Flow Cytometry

Flow Cytometry

Research Topics

The general topic of our multidisciplinary group (biochemists, biotechnologists, bioinformaticians) is to study life strategies of microbial populations and communities. Most microbial analyses are realized by measuring average properties of bulk data. However, we exploit high-troughput multi-parameter flow cytometry to obtain single cell data and use them for understanding and optimisation of biotechnological and environmental processes. With our methods we are able to provide information about individual cell characteristics along with structural and functional parameters. Fast dynamics can be analysed and resulting variation in community structure can be quantified and calculated. We developed bioinformatic tools to detect community variation almost immediately and use these tool to develop process strategies in order to stabilize complex microbial processes in managed systems like biogas production and wastewater treatment. Ecosystems analyses can also be performed on the single cell  level (groundwater, soil). Heterogeneity of cells in clonal cultures is another focus of our research. Here, specific cell chacateristics like growth, viability, productivity or plasmid stability are some of our research targets.

Topics of research are:

  • Analysis of the diversity and stability of performances of microbial populations in natural and artificial habitats. Information is available about stability of proportional constant proliferation of microbial populations within consortia cooperating in the detoxification and mineralization of xenobiotics.
  • The impact of toxic compounds on cell behaviour and viability including information on the energy providing system (membrane potential) and membrane integrity (fluidity).
  • The development of off- and on-line strategies for biotechnological processes. Microorganisms act as biological catalytical systems which perform the synthesis or the refinement of distinct products. Unlike chemical catalysts in chemistry the efficiency of microorganisms depends on their physiological status. As a consequence such information is used to control established industrial biotechnological processes as well as scarcely developed lab-scale processes. Our group has a long standing experience in optimising brewing processes and developing strategies for product production by bacteria.

AG Flow Cytometry

Bioinformatic 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.

Cytometric fingerprints for monitoring microbial community dynamics can be analyzed with the following tools:

Dalmatian Plot
Cytometric Histogram Image Comparison (CHIC)
Cytometric Barcoding (CyBar)
FlowFP


Current research


Zentrales Innovationsprogramm Mittelstand (ZIM) des BMWi – Kooperationsnetzwerke, Aktenzeichen: 16KN043222, ABOS – Entwicklung einer Abfall-Biogas-Online-Steuerung zur effektiven Überwachung des Vergärungsprozesses, Teilprojekt UFZ: ABOS – Prozesssimulation: 170 K€
(responsible: Susann Müller)
1.8.2015-3.7.2018

BMBF: Bundeshaushalt, Einzelplan 30, Kapitel 3005, Titel 68330
Aktenzeichen: 031A616K, Wissensbasierte Prozessintelligenz – Neue Wege zu stabilen Bioprozessen, Teilprojekt K, Total: 20 Mio
Partec/Sysmex in Parterschaft mit UFZ: 193 k€
(responsible: Sysmex/Partec)
1.2.2015-31.1.2018

BMEL-FNR: Förderschwerpunkt: Mikrobiologische Prozesse in Biogasanlagen, Aktenzeichen: 22008313, BiogasFingerprint-Flexible Steuerung der Biogasproduktion mittels bioinformatischer Populationsanalyse (Biogas-Fingerprint)
(responsible. Susann Müller), Total: UFZ: 364 k€
1.2.2015-31.01.2018

Deutsche Bundestiftung Umwelt (DBU), Aktenzeichen: 32062/01, Akkumulation und schadstoffarme Verfügbarmachung von Bio-P aus Klärschlamm (Bio-P)
(responsible: Susann Müller), Total: 192 k€
1.2.2015-31.1.2017

Fond zur Verbesserung der Forschungsinfrastruktur und Forschungsvorhaben mit jeweils anwendungsnaher Ausrichtung (über SMWK und SAB), Aktenzeichen: 100192205, Funktionsbeschreibungen mikrobieller Gemeinschaften mittels Zellanalyse, Zellsortierung und Massenspektrometrie (CellMassSpec)
(responsible: Susann Müller), Total: 810 k€
05.05.2014-31.03.2015

Chinese Scholarship Council (CSC), China, Ministery of Education
‘Development of stable performance of microbial communities in wastewater treatment systems’
(responsible: Susann Müller)
21.10.2013-31.08.2016


Selected Publications

Günher S, Faust K, Schumann, J, Harms H, Raes, J, Müller S.
Species-sorting and mass-transfer paradigms control managed natural metacommunities.
Environmental Microbiology (2016) accepted

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) accepted

Lieder S, Jahn M, Koepff J, Müller S, Takors R
Stress speeds up DNA replication in Pseudomonas putida in chemostat cultivations
Biotechnology Journal (2016), 11, 155-163

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.

Index:

2016 (2)
2015 (9)
2014 (9)
2013 (13)
2012 (2)
2011 (7)
2010 (7)

You could use our publication index for further requests.

2016 (2)

  • Günther, S., Faust, K., Schumann, J., Harms, H., Raes, J., Müller, S., (2016):
    Species-sorting and mass-transfer paradigms control managed natural metacommunities
    Environ. Microbiol.
    full text (url)
  • Lieder, S., Jahn, M., Koepff, J., Müller, S., Takors, R., (2016):
    Environmental stress speeds up DNA replication in Pseudomonas putida in chemostat cultivations
    Biotechnology Journal 11 (1), 155 - 163
    full text (url)
to index

2015 (9)

  • Günther, S., Müller, S., (2015):
    Facilitated gate setting by sequential dot plot scanning
    Cytom. Part A 87 (7), 661 - 664
    full text (url)
  • Jahn, M., Günther, S., Müller, S., (2015):
    Non-random distribution of macromolecules as driving forces for phenotypic variation
    Curr. Opin. Microbiol. 25 , 49 - 55
    full text (url)
  • King, N., Müller, S., (2015):
    Environmental microbiology: revisiting the physiology of microorganisms on the single cell scale. Editorial overview
    Curr. Opin. Microbiol. 25 , v - vi
    full text (url)
  • Koch, C., Kuchenbuch, A., Kretzschmar, J., Wedwitschka, H., Liebetrau, J., Müller, S., Harnisch, F., (2015):
    Coupling electric energy and biogas production in anaerobic digesters – impacts on the microbiome
    RSC Advances 5 (40), 31329 - 31340
    full text (url)
  • Lindmeyer, M., Jahn, M., Vorpahl, C., Müller, S., Schmid, A., Bühler, B., (2015):
    Variability in subpopulation formation propagates into biocatalytic variability of engineered Pseudomonas putida strains
    Frontiers in Microbiology 6 , art. 1042
    full text (url)
  • Melzer, S., Winter, G., Jäger, K., Hübschmann, T., Hause, G., Syrowatka, F., Harms, H., Tárnok, A., Müller, S., (2015):
    Cytometric patterns reveal growth states of Shewanella putrefaciens
    Microb. Biotechnol. 8 (3), 379 - 391
    full text (url)
  • Müller, S., Schleinitz, K., (2015):
    Flow cytometry and microbial community fingerprinting
    In: Wilkinson, M.G., (ed.)
    Flow cytometry in microbiology : technology and applications
    Caister Academic Press, Norfolk, p. 79 - 91
  • Pous, N., Koch, C., Vilà-Rovira, A., Balaguer, M.D., Colprim, J., Mühlenberg, J., Müller, S., Harnisch, F., Puig, S., (2015):
    Monitoring and engineering reactor microbiomes of denitrifying bioelectrochemical systems
    RSC Advances 5 (84), 68326 - 68333
    full text (url)
  • Zimmermann, M., Escrig, S., Hübschmann, T., Kirf, M.K., Brand, A., Inglis, R.F., Musat, N., Müller, S., Meibom, A., Ackermann, M., Schreiber, F., (2015):
    Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS
    Frontiers in Microbiology 6 , art. 243
    full text (url)
to index

2014 (9)

  • Bühligen, F., Lindner, P., Fetzer, I., Stahl, F., Scheper, T., Harms, H., Müller, S., (2014):
    Analysis of aging in lager brewing yeast during serial repitching
    J. Biotechnol. 187 , 60 - 70
    full text (url)
  • Jahn, M., Vorpahl, C., Türkowsky, D., Lindmeyer, M., Bühler, B., Harms, H., Müller, S., (2014):
    Population heterogeneity in Pseudomonas putida analyzed on the single cell level using proteomics and digital PCR
    New Biotech. 31 (Suppl.), S58 - S59
    full text (url)
  • Jahn, M., Vorpahl, C., Türkowsky, D., Lindmeyer, M., Bühler, B., Harms, H., Müller, S., (2014):
    Accurate determination of plasmid copy number of flow-sorted cells using droplet digital PCR
    Anal. Chem. 86 (12), 5969 - 5976
    full text (url)
  • Koch, C., Harms, H., Müller, S., (2014):
    Dynamics in the microbial cytome — single cell analytics in natural systems
    Curr. Opin. Biotechnol. 27 , 134 - 141
    full text (url)
  • Koch, C., Harnisch, F., Schröder, U., Müller, S., (2014):
    Cytometric fingerprints: evaluation of new tools for analyzing microbial community dynamics
    Frontiers in Microbiology 5 , art. 273
    full text (url)
  • Koch, C., Müller, S., Harms, H., Harnisch, F., (2014):
    Microbiomes in bioenergy production: From analysis to management
    Curr. Opin. Biotechnol. 27 , 65 - 72
    full text (url)
  • Lieder, S., Jahn, M., Seifert, J., von Bergen, M., Müller, S., Takors, R., (2014):
    Subpopulation-proteomics reveal growth rate, but not cell cycling, as a major impact on protein composition in Pseudomonas putida KT2440
    AMB Express 4 , art. 71
    full text (url)
  • Schumann, J., Koch, C., Günther, S., Fetzer, I., Müller, S., (2014):
    flowCHIC: Analyze flow cytometric data using histogram information
    R package version 1.0.0
    http://www.bioconductor.org/packages/release/bioc/html/flowCHIC.html
    October 2014: 5 downloads (distinct IPs: ~500)
    full text (url)
  • Schumann, J., Koch, C., Günther, S., Fetzer, I., Müller, S., (2014):
    flowCyBar: Analyze flow cytometric data using gate information
    R package version 1.2.0
    http://www.bioconductor.org/packages/release/bioc/html/flowCyBar.html
    October 2014: 1491 downloads (distinct IPs: December 2014: ~2000)
    full text (url)
to index

2013 (13)

  • Bühligen, F., Rüdinger, P., Fetzer, I., Stahl, F., Scheper, T., Harms, H., Müller, S., (2013):
    Sustainability of industrial yeast serial repitching practice studied by gene expression and correlation analysis
    J. Biotechnol. 168 (4), 718 - 728
    full text (url)
  • Jahn, M., Seifert, J., Hübschmann, T., von Bergen, M., Harms, H., Müller, S., (2013):
    Comparison of preservation methods for bacterial cells in cytomics and proteomics
    Journal of Integrated OMICS 3 (1), 25 - 33
    full text (url)
  • Jahn, M., Seifert, J., von Bergen, M., Schmid, A., Bühler, B., Müller, S., (2013):
    Subpopulation-proteomics in prokaryotic populations
    Curr. Opin. Biotechnol. 24 (1), 79 - 87
    full text (url)
  • Koch, C., Brumme, B., Müller, S., (2013):
    Mikrobielle Gemeinschaften im Visier der Durchflusszytometrie : Aktivitätsanalyse per Barcode
    Biospektrum 19 (4), 396 - 400
    full text (url)
  • Koch, C., Fetzer, I., Harms, H., Müller, S., (2013):
    CHIC—an automated approach for the detection of dynamic variations in complex microbial communities
    Cytom. Part A 83 (6), 561 - 567
    full text (url)
  • Koch, C., Fetzer, I., Schmidt, T., Harms, H., Müller, S., (2013):
    Monitoring functions in managed microbial systems by cytometric bar coding
    Environ. Sci. Technol. 47 (3), 1753 - 1760
    full text (url)
  • Koch, C., Günther, S., Desta, A.F., Hübschmann, T., Müller, S., (2013):
    Cytometric fingerprinting for analyzing microbial intracommunity structure variation and identifying subcommunity function
    Nat. Protoc. 8 (1), 190 - 202
    full text (url)
  • Lentendu, G., Hübschmann, T., Müller, S., Dunker, S., Buscot, F., Wilhelm, C., (2013):
    Recovery of soil unicellular eukaryotes: an efficiency and activity analysis on the single cell level
    J. Microbiol. Methods 95 (3), 463 - 469
    full text (url)
  • Mehlig, L., Petzold, M., Heder, C., Günther, S., Müller, S., Eschenhagen, M., Röske, I., Röske, K., (2013):
    Biodiversity of polyphosphate accumulating bacteria in eight WWTPs with different modes of operation
    J. Environ. Eng. Landsc. Manag. 139 (8), 1089 - 1098
    full text (url)
  • Müller, S., Hiller, K., (2013):
    From multi-omics to basic structures of biological systems
    Curr. Opin. Biotechnol. 24 (1), 1 - 3
    full text (url)
  • Neumeyer, A., Hübschmann, T., Müller, S., Frunzke, J., (2013):
    Monitoring of population dynamics of Corynebacterium glutamicum by multiparameter flow cytometry
    Microb. Biotechnol. 6 (2), 157 - 167
    full text (url)
  • Rohwerder, T., Müller, R.H., Weichler, M.T., Schuster, J., Hübschmann, T., Müller, S., Harms, H., (2013):
    Cultivation of Aquincola tertiaricarbonis L108 on the fuel oxygenate intermediate tert-butyl alcohol induces aerobic anoxygenic photosynthesis at extremely low feeding rates
    Microbiology-(UK) 159 (10), 2180 - 2190
    full text (url)
  • Vogt, J., Stahl, F., Scheper, T., Müller, S., (2013):
    Isolation of intact RNA from sorted S. cerevisiae cells for differential gene expression analysis
    In: Gupta, V.K., Tuohy, M., Ayyachamy, M., Turner, K.M., O’Donovan, A., (eds.)
    Laboratory protocols in fungal biology : current methods in fungal biology
    Fungal Biology
    Springer, New York, p. 265 - 277
    full text (url)
to index

2012 (2)

  • Günther, S., Koch, C., Hübschmann, T., Röske, I., Müller, R., Bley, T., Harms, H., Müller, S., (2012):
    Correlation of community dynamics and process parameters as a tool for the prediction of the stability of wastewater treatment
    Environ. Sci. Technol. 46 (1), 84 - 92
    full text (url)
  • Müller, S., Hübschmann, T., Kleinsteuber, S., Vogt, C., (2012):
    High resolution single cell analytics to follow microbial community dynamics in anaerobic ecosystems
    Methods 57 (3), 338 - 349
    full text (url)
to index

2011 (7)

  • Bombach, P., Hübschmann, T., Fetzer, I., Kleinsteuber, S., Geyer, R., Harms, H., Müller, S., (2011):
    Resolution of natural microbial community dynamics by community fingerprinting, flow cytometry, and trend interpretation analysis
    In: Müller, S., Bley, T., (eds.)
    High resolution microbial single cell analytics
    Adv. Biochem. Eng. Biotechnol. 124
    Springer, Berlin, Heidelberg, New York, p. 151 - 181
    full text (url)
  • Harnisch, F., Koch, C., Patil, S.A., Hübschmann, T., Müller, S., Schröder, U., (2011):
    Revealing the electrochemically driven selection in natural community derived microbial biofilms using flow-cytometry
    Energy Environ. Sci. (4), 1265 - 1267
    full text (url)
  • Müller, S., Bley, T., (eds., 2011):
    High resolution microbial single cell analytics
    Adv. Biochem. Eng. Biotechnol. 124
    Springer, Berlin, Heidelberg, New York, 233 pp.
  • Müller, S., Johnson, D.R., (2011):
    Application of cytomics to separate natural microbial communities by their physiological properties
    In: de Bruijn, F.J., (ed.)
    Handbook of molecular microbial ecology I : metagenomics and complementary approaches
    Wiley-Blackwell, Hoboken, NJ, p. 727 - 734
  • Patil, S.A., Harnisch, F., Koch, C., Hübschmann, T., Fetzer, I., Carmona-Martínez, A.A., Müller, S., Schröder, U., (2011):
    Electroactive mixed culture derived biofilms in microbial bioelectrochemical systems: the role of pH on biofilm formation, performance and composition
    Bioresour. Technol. 102 (20), 9683 - 9690
    full text (url)
  • Trutnau, M., Petzold, M., Mehlig, L., Eschenhagen, M., Geipel, K., Müller, S., Bley, T., Röske, I., (2011):
    Using a carbon-based ASM3 EAWAG Bio-P for modelling the enhanced biological phosphorus removal in anaerobic/aerobic activated sludge systems
    Bioprocess. Biosyst. Eng. 34 (3), 287 - 295
    full text (url)
  • Valet, G., Endl, E., Müller, S., (2011):
    20 years of the German Society for Cytometry: past and future concepts
    Cytom. Part A 79A (11), 891 - 893
    full text (url)
to index

2010 (7)

  • Jehmlich, N., Hübschmann, T., Gesell Salazar, M., Völker, U., Benndorf, D., Müller, S., von Bergen, M., Schmidt, F., (2010):
    Advanced tool for characterization of microbial cultures by combining cytomics and proteomics
    Appl. Microbiol. Biotechnol. 88 (2), 575 - 584
    full text (url)
  • Müller, S., Bley, T., (2010):
    Flow cytometry
    In: Flickinger, M.C., (ed.)
    Encyclopedia of industrial biotechnology: bioprocess, bioseparation, and cell technology, Vol. 4
    Wiley, Oxford, p. 2451 - 2467
    full text (url)
  • Müller, S., Harms, H., Bley, T., (2010):
    Origin and analysis of microbial population heterogeneity in bioprocesses
    Curr. Opin. Biotechnol. 21 (1), 100 - 113
    full text (url)
  • Müller, S., Nebe von Caron, G., (2010):
    Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities
    FEMS Microbiol. Rev. 34 (4), 544 - 587
    full text (url)
  • Müller, S., (2010):
    Functional flow cytometry in environmental microbiology
    In: Timmis, K.N., McGenity, T., van der Meer, J.R., de Lorenzo, V., (eds.)
    Experimental protocols and appendices
    Handbook of Hydrocarbon and Lipid Microbiology Vol. 5, Part 3
    Springer, Berlin, Heidelberg, New York, p. 4103 - 4112
    full text (url)
  • Sträuber, H., Hübschmann, T., Jehmlich, N., Schmidt, F., von Bergen, M., Harms, H., Müller, S., (2010):
    NBDT (3-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-3-toluene) - A novel fluorescent dye for studying mechanisms of toluene uptake into vital bacteria
    Cytom. Part A 77A (2), 113 - 120
    full text (url)
  • Sträuber, H., Müller, S., (2010):
    Viability states of bacteria - specific mechanisms of selected probes
    Cytom. Part A 77A (7), 623 - 634
    full text (url)
to index