paired genomic and metagenomic data of neotropical vertebrates (birds, bats, and amphibians) which inhabit ecosystems with similar ecological characteristics in the cloud forest of Honduras to understand the role of the gut microbiota in facilitating adaptive responses in inhabits with different degrees of anthropic perturbation.
Coordinators: University of Copenhagen, HN Biology Investigation
Participants: Ornithological Research Institute of Honduras
Funding:
Period: 2022-2025
Aims to understand the role of the gut microbiome in the host’s response to elevated heavy metal (mercury) levels in avian bioindicators in the Peruvian Amazon.
Coordinators: University of Copenhagen
Participators: University of California Davis
Funding: Marie Curie Postdoctoral Fellowship
Period: 2021-2024
Aims at characterising the faecal microbial communities of six different migratory passerine species during spring migration stopover. Furthermore, we will use the garden warbler (Sylvia borin) as a model species to understand whether states of fasting and refeeding influence the faecal microbiota during avian migration.
Coordinators: Konrad Lorenz Institute of Ethology (University of Veterinary Medicine Vienna)
Participants: University of Vienna
Funding: Austrian Science Fund (FWF), Intramural funds
Period: 2019-open
Center for Evolutionary Hologenomics, GLOBE Institute
University of Copenhagen
Øster Farimagsgade 5, 7
1353 Copenhagen K, Denmark
Coordinator: Antton Alberdi, PhD
Email: ehi@sund.ku.dk