Introduction to microbiomes – Methodology
Module 1

Coordinator: Prof. Dimitris Karpouzas, University of Thessaly, Greece

• Prof. D.G. Karpouzas, University of Thessaly, Greece
• Assist. Prof. S. Vasileiadis, University of Thessaly, Greece
• Assit. Prof. E.S. Papadopoulou, University of Thessaly, Greece
• Prof. K. Kormas, University of Thessaly, Greece
• Dr A. Meziti, Smallomics LP, Greece
• Prof K. Konstantinidis, Georgia Institute of Technology, USA
• Dr A. Nisiotou, Hellenic Agriculture Organization-DEMETER, Greece
• Prof. K. Ehaliotis, Agricultural University of Athens, Greece

Learning outcomes

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

• Get a good understanding and knowledge of the contribution and the role of the main components of global microbiomes in ecosystem functioning
• Have a clear understanding of the technical and biological terminology related to microbiomes
• Get a good knowledge of the tools available to study diversity and functional aspects of microbiomes
• Understand the main theories describing the interactions of microbes in the microbiome context and with their hosts
• Be able to select tools and methodological approaches to address a given microbiome scientific question

E-class: To be provided

1 Microbiome Terminology: Putting things straight
2 Lets meet the key players of global microbiome
3 Living with other microbes I – Microbial Ecology Theories
4 Living with other microbes II – Microbial Ecology theories
5 Introduction to host-microbe interactions
6 Methods to study host-microbe interactions: (i) Metataxonomics (ii) Metagenomics “Who is able to do things” (iii) Metatranscriptomics/ Metaproteomics/ Metabolomics “Who is actually doing things”
7 Host-microbe interactions in the context of One Health
8 Plasmidome/Mobilome/Volatilome/Lipidome – The new frontiers in the functional evolution of microbiomes – ARGs
9 Soil microbiomes
10 Aquatic microbiomes
11 Microbiomes in engineered environments
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 Students’ Evaluation


Students will be evaluated following a hybrid system including both written exams and evaluation of their performance in presenting their fascination paper. The weight of each of the two evaluation components will be:
• Written exams (70%)
• Fascination paper (30%)

Suggested readings

01. Tedersoo et al. (2014) Global diversity and geography of soil fungi. Science 346 (6213) DOI: 10.1126/science.1256688
02. Marchesi JR, Ravel J (2015) The vocabulary of microbiome research: a proposal. Microbiome 3:31
03. Morris JJ (2015) Black Queen evolution: the role of leakiness in structuring microbial communities. Trends Genet. 31:475-482
04. Bokulich NA., et al., (2016) Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. mBio 7(3):e00631-16.
05. Ferrer et al., (2016) Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb. Biotechnol. 9:22-34
06. Fierer N (2017) Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15:579–590
07. Alves et al. (2018) Unifying the global phylogeny and environmental distribution of ammonia oxidising archaea based on amoA genes. Nat. Comm. 9:1517.
08. Bahram et al. (2018) Structure and function of the global topsoil microbiome. Nature 560:233-237
09. Delgado-Baqureizo et al., (2018) A global atlas of the dominant bacteria found in soil. Science 359: 320-325
10. Geisen et al. (2018) Soil protists: a fertile frontier in soil biology research. FEMS Microbiol. Ecol. fuy006, 42: 293–323
11. Zengler & Zaramela (2018) The social network of microorganisms — how auxotrophies shape complex communities. Nat. Rev. Microbiol. 16:383–90
12. Kothari et al. (2019) Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multimetal resistance genes. mBio 10:e02899-18.
13. Berg et al. (2020) Microbiome definition re-visited: old concepts and new challenges. Microbiome 8:103
14. Oliveiro et al. (2020) The global-scale distributions of soil protists and their contributions to belowground systems. Sci. Adv. 6: eaax8787
15. Ryan et al. (2021) Development of Microbiome Biobanks – Challenges and Opportunities. Trends in Microbiology 29:89-92