Models4Invasion

Project reference: 2022.03060.PTDC

Funding: Portuguese Foundation for Science and Technology (FCT)

Title: Mathematical modeling of invasion resistance in multi-species ecosystems

Period: 01-03-2023  to 28-02-2026 (3 years)

DOI: https://doi.org/10.54499/2022.03060.PTDC

Abstract

In this project we propose to study with mathematical models a key aspect of health mediated by microbiota, known as colonization resistance. This refers to the protection that commensal microbes provide against invading pathogens, a huge aid to immune defenses. When the multispecies ecosystem is imbalanced, from internal composition or external perturbations, this protection is compromised and disease may follow. Although much is known on the biological mechanisms involved in system resistance to invasion, a solid theoretical quantitative understanding of the phenomenon is still missing, limiting predictive power. Here, we address this knowledge gap, linking invasibility theory in ecology with microbiology and adaptive dynamics. We study invasion resistance emergence and regulation in a multispecies system, linking microbial ecological interactions, selection, and system mean invasion fitness. Our results will offer new avenues to test, interpret and manipulate interaction networks in complex microbial consortia, quantify invasion resistance, and predict its dynamics.

Team:

PI: Erida Gjini, CEMAT, IST, University of Lisbon

Co-PI: Sten Madec, IDP, University of Tours, France

Fellows

  • PhD – Tomas Ferreira Amaro Freire (100%) 01/09/2023 – ongoing (in co-supervision with Sten Madec and Susana Vinga)
  • Visiting PhD student Carlos Andreu (Polytechnic University of Valencia)
  • Tomas Camolas 1-year IST MSc student (Project and Thesis) start: 10/09/2024
  • Marina Garcia – Master student (Universitat Politecnica de Catalunya, Barcelona)

Past members

  • Abdullah Fathi –BI  (6 months): 01/10/2024–31/03/2025
  • Nicola Cinardi – postdoc/collaborator 15/05/2024 -15/10/2024
  • Joao Duarte Alcantara Galvao (100%) 15/01/2024-15/07/2024
  • Miguel Maroco – Master student (100%) 01/06/2023- 31/12/2023
  • Louis Pailloncy 3-months (internship) June-August 2024

Outputs so far (December 2025 – month 34 of the project)

Master theses

  • Tomas Camolas: Mathematical Modelling of Microbiota Dynamics Using the Replicator Equation (2025)
  • Marina Garcia: Exploring the principles of coexistence in invader-driven replicator dynamics (2025)
  • Miguel Maroco: Modeling Coinfection Dynamics with Interacting Strains Across Patches (2023)

Scientific publications

  1. Gjini E. and Madec S. (2023) Towards a mathematical understanding of invasion resistance in multispecies communities Royal Society Open Science, https://doi.org/10.1098/rsos.231034
  2. Dekaj E. and Gjini E. (2024) Pneumococcus and the stress-gradient hypothesis: a trade-off links R0 and susceptibility to co-colonization across countries, Theoretical Population Biology, 156 pp/76-92,https://doi.org/10.1016/j.tpb.2024.02.001
  3. Freire, T. F. A., Hu, Z., Wood, K. B., & Gjini, E. (2024). Modeling spatial evolution of multi-drug resistance under drug environmental gradients. PLOS Comp. Bio https://doi.org/10.1371/journal.pcbi.1012098
  4. Le, T.M.T., Madec S. and Gjini E. (2025) Inference of pairwise interactions from strain frequency data across settings and context-dependent mutual invasibilities Bulletin of Mathematical Biology, 87(6), 1-29
  5. Freire, T. Madec, S. and Gjini E. (2025) Unpacking fitness differences between two invaders in a multispecies context, Bulletin of Mathematical Biology, doi: 10.1007/s11538-025-01491-5

Datasets:

Submitted and in preparation:

  • Le T.M.T, Garcia-Romero, M., Galvao J. D. A., Madec, S. and Gjini, E. (2025) Understanding the invader-driven replicator dynamics. (preprint pdf)
  • Marôco M. B. ,Pailloncy, L., Madec S. and Gjini E. (2025) Multi-strain SIS dynamics with coinfection across heterogeneous patches (preprint pdf)
  • Madec, S. and Gjini. E. (2025) Derivation of a spatial replicator system with environmental heterogeneity from a co-colonization SIS model with N strains and P patches (submitted, preprint pdf )
  • Paper on estimation
  • Paper on stochasticity
  • Paper on N=3
  • Paper on networks

Selected conferences and missions

  • 2023
  • Research visit in Rome at Luiss University 2023 (Erida Gjini)
  • Conference participation at Epidemics 2023 (Erida Gjini)
  • 2nd Microbiome Summit participation 2023 (Tomas Freire – poster)
  • 2024
  • Conference participation at MEEHUBS 2024 (Tomas Freire –talk and Erida Gjini – poster)
  • Conference participation at DSABNS 2024 (Tomas Freire – poster, Erida Gjini- talk, Sten Madec – talk)
  • Mission for research collaboration at University of Tours, 2024 (Joao Galvao)
  • Conference participation at SMB2024 (Erida Gjini – talk in minisymposium, Seoul, South Korea)
  • Invited talk at L24EEDs workshop “Mathematical modelling of microbial communities: cooperation, dynamics, and resistance” (Erida Gjini) – July 2024, University of Leeds, UK
  • Coinfection workshop, Montpellier September 2024- Erida Gjini
  • SFE² symposium & Theoretical Ecology workshop, Lyon, October 2024 – Erida Gjini
  • Biomathematics meeting in Braga, October 2024 (Tomas Freire)
  • 2025
  • DSABNS 2025 in Naples, Italy, January 2025 (Erida Gjini)
  • Invited talk at University of Coimbra, February 2025 (Erida Gjini)
  • Invited talk at ESCMID Global 2025, Vienna, April 2025 (Erida Gjini)
  • INTP Spring School in Toulouse, May 2025 (Sten Madec and Tomas Freire)
  • Invited talk at MME&HB 2025 in Valencia, July 2025 (Erida Gjini)
  • Talk at Vaginal Microbiota and STI conference 2025 , September 2025 (Tomas Freire)
  • Workshop on Population Models in Biology, November 2025 (Erida Gjini)

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