Florence Computational Biology Group

Microbiome Assembly: A multilevel approach to predict establishment and variation of microbiomes


Research Units involved: 

  • MARTINO Maria Elena - University of Pavia
  • FONDI Marco - University of Florence
  • BOSI Emanuele - University of Genova

Project details:

  • Coordinator: MARTINO Maria Elena
  • Project code: 2022Z88RK4
  • Budget:      206.296,00 Euros

Project description:

The mechanisms by which host-associated microbiomes assemble is unresolved and controversial. Microbial ecologists have hypothesized that genetic and environmental processes may explain the characteristics of the vertebrate microbiomes. However, how these factors converge to determine microbiome assembly and variation across hosts remains largely elusive. MicroACE will examine aspects of microbial ecology, evolution and animal biology to reveal the ecological mechanisms involved both in short- and long-term establishment, variation, transmission and function of host-associated microbiomes.
The overall hypothesis behind this project is that microbiome assembly is predominantly and temporally driven by adaptation to the external environment, transmission capacity, and colonization history. By combining genomics, genetic engineering, mathematical modelling and animal behavioural studies, we will 1) reveal to what extent microbial dispersal through the environment and host-mediated transmission contribute to microbiomes’ assembly and 2) identify how environmental heterogeneity drives the establishment, function and evolution of host-associated microbiomes. Moreover, we will identify fundamental principles about how microbiome assembly processes influence host behaviour and physiology. We will use the guppy as a novel animal model in host-microbiome ecology. Having many advantages over other species, the guppy is a tractable system to study the mechanistic foundations of microbiome assembly, as all ecological processes can be strictly controlled.
This project is innovative as it offers the first comprehensive assessment of the mechanisms that drive microbiomes’ assembly throughout host development. Our results will also provide a greater understanding relevant to most host-microbe interactions, including those occurring in mammals.

Our reseach scheme:





What we do:







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