Animal-microbe interactions
Module 4

Prof. K. Kormas, University of Thessaly, Greece


  • Assoc. Prof. P. Berillis, University of Thessaly, Greece
  • Assoc. Prof. I. Karapanagiotidis, University of Thessaly, Greece
  • Assist. Prof. Fotini Kokou, Wageningen University & Research, The Netherlands
  • Prof. K. Kormas, University of Thessaly, Greece
  • Dr A. Meziti, Smallomics LP, Greece
  • Assist. Prof. G. Michail, University of Thessaly, Greece
  • Prof. Itzhak Mizrahi, Ben Gurion University, Israel
  • Prof. Tamara Tal, Helmholtz Centre for Environmental Research – UFZ, Germany
  • Prof. Lifeng Zhu, Nanjing Normal University, China
  • Prof. Elena Mente, Aristotle University of Thessaloniki, Greece
Learning outcomes

The students are expected at the end of the module to:

• Display knowledge of microbe-animal biology that applies to a wide variety of animal species (including wildlife, production and companion animals).
• Clarify major issues of shaping and regulating microbe-animal relations across animal species.
• Demonstrate an understanding of animal holobionts interactions.
• Develop skills in setting hypothesis-based and designing animal-microbes scientific investigations.


E-class: To be provided

01. Microscopy & visualization for animal microbiomes.
02. Terrestrial animal microbiomes I – Insects.
03. Terrestrial animal microbiomes II – Ruminants.
04. Manipulating animal microbiomes.
05. Sponges, corals and other invertebrates.
06. Marine mammals.
07. Fish.
08. Animal wildlife.
09. Chemical-microbiome interactions and their effects on the host.
10. Animal pathobiomes.
11. Microbiomes in animal physiology.
12. • Fascination paper: Students read a paper of their choice (relevant to the module), make an infographic or graphical abstract about it, and present it in 3 minutes.
• Recapitulation
13. Evaluation


• Written exams (70%)
• Fascination paper (30%)

Suggested readings

01. Flint HJ (2020) Why gut microbes matter. Understanding our microbiome. Springer, Cham
02. Ishiguro et al. (2018) Gut microbiota. Interactive effects on nutrition and health. Academic Press, London
03. Butt & Volkoff (2019) Gut Microbiota and Energy Homeostasis in Fish. Front. Endocrinol. 10,9.
04. Ikeda-Ohtsubo et al. (2018) How can we define “optimal microbiota?”: A comparative review of structure and functions of microbiota of animals, fish, and plants in agriculture. Front. Nutrit. 5,90.
05. Levin et al. (2021) Diversity and functional landscapes in the microbiota of animals in the wild. Science 372:eabb5352
06. Ley et al. (2008) Evolution of Mammals and Their Gut Microbes. Science 320:1647-1651
07. Lind & Pollard (2021) The gut microbiomes of 180 species. Science 372:238-239
08. Lindsay et al. (2020) The potential role of the gut microbiota in shaping host energetics and metabolic rate. J. Anim. Ecol. 89:2415-2426
09. Nayfach et al. (2021) A genomic catalog of Earth’s microbiomes. Nature Biotechnology 39:499-509
10. Mizrahi et al. (2021) The rumen microbiome: balancing food security and environmental impacts. Nat. Rev. Microbiol. 19, pages 553–566
11. Reinoso et al. (2016) Protective and pro-inflammatory roles of intestinal bacteria. Pathophysiology 23:67-80
12. Shetty et al. (2019) Reconstructing functional networks in the human intestinal tract using synthetic microbiomes. Curr. Opin. Biotechnol. 58:146-154
13. Youngblut et al. (2019) Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat. Comm. 10:2200