The process control of bioreactor grown microbial communities must handle a niche with certain boundaries and also with fast growth and assembly dynamics of the community members. In order to probe, monitor, and eventually control artificial or natural communities in managed systems, rapid detection and evaluation methods are required. We apply microbial community flow cytometry, which provides single cell-based high-dimensional data. To interpret the resulting time series data, we draw inspiration from macroecology, in which a rich set of concepts has been developed for describing population dynamics. We focused, 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. We use various diversity indices and interaction profiles to describe community assembly strategies and functional dependencies of community members.
In addition, we are working in projects connected to a future bio-based circular economy. The carboxylate platform is one of these proposals and a promising technology for substituting fossil resources for the provision of platform chemicals and liquid fuels. We also aim to develop a biological system for phosphate recovery from wastewater thus using waste streams as raw materials.

AG Flow Cytometry

Bioinformatische Tools

Natural microbial systems are highly dynamic due to the short generation times of the comprised organisms and their rapid and distinct reactions to changing environments. Microbial flow cytometry approaches are capable techniques for following such community dynamics in a fast and inexpensive way. Newly developed bioinformatics tools not only enable quantification of single cell dynamics, they also make nearly on-line evaluation of community attributes possible, enable interpretation of community trends, and reveal possible constraints that influence community structure and function. Microbial flow cytometry is poised to make the microbial cytome accessible for ambitious ecosystem studies. Functions of cells within the cytome can be determined either by cell sorting in combination with other -omics.

Zytometrische Datensätze ("cytometric fingerprints") von komplexen mikrobiellen Gemeinschaften können mithilfe der folgenden vier Tools ausgewertet werden:

Cytometric Histogram Image Comparison (flowCHIC: https://www.bioconductor.org/packages/release/bioc/html/flowCHIC.html)

Cytometric Barcoding (flowCyBar:https://bioconductor.org/packages/release/bioc/html/flowCyBar.html)

Automated GateSetting (flowEMMi; http://www.bioinf.uni-leipzig.de/Software/flowEMMi/)

Aktuelle Forschung

Deutsche Bundestiftung Umwelt (DBU), Aktenzeichen:33960/01-32
On-demand Produktion von Phosphatdünger aus Reststoffen von Brauerei und Kläranlage (Bio-P2)
(responsible: Susann Müller),
1.2.2018 - 31.1.2021
Total: 692.516 €

Zentrales Innovationsprogramm Mittelstand (ZIM) des BMWi – Kooperationsnetzwerke
Aktenzeichen: 16KN043226, INAR - BioPRec
BioP-Rec - Die Entwicklung eines automatisierten, rein biologischen, chemiefreien Phosphorrückgewinnungsverfahrens (im Zuge einer klassischen Abwasserreinigungsanlage) zur Herstellung eines hocheffizienten schwermetallfreien, organischen Phosphordüngers'
Responsible: Susann Müller
01.03.2019 – 28.02.2022
Total: 187.919 €

Zentrales Innovationsprogramm Mittelstand (ZIM) des BMWi – Kooperationsnetzwerke
Aktenzeichen: 16KN074623 INET - BitCa
Entwicklung einer Bioinformatischen Community Analyse zur Regelung von komplexen mikrobiellen biotechnischen Prozessen – BitCA
Responsible: Susann Müller
01.01.2019 – 31.12.2021
Total: 181.071 €

Chinese Scholarship Council (CSC)
China, Ministery of Education
‘Harnessing microbial community assembly and plasticity for resiliencing heterogeneous cell systems’
(responsible: Susann Müller)
Total: Scholarship

Bundesministerium für Bildung und Forschung BMBF
Aktenzeichen: 031L0192B
Culture Challenge - Geltropfenbasierte Hochdurchsatz-Isolation und -Kultivierung von Bakterien unter Verwendung von
Helferstämmen (Association)
Sondierungsphase (plus U Tübingen, EMBL Heidelberg)
Total: 200.000 €

Ausgewählte Publikationen

Vučič V, Süring C, Harms H, Müller S, Günther S.
A framework for P-cycle assessment in wastewater treatment plants.
Science of the Total Environment (2020) in print

Cichocki N, Hübschmann T, Schattenberg F, Kerckhof FM, Overmann J, Müller S.
Bacterial mock communities as standards for reproducible cytometric microbiome analysis.
Nature Protocols (2020) 15, 2788-2812. DOI: 10.1038/s41596-020-0362-0

Haange SB, Jehmlich N, Krügel U, Hintschich C, Wehrmann D, Hankir M, Seyfried F, Froment J, Hübschmann T, Müller S, Wissenbach DK, Kang K, Buettner C, Panagiotou G, Noll M, Rolle-Kampczyk U, Fenske W, von Bergen M.
Gastric bypass surgery alters the community structure and functional composition of the intestinal microbiota independently of weight loss.
Microbiomes (2020) 8/13

Krause JL, Schaepe SS, Fritz-Wallace K, Engelmann B, Rolle-Kampczyk U, Kleinsteuber S, Schattenberg F, Liu Z, Mueller S, Jehmlich N,Von Bergen M, and Herberth G.
Following the community development of SIHUMIx – a new intestinal in vitro model for bioreactor use.
Gut Microbes (2020) doi.org/10.1080/19490976.2019.1702431

Liu Z, Müller S.
Bacterial community diversity dynamics highlight degrees of nestedness and turnover patterns.
Cytometry Part A (2020) doi.org/10.1002/cyto.a.23965

Lambrecht J, Cichocki N, Schattenberg F, Kleinsteuber S, Harms H, Müller S, Sträuber, H
Key sub-community dynamics of medium-cain carboxylate production
Microbial Cell Factory (2019) 18:92.

Ludwig J, Höner zu Siederdissen C, Liu Z, Stadler PF, Müller S
flowEMMi: An automated model-based clustering tool for microbial cytometric data.
BMC Bioinformatics (2019), 20:643

Liu Z, Cichocki N, Hübschmann T, Süring C, Ofiţeru ID, Sloan WT, Grimm V, Müller S
Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis.
Environmental Microbiology (2019), 21/1, 164-181.

Liu Z, Cichocki N, Bonk F, Günther S, Schattenberg F, Harms H, Centler F, Müller S. Ecological stability properties of microbial communities assessed by flow cytometry.

mSphere (2018), 3/1, e00564-17

Koch C, Müller S.
Personalized microbiome dynamics – Cytometric fingerprints for routine diagnostics.
Molecular Aspects of Medicine (2018), 59, 123-134

Günther S, Faust K, Schumann, J, Harms H, Raes, J, Müller S.
Species-sorting and mass-transfer paradigms control managed natural metacommunities.
Environmental Microbiology (2016); 18(12):4862-4877.

Zimmermann J, Hübschmann T, Schattenberg F, Schumann J, Durek P, Riedel R, Friedrich M, Glauben R, Siegmund B, Radbruch A, Müller S, Dong HD
High-resolution Microbiota flow cytometry reveals dynamic colitis-associated changes in fecal bacterial composition.
European Journal of Immunology (2016) 46, 1300-1303

Jahn M, Günther S, Müller S
Non-random distribution of macromolecules as driving forces for phenotypic variation
Current Opinion Microbiology (2015) 25, 49-55.

Koch C, Harnisch F, Schröder U and Müller S
Cytometric fingerprints: evaluation of new tools for analyzing microbial community dynamics
Frontiers in Microbiology Section Systems Microbiology (2014) Vol. 5 Article 273, 1-11.

Jahn M, Vorpahl C, Türkowsky D, Lindmeyer M, Bühler B, Harms H, Müller S
Accurate Determination of Plasmid Copy Number of Flow-Sorted Cells using Droplet Digital PCR
Analytical Chemistry (2014) 86 5969-5976.

Koch C, Harms H, Müller S
Dynamics in the microbial cytome – single cell analytics in natural systems
Current Opinion Biotechnology (2014) 27 134-141.

Koch C, Müller S, Harms H, Harnisch F
Microbiomes in bioenergy production: From analysis to management
Current Opinion Biotechnology (2014) 27, 65-72.

Koch C, Fetzer I, Schmidt T, Harms H, Müller S
Monitoring functions in managed microbial systems by cytometric bar coding
Environmental Science and Technology (2013) 47, 1753-1760

Jahn M, Seifert J, von Bergen M, Schmid A, Bühler B, Müller S
Subpopulation-proteomics in prokaryotic populations
Current Opinion Biotechnology (2013) 24, 79-87.

Koch C, Günther S, Desta AF, Hübschmann T, Müller S
Cytometric fingerprinting for analysing microbial intra-community structure variation and identifying sub-community function
Nature Protocols (2013) 8/1, 190-202.

Günther S, Koch C, Hübschmann T, Röske I, Müller RA, Bley T, Harms H, Müller S
Correlation of community dynamics and process parameters as a tool for the prediction of the stability of wastewater treatment.
Environmental Science and Technology (2012) 46(1), 84-92.

Harnisch F, Koch C, Patil SA, Hübschmann T, Müller S, Schröder U
Revealing the electrochemically driven selection in natural community derived microbial biofilms using flow–cytometry
Energy & Environmental Science (2011) 4 (4) 1265 – 1267.

Müller S and Nebe-von-Caron G
Functional single-cell analyses – flow cytometry and cell sorting of microbial populations and communities.
FEMS Microbiol Rev (2010) 34, 554–587.

Müller, S.
Modes of cytometric bacterial DNA pattern – A tool for pursuing growth
Cell Proliferation (2007) 40, 621-635.

Achilles J., Stahl F., Harms H., Müller S.
Isolation of intact RNA from cytometrically sorted S. cerevisiae for the analysis of intra-population diversity of gene expression
Nature Protocols (2007) 2/9, 2203-2211.


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