Flow-Cytometrie
Forschungsthemen
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.
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.
Cytometric fingerprints of complex microbial communities can be evaluated using the following tools:
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 Forschungsgemeinschaft (DFG)
Aktenzeichen: GZ: MU 1089/10-1, AOBJ: 687645
Projektnummer: 503905203
Schwerpunktprogramms (SPP) "Emergente Funktionen der bakteriellen Multizellularität"
Analyse der lokalen Struktur und Funktion von bakteriellen Kolonien und Biofilmen auf Einzelzellebene mittels Durchflusszytometrie, Zellsortierung, Multi-omics und Datenwissenschaft -
Z-PROJECT“
1.11.2022-31.10.2025
Total: 556.550 €
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 – 31.08.2022
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
01.07.2019 – 30.10.2022
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)
01.03.2019-30.2.2023
Total: Scholarship
Gordon and Betty Moore Foundation
Grant Number: GBMF9730
Resolving archaeal contributions to the first eukaryotic common ancestor: Developing new tools for accessing the genomes of uncultivated archaea.
In cooperation with the University of California, Santa Barbara Earth Research Institute
13.08.2020-01.09.2023
23 K€
EU- H2020- Horizon 2020 Societal Challenge 2
Aktenzeichen: Proposal 101000733 – PROMICON
PROMICON - FNR-12-2020 - Industrial microbiomes – learning from nature
Harnessing the power of nature through productive microbial consortia in biotechnology – Measure, Model & Master (PROMICON)
01.06.2021-31.12.2024
Total: 200 k€ UFZ, AG Flow Cytometry
Chinese Scholarship Council (CSC)
China, Ministery of Education
‘Construction of functionally active artificial communities based on individual cell analyses and ecological theory’
01.10.2021-31.09.2025
Total: Scholarship
Ausgewählte Publikationen
Jurburg SD, Eisenhauer N, Buscot F, Chatzinotas A, Chaudhari NM, Heintz-Buschart A, Kallies R, Küsel K, Litchman E, Macdonald CA, Müller S, Reuben RC, da Rocha UN, Panagiotou G, Rillig MC, Singh BK.
Potential of microbiome-based solutions for agrifood systems
Nature Food (2022) DOI - 10.1038/s43016-022-00576-x
Li S, Abdulkadir N, Schattenberg F, Rocha UN, Grimm V, Müller S, Liu Z
Stabilising microbial communities by looped mass transfer
Proceedings of the National Academy of Sciences (PNAS) (2022) 119/17, e2117814119
Cohen Y, Pasternak Z, Müller S, Hübschmann T, Schattenberg F, Sivakala KK, Abed-Rabbo A,
Chatzinotas A & Jurkevitch E
Community and single cell analyses reveal complex predatory interactions between bacteria in high-diversity systems.
Nature Communications (2021) 12, 5481.
A framework for P-cycle assessment in wastewater treatment plants.
Science of the Total Environment (2021) 760C, 143392.
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.
Inhalt:
2021 (5)2020 (8)
2019 (10)
2018 (7)
2017 (4)
2016 (4)
2015 (9)
2014 (9)
2013 (13)
2012 (2)
2011 (7)
2010 (7)
Weiterführende Recherchen können Sie in unserem Publikationsverzeichnis durchführen.
2021 (5)
- Cohen, Y., Pasternak, Z., Müller, S., Hübschmann, T., Schattenberg, F., Sivakala, K.K., Abed-Rabbo, A., Chatzinotas, A., Jurkevitch, E. (2021):
Community and single cell analyses reveal complex predatory interactions between bacteria in high diversity systems
Nat. Commun. 12 , art. 5481
Volltext (DOI) - Heyse, J., Schattenberg, F., Rubbens, P., Müller, S., Waegeman, W., Boon, N., Props, R. (2021):
Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting
mSystems 6 (5), e00551-21
Volltext (DOI) - Qin, W., Stärk, H.-J., Müller, S., Reemtsma, T., Wagner, S. (2021):
Determination of elemental distribution and evaluation of elemental concentration in single Saccharomyces cerevisiae cells using single cell-inductively coupled plasma mass spectrometry
Metallomics 13 (6), mfab032
Volltext (DOI) - Vučić, V., Müller, S. (2021):
New developments in biological phosphorus accessibility and recovery approaches from soil and waste streams
Eng. Life Sci. 21 (3-4), 77 - 86
Volltext (DOI) - Vučić, V., Süring, C., Harms, H., Müller, S., Günther, S. (2021):
A framework for P-cycle assessment in wastewater treatment plants
Sci. Total Environ. 760 , art. 143392
Volltext (DOI)
2020 (8)
- Alvarez Esquivel, D.Y., Guo, Y., Brown, R.K., Müller, S., Schröder, U., Harnisch, F. (2020):
Investigating community dynamics and performance during microbial electrochemical degradation of whey
ChemElectroChem 7 (4), 989 - 997
Volltext (DOI) - Cichocki, N., Hübschmann, T., Schattenberg, F., Kerckhof, F.M., Overmann, J., Müller, S. (2020):
Bacterial mock communities as standards for reproducible cytometric microbiome analysis
Nat. Protoc. 15 , 2788 - 2812
Volltext (DOI) - Guo, Y., Rosa, L.F.M., Müller, S., Harnisch, F. (2020):
Monitoring stratification of anode biofilms in bioelectrochemical laminar flow reactors using flow cytometry
Environ. Sci. Ecotechnol. 4 , art. 10062
Volltext (DOI) - Haange, S.-B., Jehmlich, N., Krügel, U., Hintschich, C., Wehrmann, D., Hankir, M., Seyfried, F., Froment, J., Hübschmann, T., Müller, S., Wissenbach, D.K., Kang, K.H., Buettner, C., Panagiotou, G., Noll, M., Rolle-Kampczyk, U., Fenske, W., von Bergen, M. (2020):
Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss
Microbiome 8 , art. 13
Volltext (DOI) - Krause, J.L., Schaepe, S.S., Fritz-Wallace, K., Engelmann, B., Rolle-Kampczyk, U., Kleinsteuber, S., Schattenberg, F., Liu, Z., Müller, S., Jehmlich, N., von Bergen, M., Herberth, G. (2020):
Following the community development of SIHUMIx – a new intestinal in vitro model for bioreactor use
Gut Microbes 11 (4), 1116 - 1129
Volltext (DOI) - Krause, J.L., Schäpe, S.S., Schattenberg, F., Müller, S., Ackermann, G., Rolle-Kampczyk, U.E., Jehmlich, N., Pierzchalski, A., von Bergen, M., Herberth, G. (2020):
The activation of mucosal-associated invariant T (MAIT) cells is affected by microbial diversity and riboflavin utilization in vitro
Front. Microbiol. 11 , art. 755
Volltext (DOI) - Liu, Z., Müller, S. (2020):
Bacterial community diversity dynamics highlight degrees of nestedness and turnover patterns
Cytom. Part A 97 (7), 742 - 748
Volltext (DOI) - Müller, S., Chang, H.-D. (2020):
Microorganisms and their activities within microbial communities
Cytom. Part A 97 (7), 681 - 682
Volltext (DOI)
2019 (10)
- Calabrese, F., Voloshynovska, I., Musat, F., Thullner, M., Schlömann, M., Richnow, H.H., Lambrecht, J., Müller, S., Wick, L.Y., Musat, N., Stryhanyuk, H. (2019):
Quantitation and comparison of phenotypic heterogeneity among single cells of monoclonal microbial populations
Front. Microbiol. 10 , art. 2814
Volltext (DOI) - Cossarizza, A., Chang, H.-D., Radbruch, A., Acs, A., Adam, D., Adam-Klages, S., Müller, S., Agace, W.W., et al. (2019):
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
Eur. J. Immunol. 49 (10), 1457 - 1973
Volltext (DOI) - Czechowska, K., Lannigan, J., Wang, L., Arcidiacono, J., Ashhurst, T.M., Barnard, R.M., Bauer, S., Bispo, C., Bonilla, D.L., Brinkman, R.R., Cabanski, M., Chang, H.-D., Chakrabarti, L., Chojnowski, G., Cotleur, B., Degheidy, H., Dela Cruz, G.V., Eck, S., Elliott, J., Errington, R., Filby, A., Gagnon, D., Gardner, R., Green, C., Gregory, M., Groves, C.J., Hall, C., Hammes, F., Hedrick, M., Hoffman, R., Icha, J., Ivaska, J., Jenner, D.C., Jones, D., Kerckhof, F.M., Kukat, C., Lanham, D., Leavesley, S., Lee, M., Lin‐Gibson, S., Litwin, V., Liu, Y., Molloy, J., Moore, J.S., Müller, S., Nedbal, J., Niesner, R., Nitta, N., Ohlsson‐Wilhelm, B., Paul, N.E., Perfetto, S., Portat, Z., Props, R., Radtke, S., Rayanki, R., Rieger, A., Rogers, S., Rubbens, P., Salomon, R., Schiemann, M., Sharpe, J., Sonder, S.U., Stewart, J.J., Sun, Y., Ulrich, H., Van Isterdael, G., Vitaliti, A., van Vreden, C., Weber, M., Zimmermann, J., Vacca, G., Wallace, P., Tárnok, A. (2019):
Cyt‐Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops
Cytom. Part A 95 (6), 598 - 644
Volltext (DOI) - Donnenberg, V.S., Müller, S., Houston, J.P., Holden, E. (2019):
Cytometry score: 23 to 4
Cytom. Part A 95 (3), 259 - 260
Volltext (DOI) - Engel, C., Schattenberg, F., Dohnt, K., Schröder, U., Müller, S., Krull, R. (2019):
Long-term behavior of defined mixed cultures of Geobacter sulfurreducens and Shewanella oneidensis in bioelectrochemical systems
Front. Bioeng. Biotechnol. 7 , art. 60
Volltext (DOI) - Guo, Y., Cichocki, N., Schattenberg, F., Geffers, R., Harms, H., Müller, S. (2019):
AgNPs change microbial community structures of wastewater
Front. Microbiol. 9 , art. 3211
Volltext (DOI) - Lambrecht, J., Cichocki, N., Schattenberg, F., Kleinsteuber, S., Harms, H., Müller, S., Sträuber, H. (2019):
Key sub‑community dynamics of medium‑chain carboxylate production
Microb. Cell. Fact. 18 , art. 92
Volltext (DOI) - Liu, Z., Cichocki, N., Hübschmann, T., Süring, C., Ofiţeru, I.D., Sloan, W.T., Grimm, V., Müller, S. (2019):
Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis
Environ. Microbiol. 21 (1), 164 - 181
Volltext (DOI) - Ludwig, J., Höner zu Siederdissen, C., Liu, Z., Stadler, P.F., Müller, S. (2019):
flowEMMi: an automated model-based clustering tool for microbial cytometric data
BMC Bioinformatics 20 , art. 643
Volltext (DOI) - Schäpe, S.S., Krause, J.L., Engelmann, B., Fritz-Wallace, K., Schattenberg, F., Liu, Z., Müller, S., Jehmlich, N., Rolle-Kampczyk, U., Herberth, G., von Bergen, M. (2019):
The simplified human intestinal microbiota (SIHUMIx) shows high structural and functional resistance against changing transit times in in vitro bioreactors
Microorganisms 7 (12), art. 641
Volltext (DOI)
2018 (7)
- Günther, S., Becker, D., Hübschmann, T., Reinert, S., Kleinsteuber, S., Müller, S., Wilhelm, C. (2018):
Long-term biogas production from glycolate by diverse and highly dynamic communities
Microorganisms 6 (4), art. 130
Volltext (DOI) - Günther, S., Grunert, M., Müller, S. (2018):
Overview of recent advances in phosphorus recovery for fertilizer production
Eng. Life Sci. 18 (7), 434 - 439
Volltext (DOI) - Koch, C., Müller, S. (2018):
Personalized microbiome dynamics – Cytometric fingerprints for routine diagnostics
Mol. Asp. Med. 59 , 123 - 134
Volltext (DOI) - Lambrecht, J., Schattenberg, F., Harms, H., Müller, S. (2018):
Characterizing microbiome dynamics – flow cytometry based workflows from pure cultures to natural communities
J. Vis. Exp. (137), e58033
Volltext (DOI) - Liu, Z., Cichocki, N., Bonk, F., Günther, S., Schattenberg, F., Harms, H., Centler, F., Müller, S. (2018):
Ecological stability properties of microbial communities assessed by flow cytometry
mSphere 3 (1), e00564-17
Volltext (DOI) - van Gelder, S., Röhrig, N., Schattenberg, F., Cichocki, N., Schumann, J., Schmalz, G., Haak, R., Ziebolz, D., Müller, S. (2018):
A cytometric approach to follow variation and dynamics of the salivary microbiota
Methods 134–135 , 67 - 79
Volltext (DOI) - Zimmermann, J., Durek, P., Kühl, A.A., Schattenberg, F., Maschmeyer, P., Siracusa, F., Lehmann, K., Westendorf, K., Weber, M., Riedel, R., Müller, S., Radbruch, A., Chang, H.-D. (2018):
The intestinal microbiota determines the colitis-inducing potential of T-bet-deficient Th cells in mice
Eur. J. Immunol. 48 (1), 161 - 167
Volltext (DOI)
2017 (4)
- Cossarizza, A., Chang, H.-D., Radbruch, A., Akdis, M., Andrä, I., Annunziato, F., Bacher, P., Barnaba, V., Battistini, L., Bauer, W.M., Baumgart, S., Becher, B., Beisker, W., Berek, C., Blanco, A., Borsellino, G., Boulais, P.E., Brinkman, R.R., Büscher, M., Busch, D.H., Bushnell, T.P., Cao, X., Cavani, A., Chattopadhyay, P.K., Cheng, Q., Chow, S., Clerici, M., Cooke, A., Cosma, A., Cosmi, L., Cumano, A., Dang, V.D., Davies, D., De Biasi, S., Del Zotto, G., Müller, S., Müller, W., et al. (2017):
Guidelines for the use of flow cytometry and cell sorting in immunological studies
Eur. J. Immunol. 47 (10), 1584 - 1797
Volltext (DOI) - Guo, Y., Baumgart, S., Stärk, H.-J., Harms, H., Müller, S. (2017):
Mass cytometry for detection of silver at the bacterial single cell level
Front. Microbiol. 8 , art. 1326
Volltext (DOI) - Guo, Y., Stärk, H.J., Hause, G., Schmidt, M., Harms, H., Wick, L.Y., Müller, S. (2017):
Heterogenic response of prokaryotes toward silver nanoparticles and ions is facilitated by phenotypes and attachment of silver aggregates to cell surfaces
Cytom. Part A 91 (8), 775 - 784
Volltext (DOI) - Lambrecht, J., Cichocki, N., Hübschmann, T., Koch, C., Harms, H., Müller, S. (2017):
Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence
Microb. Cell. Fact. 16 , art. 180
Volltext (DOI)
2016 (4)
- 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. 18 (12), 4862 - 4877
Volltext (DOI) - Jahn, M., Vorpahl, C., Hübschmann, T., Harms, H., Müller, S. (2016):
Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR
Microb. Cell. Fact. 15 , art. 211
Volltext (DOI) - Lieder, S., Jahn, M., Koepff, J., Müller, S., Takors, R. (2016):
Environmental stress speeds up DNA replication in Pseudomonas putida in chemostat cultivations
Biotechnol. J. 11 (1), 155 - 163
Volltext (DOI) - Zimmermann, J., Hübschmann, T., Schattenberg, F., Schumann, J., Durek, P., Riedel, R., Friedrich, M., Glauben, R., Siegmund, B., Radbruch, A., Müller, S., Chang, H.-D. (2016):
High-resolution microbiota flow cytometry reveals dynamic colitis-associated changes in fecal bacterial composition
Eur. J. Immunol. 46 (5), 1300 - 1303
Volltext (DOI)
2015 (9)
- Günther, S., Müller, S. (2015):
Facilitated gate setting by sequential dot plot scanning
Cytom. Part A 87 (7), 661 - 664
Volltext (DOI) - Jahn, M., Günther, S., Müller, S. (2015):
Non-random distribution of macromolecules as driving forces for phenotypic variation
Curr. Opin. Microbiol. 25 , 49 - 55
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI) - 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
Front. Microbiol. 6 , art. 1042
Volltext (DOI) - 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
Volltext (DOI) - 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. 77 - 89 - 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
Volltext (DOI) - 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
Front. Microbiol. 6 , art. 243
Volltext (DOI)
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
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI) - Koch, C., Harms, H., Müller, S. (2014):
Dynamics in the microbial cytome — single cell analytics in natural systems
Curr. Opin. Biotechnol. 27 , 134 - 141
Volltext (DOI) - Koch, C., Harnisch, F., Schröder, U., Müller, S. (2014):
Cytometric fingerprints: evaluation of new tools for analyzing microbial community dynamics
Front. Microbiol. 5 , art. 273
Volltext (DOI) - Koch, C., Müller, S., Harms, H., Harnisch, F. (2014):
Microbiomes in bioenergy production: From analysis to management
Curr. Opin. Biotechnol. 27 , 65 - 72
Volltext (DOI) - 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
Volltext (DOI) - 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)
Volltext (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)
Volltext (URL)
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
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI) - Koch, C., Brumme, B., Müller, S. (2013):
Mikrobielle Gemeinschaften im Visier der Durchflusszytometrie : Aktivitätsanalyse per Barcode
Biospektrum 19 (4), 396 - 400
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI) - 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.-ASCE 139 (8), 1089 - 1098
Volltext (DOI) - Müller, S., Hiller, K. (2013):
From multi-omics to basic structures of biological systems
Curr. Opin. Biotechnol. 24 (1), 1 - 3
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI)
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
Volltext (DOI) - 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
Volltext (DOI)
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, p. 151 - 181
Volltext (DOI) - 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
Volltext (DOI) - Müller, S., Bley, T. (eds., 2011):
High resolution microbial single cell analytics
Adv. Biochem. Eng. Biotechnol. 124
Springer, Berlin, Heidelberg, 233 pp.
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI) - 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
Volltext (DOI)
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
Volltext (DOI) - 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
Volltext (DOI) - Müller, S., Harms, H., Bley, T. (2010):
Origin and analysis of microbial population heterogeneity in bioprocesses
Curr. Opin. Biotechnol. 21 (1), 100 - 113
Volltext (DOI) - 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
Volltext (DOI) - 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 International Publishing, Cham, p. 4103 - 4112
Volltext (DOI) - 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
Volltext (DOI) - Sträuber, H., Müller, S. (2010):
Viability states of bacteria - specific mechanisms of selected probes
Cytom. Part A 77A (7), 623 - 634
Volltext (DOI)