Prof. Dr. Susann Müller


Prof. Dr. Susann Müller
Group Leader Flow Cytometry

Department of Applied Microbial Ecology
Working Group Flow Cytometry
Helmholtz Centre for
Environmental Research - UFZ
Permoserstr. 15, 04318 Leipzig, Germany

Phone +49 341 6025-1318

Web of Science ResearcherID K-1293-2013:

Susann Müller

CV / Scientific Career


Diploma in Biochemistry, Martin-Luther-University Halle-Wittenberg


Scientific assistant at the Institute of Biotechnology of the Academy of Science of the GDR, Leipzig


PhD, University of Halle-Wittenberg, subject: 'Population dynamics of S. cerevisiae'


Scientific assistant in the Scientist Integration Programme of the Coordination and Development Initiative for institutes of the former Academy of Sciences of the GDR


Scientific assistant at the University of Leipzig; Faculty of Biosciences, Pharmacy and Psychology; Department Biotechnology


Grant for habilitation of the Saxon Ministry of Science and Art (SMWK), Dresden

since 2001

Senior scientist at the Department of Environmental Microbiology, UFZ Centre for Environmental Research Leipzig-Halle


Habilitation at the Technical University Dresden, Faculty of Natural Science and Mathematics; subject: 'Multiparametric Cytometry'


apl. Professor for Microbiology at the Leipzig University, Faculty of Life Sciences

Research interests

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.

Current research

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 -
Total: 556.550 €

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
Total: 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)
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’
Total: Scholarship

Current classes

Modul: Structure, Function and Ecology of Microbial Communities 11-BIO-204
Master of Science Integrative Biology, Focus Biodiversity, Ecology, and Evolution (BEE)
Vorlesung (2SWS), Seminar (2SWS), Praktikum (5SWS)
Zusammenarbeit mit Prof. Dr. Chatzinotas
Masterstudiengang Biologie, 1. Semester

Modul: Quantitative Biologie und Biotechnologie 11-BCH-0822
Mitarbeit im Rahmen der Vorlesung
Masterstudiengang Biochemie, 1. Semester

Modul: Mikrobielle Ökologie und Umweltbiotechnologie 11-BCH-0707
Mitarbeit im Rahmen des Seminars und Praktikums
Masterstudiengang Biochemie, 1. Semester

Modul: Interaktionen in aquatischen und terrestrischen Ökosystemen 11-BIO-205
Mitarbeit im Rahmen der Vorlesung
Masterstudiengang Biologie, 1. Semester

Other Professional Activities

  • President of the German Society of Cytometry (DGfZ, 2008 -2010)
  • Associate Editor for Microbiology for CYTOMETRY Part A
  • Member of the Educational Committee of ISAC (2011 - 2012)
  • Board member of ISAC Scholars Program Committee (ISPC, 2013-2015)

Selected Publications

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.

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 (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)

Liu Z, Müller S.
Bacterial community diversity dynamics highlight degrees of nestedness and turnover patterns.
Cytometry Part A (2020)

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.

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
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.

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.

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.


You could use our publication index for further requests.

2024 (2)

to index

2023 (5)

to index

2022 (6)

to index

2021 (5)

to index

2020 (8)

to index

2019 (10)

to index

2018 (7)

to index

2017 (4)

to index

2016 (4)

to index

2015 (9)

to index

2014 (9)

to index

2013 (13)

to index

2012 (2)

to index

2011 (7)

to index

2010 (7)

to index