Meta_Microbial Workshop 4-5 July

Meta_Microbial Workshop

Metagenomic and bioinformatic insights into microbial communities

The Meta_Microbial workshop aims at providing academic researchers, students, and fellows with an overview of current tools to analyze next-generation sequence data and to make insightful interpretation towards the fields of microbial ecology and environmental microbiology. It will be a short-course (2 days) with lectures, paper/topic discussions, and practical examples. The workshop will be given in-person at CIIMAR on July 4th and 5th, 2023. 


Coordination: Miguel Semedo, Postdoctoral Researcher at CIIMAR (


-              Adriana Rego. PhD Student at CIIMAR and ICBAS. ORCID: 0000-0001-9647-1197.

-              Francisco Pascoal. PhD Student at CIIMAR and FCUP. ORCID: 0000-0003-2315-358X.

-              Miguel Semedo. Postdoctoral Researcher at CIIMAR. ORCID: 0000-0003-2263-2212.

Organization: Rafaela Mendes, Rúben Pereira (CIIMAR PhD student’s committee), Miguel Semedo, Catarina Magalhães.



-              Introduction. Sequencing technologies. Data generation.

-              R tools for microbial ecology studies in the “Omics Era”.

-              Metabarcoding/Targeted Metagenomics. Diversity, taxonomy, and functional inference.

-              Untargeted Metagenomics (shotgun/whole genome sequencing) and functional interpretations.

-              Exploring Online Resources and Repositories.

-              Alternative statistical and data analysis tools to explore the microbial realm.

-              Further insights on data visualization and analysis.



Graduate students, academic researchers, and other members of the research community interested in microbial ecology, environmental microbiology, and metagenomics.

Estimated number of participants: 10-30.

Registration Fee: 30€. Fee waivers will be available to attendants without specific funds to support participation (projects, tuition, etc.). Registration fee waivers are available through the support from the International Society for Microbial Ecology (ISME). Please submit a waiver justification in the registration form. The payment details will be given by email to each participant after acceptance notification.



-              Own laptop with R and R Studio installed (installation guidance will be provided, if needed). Some experience with programming languages, such as R or Python, would be beneficial but are not a requirement.



Please fill the application form by May 15th.


AGENDA (preliminary)

Day 1 - July 4th, 2023

09:30 - 10:00h    Welcoming / Opening  by Miguel Semedo (CIIMAR) e Rodrigo Costa (IST-UL, ISME Ambassador)

10:00 - 10:30h    Next-generation sequencing technologies and data generation (Miguel S.)

10:30 - 11:00h    R tools for microbial ecology in the “Omics Era” (Francisco P.)

11:00 - 11:30h    Break

11:30 - 13:00h    Metabarcoding (16S) upstream analysis (Miguel S.)

-              Lecture

-              Practical example (Dada2 in R)

13:00 - 14:00h    Lunch

14:00 - 16:00h    Metabarcoding (16S) downstream analysis (Miguel S.)

-              Practical example (Phyloseq, vegan, DESeq2, etc.)

-              Paper Discussion

16:00 - 16:30h    Break

16:30 - 17:15h    Phylogenetic trees from high-throughput sequence data (Adriana R.)

-              Lecture

-              Practical example (iTOL, etc.)

17:15 - 18:00      Functional inference from amplicon data (Miguel S.)

-              Lecture

-              Practical example (PICRUSt2, PAPRICA, etc.)



Day 2 - July 5th, 2023


09:30 - 11:00h    Untargeted Metagenomics - Data Processing (Miguel S.)

-              Lecture

-              Practical examples (Trimmomatic, Megahit, Bowtie2, etc.)

11:00 - 11:30h    Break

11:30 - 13:00h    Untargeted Metagenomics - Taxa and Functional Annotation (Adriana R.)

-              Lecture

-              Practical examples

13:00 - 14:00h    Lunch

14:00 - 15:00h    Untargeted Metagenomics - Taxa and Functional Annotation (Miguel S.)

-              Paper Discussion

15:00 - 16:00h    Exploring Online Resources and Repositories (Miguel S.)

-              Lecture

-              Practical examples (IMG, MG-RAST, KBase)

16:00 - 16:30h    Break

16:30 - 17:15h    Alternative statistical and data analyses (Miguel S.)

-              Lecture

-              Practical examples (AIC, Networks, etc.)

17:15 - 18:00h    Insights on data visualization and analysis (Francisco P.)

-              Lecture

-              Paper discussion