Flow cytometry (FCM) is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. Microbial FCM data have a number of different characteristics and challenges compared to immunophenotyping FCM data. Most prokaryotic cells are much smaller in size and volume than human or mammalian cells, and although most cells are small, the size range within which microbial cells lie is larger than for mammalian cells, covering a range between 0.2 and 500µm. Microbial communities also comprise high levels of phenotypic and phylogenetic complexity (e.g. 1000s of taxa). In this talk, I will provide an overview of common pitfalls of traditional FCM computational techniques on these microbial data, and describe how we can move towards a tailored and reproducible approach for microbial ecology studies. Finally, I will list a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.
A great collaboration with INVE aquaculture, Benchmark’s Advanced Nutrition group, and Jasmine Heyse (PhD candidate at CMET) resulted in novel insights into the way microbial communities assemble, and are influenced by artemia-, algae-, and dry feed-associated microbiomes, in shrimp hatchery systems.
In this study, we found that the microbial community assembly in the hatchery rearing water over time was dominated by stochastic effects. This demonstrates that random fluctuations in growth and death of bacterial species cause microbiomes in identical shrimp tanks to become more dissimilar over time. Two major shifts in microbial community structure that were tightly coupled to the abundance of Chaetoceros algae were observed. Using a newly developed source tracking algorithm we could quantify that 37% of all bacteria in the hatchery rearing water were introduced either by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds.
These findings have significantly improved our fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of the peripheral microbiomes in maintaining health-promoting rearing water microbiomes.
His main take-away: “In the very near future we will be able to translate these complex microbial fingerprints into specific management advice that empowers farmers with actionable microbial management“