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Online workshop on Microbiota-related research tools

Discover the main methodology used in microbiome research and computational tools used to characterize and study the microbiome

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CIVIS focus area
Open to
  • Bachelor's
  • Master's
  • Phd
Field of studies
  • Medicine and Health
  • Short-term
  • CIVIS Hub 3
Course dates
4 May 2022

This CIVIS workshop will be consisting of 2 sessions:

  • The first session will be delivered by Universidad Autónoma de Madrid and will describe the main methodology used in microbiome research including sample collection, sample storage and processing, and sequencing, and provide some ideas for translational microbiome studies in IBD and other pathologies.
  • The second session, delivered by the University of Bucharest, will present the technologies and computational tools used to characterize and study the microbiome. Sapienza Università di Roma and Universidad Autónoma de Madrid academics will be chairing and moderating and offering matters of discussion.

Main topics addressed

  • Methodological aspects in the study of the microbiota and Inflammatory Bowel disease

Presenters: Laila Aldars Garcia and Sebastian Mas-Fontao

Gut microbiome analysis is used to understand many diseases, and preparation, handling, and storage of samples are critical processes that alter the outcomes of downstream DNA-based microbial community analyses. The widespread application of high-throughput genomic approaches has revolutionized the study of complex microbial communities and allowed for the development of sequencing-based approaches. Each methodological stage, from sampling to sequencing, can introduce biases.

Studies in animal models and humans have shown that there is a persistent imbalance in the intestinal microbiome related to IBD, with a substantial body of literature providing evidence for the role of the human gut microbiome on IBD. In general, these studies have a number of limitations, such as the small sample size, the lack of a valid gold standard (such as endoscopic evaluation) to classify the presence of disease activity, most of them do not take into account previous and current treatments (which can modify the biological state), lack of information about the accuracy of the biomarkers, lack of longitudinal studies, and they find heterogeneous results which have not been validated in independent cohorts. In this session, we will describe the main methodology used in microbiome research including sample collection, sample storage and processing, and sequencing, and provide some ideas for IBD translational microbiome studies.

  • Data analysis and statistical approach in microbiota research

Presenter: Gratiela Gradisteanu

Over the past decade, it has become very clear that the microbiome is an essential player in human health and disease and thus should be analysed to develop innovative treatment strategies. To this end, the field of metagenomics has come a long way in leveraging the advances of next-generation sequencing technologies resulting in the capacity to identify and quantify almost all microorganisms present in human specimens. Nevertheless, the field of metagenomics is still in its infancy, specifically in terms of the limitations in standardization, statistical assessments, computational analysis, and validation due to vast variability in bioinformatic workflows and the experimental design. Our workshop will present the technologies and computational tools used to characterize and study the microbiome. We expect our students to get a flavour of the steps needed to analyze the microbiome as this is an exciting field of research.

Learning outcomes

  • Knowledge of microbiota-related methodology and research tools
  • Contact opportunity with researchers from CIVIS universities
Dates: 4 May 2022 ECTS: 0.2*
Format: Virtual Language: English
Duration: 2h30

* The workshop is equivalent to 0.2 ECTS. The recognition of ECTS depends on your home university. Reach out to the CIVIS contact point within your university for further information.


This CIVIS course is open to Bachelor, Master and PhD students at one of the 10 CIVIS member universities. Applicants should be enrolled or have a strong interest in the following fields of studies: medicine, surgery, biotechnologies, medical biology, microbiology, applied immunology, medical bioinformatics, medical biology, medical laboratory, molecular biology and biochemistry courses.

Application process

The workshop will be held on Zoom. Interested students should fill in the online registration form by 3 May 2022.

General Eligibility Criteria for CIVIS Courses

Applicants need to be enrolled at their home university in order to be eligible for selection and participation.  If uncertain about your status at your home university (part-time or exchange students etc) please check with your home university’s website or International Office. 

Applicants who will be receiving other Erasmus funds for the duration of the course are not entitled to funding. Participation in the course may still be possible under “zero-grant” status, but applicants should contact their home university in order to confirm this. 

A list of links and contacts for each university can be found in this Q&A.

GDPR Consent

The CIVIS alliance and its member universities will treat the information you provide with respect. Please refer to our privacy policy for more information on our privacy practices. By applying to this course you agree that we may process your information in accordance with these terms.

Universidad Autónoma de Madrid

Laila Aldars-Garcia  – Postdoctoral Researcher. She has a degree in Nutrition, Food Science and Technology from the Universidad Autonoma de Madrid (Spain) and she continued her training in health sciences by taking the Official Master's Degree in Pharmaceutical Sciences at the Universidad Complutense de Madrid (Spain). She completed her doctoral thesis at the University of Lleida (Spain) where she focused on microbiology, as well as on the design of predictive models. During her PhD, she had the opportunity to work at Cranfield University (UK). During her research career she has specialised in microbiology and in recent years she has focused on the study of gut microbiota. Since 2020, Dr Laila Aldars-García has been working in Dr Javier P. Gisbert's group at the Hospital de La Princesa in Madrid investigating the microbiome and metabolome of patients with Inflammatory Bowel Disease using metagenomic and metabolomic approaches.

Sebastián Mas Fontao – Principal investigator and group leader of the renal pathology and diabetes laboratory. Degree and PhD in Biochemistry and Molecular Biology (UCM). His field of research focuses on diagnostic, prognostic and therapeutic biomarkers of diabetes complications using -omics approaches (including microbiome analysis) in clinical trials and preclinical models.

Javeir P. Gisbert – Specialist in Gastroenterology (Senior Consultant), Chief of Section and Director of the Inflammatory Bowel Disease Unit at La Princesa University Hospital, Madrid, Spain. Past-President of the Spanish Inflammatory Bowel Disease Group (GETECCU). Spanish representative/past-President of the European Helicobacter and Microbiota Study Group. Doctor (PhD), Magister in Methodology in Clinical Investigation, and Tenure Professor. Speaker at >200 conferences.>1,000 articles published in journals. Coordinator/Principal Investigator in >250 Research Projects. Member of 15 Medical Societies. Expert reviewer for 28 Scientific Organizations. International Editor of the Cochrane Collaboration. Reviewer for >300 scientific journals. Member of the Editorial Board of >15 journals.

Sapienza Università di Roma

Daniela De Biase - Associate Professor (Hab. Full Professor). She teaches Biochemistry (12 CFU) to students of the Health area: Medicine (including International Medical School, fully taught in English) and Midwifery. She is Erasmus Coordinator of the Faculty of Pharmacy and Medicine (medical area), and a member of CIVIS Health Hub Council and CIVIS WP6 (Task Force Mobility). She is on the teachers’ board of the PhD course in Life Sciences. Her scientific interests are at the crossroad between microbiology, biochemistry and biotechnology. She is an expert on microbial responses to acid stress relying on glutamate/glutamine use and leading to GABA production/release. She is recently shifting her research interest to the study of the human microbiota. Vice-chair of a COST Action 2019-2023. Associate Editor for Frontiers in Microbiology, Microbial Physiology and Metabolism section.

University of Bucharest 

Gratiela (Pircalabioru) Gradisteanu – Senior Researcher at the Research Institute of the University of Bucharest (ICUB), she teaches Medical Microbiology (6 ECTS) and New targets for developing antimicrobial agents (5 ECTS) to Master Students at the Faculty of Biology. She is a member of the CIVIS Health Hub Council. Her research interests include microbiome changes in diabetes and metabolic syndrome, in vivo and ex-vivo investigation of host-pathogen crosstalk during the infectious process, oxidative stress in health and disease, assessment of the antimicrobial activity of novel antimicrobial compounds, SARS-CoV-2 diagnostic and omic technologies. She coordinates the microbiome analysis platform at ICUB.