CYTO Virtual Interactive 2021 Oral Presentation - Tools to Unravel the Ecology of Microbial Communities
Microbiomes accompany human life in countless ways. They are an essential part of the human body and interact with its host in countless ways. Currently, extensive microbiome analyses assessing the microbiomes’ composition and functions based on sequencing information are still far away from being routine analyses due to the complexity of applied techniques and data analysis, their time demand, and high costs. With the growing demand for on-time community assessment and monitoring of its dynamic behavior with high resolution, alternative high-throughput methods such as microbial community flow cytometry come into focus (Molecular Aspects of Medicine (2018), 59, 123-134). Our flow cytometric approach provides single-cell based high-dimensional data by using only three parameters but for every cell in a system, which is enough to characterize whole communities’ attributes with high acuity over time (Nature Protocols, 2020, 15, 2788-2812). To interpret such complex cytometric time-series data, novel concepts are required (e.g., Cytometry Part A (2020) 97A: 742–748). We provide a workflow, which is applicable for easy-to-use handling and measurement of microbiomes. Drawing inspiration from macroecology, in which a rich set of concepts has been developed for describing population dynamics, we interpret huge sets of community single cell data in an intuitive and actionable way using a series of bioinformatics tools which we either developed or adapted from sequence-based evaluation approaches for the interpretation of single cell data. The developed evaluation pipeline tests for ecological measures such as community assembly, functioning, and evolution. We also addressed the metacommunity concept, which is a well-acknowledged idea in macroecology on how interconnected communities perform (Environmental Microbiology (2019), 21/1, 164-181). The last concept discusses stability, which is a metrics of paramount importance for the operation of microbiomes (mSphere (2018), 3/1, e00564-17). A fast quantification of stability properties may not only detect disturbances and their impact on the organisms but would also allow for on-time microbiome treatment. The workflow's immanent ability to support high temporal sample densities below bacterial generation times provides new insight into the ecology of microbiomes and may also provide access to community control for microbiome-based health management (Microbiomes (2020) 8/13).
Helmholtz Centre for Environmental Research-UFZ
Müller applies microbial community flow cytometry to analyze and interpret structure and function of natural and artificial microbial communities within their respective boundaries. To interpret time-series data, they draw inspiration from macroecology, in which a rich set of concepts has been developed for describing population dynamics. They focus, for example, on stability concepts and developed a workflow to monitor and compute the stability properties resistance, resilience, displacement speed, and elasticity. In addition, metacommunity paradigms are studied on the single-cell level. They use various diversity indices and interaction profiles to describe community assembly strategies and functional dependencies of community members. Professor Müller was president of the German Society for Flow Cytometry (2008-2010) and is now Senior Scientist at Helmholtz Centre for Environmental Research—UFZ in Leipzig, Germany.
CMLE Credit: 1.0