The role the gut microbiome in responding to environmental changes, within and between generations, and species

The ERC consolidator project 2024-2029 (2.0 M€) led by Suvi Ruuskanen

The gut microbiome is strongly linked to health and sickness. A current key challenge is to understand how the microbiome helps the host adapt to environmental variation. Yet, most research originates from few laboratory animal models and thus misses large parts 
of environmental, physiological and life-history variation, while data from wild populations and species is needed. Thus, our overarching aim is to unravel how the microbiome mediates host’s responses to environmental variation, covering molecular to evolutionary scale, using wild birds as a study system. We focus on how gut microbiome helps hosts to cope with temperature variation, given the pervasiveness of temperature as a challenge across taxa, and climate-crisis driven thermal challenges. We use birds as our study system. See below our five major objectives and progress:

(O1) We study the role of the microbiome in mediating host (adaptive) reversible thermal plasticity in adulthood 

Here, we have experimentally manipulated ambient temperatures, via simulating fluctuations (heat waves and cold snaps), to understand temporal changes in gut microbiome and thermal physiology (led by Maria Correia). We further manipulate directly the microbiome via probiotics and via transplants from high and low cold-tolerant birds (led by Mari-Ann Lind) within a population, and test the role of microbiome mediating local adaptation via microbiome transplants across populations (led by Stijn Kouwenberg, collaboration Andreas Nord). 

(O2) To assess the role of the microbiome in mediating host (adaptive) developmental and transgenerational thermal plasticity, and explore the underlying epigenetic changes  

We have experimentally manipulated early-life thermal environment (nest-box cooling heating) and microbiome (via antibiotics), to understand long-lasting effects on adult thermal physiology, and role of microbiome and epigenetics as underlying mechanisms (led by Charli Davies, in collaboration with Sophie Reichert, Clemence Furic and Julie Fleitz). We have further manipulated transfer of microbiome from parents via microbiome transplants, to understand the role on thermal development of the offspring (led by Maria Correia).

(O3) To quantify the contribution of host genetic variation and the microbiome on host thermal physiology  

We collect data on the heritability of microbiome using pedigree population and the heritability of reaction temperature-microbiome reaction norm (led by Stijn Kouwenberg, collaboration Kees van Oers, David  Diez Mendez). We also study the role of genetic and environemntal effects using common garden reared birds originating from populations across different latitudes (led by Stijn Kouwenberg, collaboration Kees van Oers, Xieomei Chi, David  Diez Mendez). Finally, by creating selection lines on cold tolerance (cost of thermoregulation), we distinguish the contribution of genetic and microbiome (led by Lisandrina Mari).
(O4) To explore the macroevolutionary patterns of microbiome and host thermal physiology  

To understand how evolutionary conserved are the associations between temperature microbiome and thermal physiology,  we have collected >1500 samples across >70 taxa with tens of collaborators. 

(O5) To examine the underlying molecular mediators of host-microbiome interactions 

We have experimentally manipulated putative key bacterial metabolites, short-chained fatty acids (butyrate) both in adults and during development to understand its role on mediating effects of gut microbes on host thermal physiology (led by Maria Correia). We characterize novel mechanisms, metabolomic profiles and extracellular vesicle contents in response to environmental challenges (led by Heloise Duvignau, collaboration Lisandrina Mari, Phill Watts