By JCVI Staff

South Africa Microbiome Workshops

In April 2016, researchers from JCVI led two microbiome data analysis workshops in South Africa. Both workshops were co-sponsored by the NIAID-funded JCVI Genomic Center for Infectious Disease and the H3Africa Initiative.

The first workshop was held from April 21 - 22 at the Durban University of Technology (DUT). Forty-five participants attended the workshop led by JCVI scientists Alex Voorhies, PhD, Derek Harkins, and Andres Gomez, PhD.

The second workshop was held from April 25 – 29 at the University of Cape Town (UCT).  The DUT JCVI team was joined by Stephanie Mounaud and partnered with UCT faculty, Gerrit Botha, PhD and Katie Lenard, PhD, and UCT PI Mark Nicol to teach a four-day microbiome analysis course. Twenty-two researchers from Nigeria, The Gambia, Malawi, Tunisia, Zimbabwe and South Africa were selected from over 70 applicants to participate.

The workshops provided participants with a background to microbiome studies and covered topics such as sample preparation, sequencing, and data interpretation for purposes of planning and conducting microbiome related projects. Students were also taught each step of working with a 16S rRNA gene dataset, from processing raw reads to statistical analysis and figure generation. This included how to use various taxonomic classification pipelines and perform data analysis using R with hands on, step-by-step presentations. Participants were then provided with a sample data set to process individually with guided assistance. Students explored alpha and beta diversity, as well as indicator species analysis and statistical significance of their findings.  The hands-on workshop concluded with various ways to display 16S microbiome data in publication quality figures. Each student received a flash drive with sample data sets and relevant instructions along with workshop content to allow them to practice and share their experience with their home institutes.

Topics Covered in the Workshops

History of Microbiome Research

MOTHUR: Interactive application

Statistical approaches: Exploratory analysis of microbiome data

Sample Preparation

UPARSE: Interactive application

Statistical approaches: Association measures and beta diversity


Assessing Contamination in Dataset

Statistical approaches: Microbiome pattern recognition and marker discovery

16S Ribosomal RNA and Metagenomics Approaches

Statistical approaches: Moving through the microbiome data space

Data analysis: Predicting ecosystem phenotype (Hands-on individual exercises)

Pipeline processing for taxonomic classification:

Statistical approaches: R software

Data analysis: Hands on individual exercises

Feedback from both workshops was overwhelmingly positive:

Thank you for sending out a wonderful, and extremely knowledgeable team to ignite one of many workshops at DUT. It was truly a great exposure for many of my students and staff. They enjoyed the theoretical and hands on sessions alike. Let’s continue this association for many more years ahead.”– Dr. Suren Singh, Durban University of Technology
From my interactions with the participants it was really clear how informative and useful the workshop was. It’s evident that an enormous amount of effort went into planning and putting together the programme, which was very well received and professionally delivered” – Dr. Mark Nicol, University of Cape Town
This was a great workshop, and I would not hesitate to recommend it to researchers getting started in microbiome research. The presenters were excellent and really dedicated to assisting us and answering our questions.” – Cape Town Workshop Participant

JCVI Principal Investigators Bill Nierman, PhD and Rembert Pieper, PhD are current awardees under the H3Africa Initiative which aims to facilitate a contemporary research approach to the study of genomics and environmental determinants of common diseases with the goal of improving the health of African populations. To accomplish this, the H3Africa Initiative assists in the development of the necessary expertise among African scientists to establish networks of African investigators.

These workshops are just one of the ways JCVI has taught and collaborated with the next generation of African researchers. In previous years JCVI has conducted workshops at the University of Limpopo in South Africa (2011), the International Livestock Research Institute in Nairobi, Kenya (2013), and IITA in Ibadan, Nigeria (2014). JCVI has also hosted trainings at its Rockville campus, such as the Proteomics Training Course (2015) taught by Drs. Pieper and Yanbao Yu, and a 5-week Microbiome Workshop (2014) focusing on sample preparation, designed and conducted by Stephanie Mounaud. Dr. Pieper also co-organized the fellows’ poster session at the Eighth H3Africa Consortium Meeting (2016).


These workshops were supported by the NIAID funded JCVI Genomic Center for Infectious Disease and the H3 Africa Initiative.