We warmly invite you to join Workshop 15 at CYTO2018!
Workshop 15 (117) will take place in the panorama hall from 17:00-18:30 on the 1st of May. The pre-workshop survey (which will not take up more than 10 min of your time) can be found here
Cytometric Fingerprinting for Routine Diagnostics of Microbiome Dynamics in Medical and Environmental Settings
Facilitators: Hyun-Dong Chang, Jakob Zimmerman, Frederik Hammes, Susann Müller, Peter Rubbens, Ruben Props, Frederiek - Maarten Kerckhof
Overview
Microbiomes perform essential services, ranging from the human microbiome to man-made and natural ecosystems. Human microbiome dysbiosis can be indicative of the host health status, while environmental microbiome changes can impact global biogeochemical cycling, which is intricately linked with climate change.
Agenda
- 17:10-17:15 Part 1: Set-up and standardized methods for microbial community flow cytometry (MCFC) – Hyun-Dong Chang Many methods exist for differentiation of microbial cell types by fluorescent dyes ranging from the whole microbiome to specific functional or phylogenetic groups. Standardization of measurements is an essential issue here. This involves decisions on cytometer setup but also automation for fast response assessment of microbial communities.
- 17:15-17:25 Discussion pt. 1
- 17:25-17:30: Part 2: Screening microbiomes in human environments- Jakob Zimmerman In a real world example, we will show how flow cytometry and cell sorting in conjunction with gnotobiotic mouse models were relevant to microbiome research.
- 17:30-17:40 Discussion pt. 2
- 17:40-17:45 Part 3: Complementarity of MCFC in combination with other ‘omics’-approaches – Ruben Props To increase the (phylo)genomic resolution of MCFC, it can be used in tandem with “-omics” approaches. Current challenges and opportunities of integrating MCFC with “omics” will be discussed (with a specific focus on cell sorting).
- 17:45-17:55 Discussion pt. 3
- 17:55-18:00 Part 4: Ecological measures derived from flow cytometric fingerprinting (FCFP) – Susann Müller MCFC single-cell data can be evaluated using macro-ecological concepts in an intuitive and actionable way. These ecological metrics can be of interest for both medical and environmental applications. The high temporal sample densities provide new insight into the ecology of microbiomes and may also lead to strategies for microbiome based health management.
- 18:00-18:10 Discussion pt. 4
- 18:10-18:15 Part 5: Computational challenges for FCFP – Peter Rubbens The analysis of FCFPs requires high-dimensional multivariate analysis techniques. In addition, temporal aspects need to be addressed, as routine diagnostics require on-line measurement. Therefore, FCFP faces computational challenges, which will be highlighted in this workshop, followed by possible strategies to resolve them.
- 18:15-18:25 Discussion pt. 5 and Concluding remarks + data challenge
Data challenge for microbial community flow cytometry
Welcome to the Github pages website of the microbial community flow cytometry data challenge which will be launched on CYTO2018. Here you will soon find background and more information on the different data sets.
Contact
A general email address will be active from Cyto 2018 on