Micro-organisms biophysics

Permanent staff: Nicolas Biais, Didier Chatenay, Maxime Deforet, Nicolas Fix-Boulier, Nelly Henry, Frédéric Joubert.
Non-permanent staff: Irshad Abibouraguimane, Martin Maliet.

Microorganisms represent the dominant forms of life on Earth. They display a huge diversity of geometric shapes, behaviours and habitats. We are particularly interested in bacteria. Their size — on the order of microns — and their lifetime — on the order of hours — enable exploring from single cell level to heterogeneous, socially organized populations. We study these systems based on the development of dedicated microfabricated microfluidic devices, coupled with the most recent advances in genetics and video-microscopy and fluorescence imaging approaches. Our objective is to understand the mechanisms underpinning the behaviour of these systems under controlled environments, unveiling the causal relationships linking their physical and biological properties.


Spatio-temporal physiology Multi-species adherent communities Biofilm under flow Bacterial Mechano-biology Compressive Raman Imaging of bacterial biofilm Physics of bacterial colony spreading

Post-docs (since 2018)

  • 2023-2024 Gaspard Junot
  • 2021-2023 Nidia Maldonado-Carmona
  • 2020-2021 Jerko Rosko
  • 2015-2019 Jean Ollion

PhD students (defense 2018->)

  • 2025 Martin Maliet

  • 2023 Vui-Yin Seow

  • 2022 Wafa Ben Youssef

  • 2019 Amaury Monmeyran

  • 2018 Alexandre Deloupy

Master students (since 2018)

Master 1:

  • 2024 Bilge Demerci
  • 2024 Nicolaj Velikinac
  • 2024 Miriam Koch
  • 2024 Pauline Autin
  • 2023 Adrien Bérard
  • 2023 Jinghan Huang
  • 2022 Elif Uyar 
  • 2021 Assia Benachir
  • 2020 Valentin Bonnet

Master 2:

  • 2024 Helene Zhou
  • 2022 Naicen Naourra
  • 2022 Martin Maliet
  • 2022 Nicolas Pellet
  • 2021 Candice hermant
  • 2020 Elif Elçin
  • 2019 Raphaël Monteil
  • 2018 Wafa Benyoussef
  • 2018 Yvan Bourrigault

Licence / BTS students

  • 2025 Amandine Hwang
  • 2024 Berhan Simsek

Related job openings

2024
2026
Master 2
Functional Raman imaging of a bacterial adherent community
2024
2024
Master 2
Membrane Potential dynamics in Neisseria gonorrhoeae microcolonies
2025
2025
Licence
Study of major pathogenic bacteria through the development of genetically modified strains
2025
2027
PostDoc
Bacterial Biofilm Compressive Raman Imaging

Publications

2025

⊞ Experimental and theoretical approaches reveal that antimicrobial blue light killing efficiency decreases with biofilm growth in a Pseudomonas aeruginosa model - BioRxiv (Mar. 2025)
G. Insero, , N. Maldonado-Carmona, , T. Panier , G. Romano, , N. Henry
  URL Full text PDF Bibtex doi:https://doi.org/10.1101/2025.02.26.636652
⊞ Cooperative nutrient scavenging is an evolutionary advantage in cancer - Nature (Feb. 2025)
G. Guzelsoy , S.D. Elorza , M. Ros , L.T. Schachtner , M. Hayashi , S. Hobson-Gutierrez , P. Rundstrom , J.S. Brunner , R. Pillai , W.E. Walkowicz , L.W.S. Finley , M. Deforet , T. Papagiannakopoulos , C. Carmona-Fontaine
  URL Full text PDF Bibtex doi:

2024

⊞ DiSTNet2D: Leveraging Long-Range Temporal Information for Efficient Segmentation and Tracking - PRX Life (Apr. 2024)
J. Ollion , M. Maliet , C. Giuglaris , E. Vacher , M. Deforet
  URL Full text PDF Bibtex doi:https://doi.org/10.1103/PRXLife.2.023004

2023

⊞ Direct comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities - Nature communications (Nov. 2023)
Y. Dergham , D. Le Coq , P. Nicolas , E. Bidnenko , S. Dérozier , M. Deforet , E. Huillet , P. Sanchez-Vizuete , J. Deschamps , K. Hamze , R. Briandet
  URL Full text PDF Bibtex doi:https://doi.org/10.1038/s41467-023-43386-w
⊞ Multisite transformation in Neisseria gonorrhoeae: insights on transformations mechanisms and new genetic modification protocols - Frontiers in Microbiology (Jun. 2023)
V.Y.M. Seow , O. Tsygelnytska , N. Biais
  URL Full text PDF Bibtex doi:https://doi.org/10.3389/fmicb.2023.1178128
⊞ Emergence of Exopolysaccharides Overproducers Is Linked to Environmental Spatial Structure via Redox State - mSphere (Apr. 2023)
M. Ardré , M. Deforet
  URL Full text PDF Bibtex doi:https://doi.org/10.1128/msphere.00123-23
⊞ Long-range alteration of the physical environment mediates cooperation between Pseudomonas aeruginosa swarming colonies - Environmental Microbiology (Mar. 2023)
M. Deforet
  URL Full text PDF Bibtex doi:https://doi.org/10.1111/1462-2920.16373

2022

⊞ Flagellar Motility During E. coli Biofilm Formation Provides a Competitive Disadvantage Which Recedes in the Presence of Co-Colonizers - Front Cell Infect Microbiol (Jul. 2022)
W. Benyoussef , M. Deforet , A. Monmeyran , N. Henry
  URL Full text PDF Bibtex doi:10.3389/fcimb.2022.896898
⊞ Spatial-temporal dynamics of a microbial cooperative behavior resistant to cheating - Nature communications (Jun. 2022)
H. Monaco , K.S. Liu , T. Sereno , M. Deforet , B.P. Taylor , Y. Chen , C.C. Reagor , J.B. Xavier
  URL Full text PDF Bibtex doi:https://doi.org/10.1038/s41467-022-28321-9

2021

⊞ An In Vitro Model System to Test Mechano-Microbiological Interactions Between Bacteria and Host Cells - Cytoskeleton : Methods and Protocols (Sep. 2021)
L.C. Santos , E.L. Munteanu , N. Biais
  URL Full text PDF Bibtex doi:https://doi.org/10.1007/978-1-0716-1661-1_11
⊞ Cooperation between melanoma cell states promotes metastasis through heterotypic cluster formation - Developmental Cell (Aug. 2021)
N.R. Campbell , A. Rao , M.V. Hunter , M.K. Sznurkowska , L. Briker , M. Zhang , M. Baron , S. Heilmann , M. Deforet , C. Kenny , L. Ferretti , T.H. Huang , S. Perlee , M. Garg , J. Nsengimana , M. Saini , E. Montal , M. Tagore , J. Newton-Bishop , M.R. Middleton , P. Corrie , D.J. Adams , R. Rabbie , N. Aceto , M.P. Levesque , R.A. Cornell , I. Yanai , J.B. Xavier , R.M. White
  URL Full text PDF Bibtex doi:https://doi.org/10.1016/j.devcel.2021.08.018
⊞ Fresh Extension of Vibrio cholerae Competence Type IV Pili Predisposes Them for Motor-Independent Retraction - Applied and Environmental Microbiology (Jun. 2021)
J.L. Chlebek , T.N. Dalia , N. Biais , A.B. Dalia
  URL Full text PDF Bibtex doi:https://doi.org/10.1128/AEM.00478-21
⊞ Open science saves lives: lessons from the COVID-19 pandemic - BMC MEDICAL RESEARCH METHODOLOGY (Jun. 2021)
L. Besancon , N. Peiffer-Smadja , C. Segalas , H. Jiang , P. Masuzzo , C. Smout , E. Billy , M. Deforet , C. Leyrat
  URL Full text PDF Bibtex doi:10.1186/s12874-021-01304-y
⊞ Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel - NPJ Biofilms Microbiomes (Jan. 2021)
A. Monmeyran , W. Benyoussef , P. Thomen , N. Dahmane , A. Baliarda , M. Jules , S. Aymerich , N. Henry
  URL Full text PDF Bibtex doi:10.1038/s41522-021-00233-4

2020

⊞ Spatiotemporal pattern formation in E. coli biofilms explained by a simple physical energy balance - Soft Matter (Jan. 2020)
P. Thomen , J. Valentin , A.F. Bitbol , N. Henry
  URL Full text PDF Bibtex doi:10.1039/c9sm01375j

2019

⊞ Evolution at the edge of expanding populations - The American Naturalist (Sep. 2019)
M. Deforet , C. Carmona-Fontaine , K.S. Korolev , J.B. Xavier
  URL Full text PDF Bibtex doi:

2018

⊞ Environmentally Mediated Social Dilemmas - Trends in Ecology and Evolution (Nov. 2018)
S. Estrela , E. Libby , J. Van Cleve , F. Débarre , M. Deforet , W. R. Harcombe , J. Peña , S. P. Brown , M. E. Hochberg
  URL Full text PDF Bibtex doi:https://doi.org/10.1016/j.tree.2018.10.004
⊞ The inducible chemical-genetic fluorescent marker FAST outperforms classical fluorescent proteins in the quantitative reporting of bacterial biofilm dynamics - Scientific Reports (Oct. 2018)
A. Monmeyran , P. Thomen , H. Jonquiere , F. Sureau , C. Li , M.A. Plamont , C. Douarche , J.F. Casella , A. Gautier , N. Henry
  URL Full text PDF Bibtex doi:10.1038/s41598-018-28643-z
⊞ Intermittent Pili-Mediated Forces Fluidize Neisseria meningitidis Aggregates Promoting Vascular Colonization - Cell (Jun. 2018)
D. Bonazzi , V. Lo Schiavo , S. Machata , I. Djafer-Cherif , P. Nivoit , V. Manriquez , H. Tanimoto , J. Husson , N. Henry , H. Chate , R. Voituriez , G. Dumenil
  URL Full text PDF Bibtex doi:10.1016/j.cell.2018.04.010
⊞ Archaeal cells share common size control with bacteria despite noisier growth and division - Nature Microbiology (Feb. 2018)
Y.J. Eun , P.Y. Ho , M. Kim , S. LaRussa , L. Robert , L. Renner , A. Schmid , E. Garner , A. Amir
  URL Full text PDF Bibtex doi:10.1038/s41564-017-0082-6
⊞ Method for Detecting and Studying Genome-Wide Mutations in Single Living Cells in Real Time - Methods Mol Biol (Jan. 2018)
M. Elez , L. Robert , I. Matic
  URL Full text PDF Bibtex doi:https://doi.org/10.1007/978-1-4939-7638-6_3

2017

⊞ Bacterial biofilm under flow: First a physical struggle to stay, then a matter of breathing - PLOS ONE (Apr. 2017)
P. Thomen , J. Robert , A. Monmeyran , A.F. Bitbol , C. Douarche , N. Henry
  URL Full text PDF Bibtex doi:10.1371/journal.pone.0175197

2016

⊞ Single-cell analysis of growth in budding yeast and bacteria reveals a common size regulation strategy - Current Biology (Feb. 2016)
I. Soifer , L. Robert , A. Amir
  URL Full text PDF Bibtex doi:10.1016/j.cub.2015.11.067

2015

⊞ Single-Cell Analysis of Growth and Cell Division of the Anaerobe Desulfovibrio vulgaris Hildenborough - Frontiers in Microbiology (Dec. 2015)
A. Fievet , A. Ducret , T. Mignot , O. Valette , L. Robert , R. Pardoux , A. Dolla , C. Aubert
  URL Full text PDF Bibtex doi:10.3389/fmicb.2015.01378
⊞ Size sensors in bacteria, cell cycle control, and size control - Frontiers in Microbiology (May. 2015)
L. Robert
  URL Full text PDF Bibtex doi:10.3389/fmicb.2015.00515
⊞ Statistical estimation of a growth-fragmentation model observed on a genealogical tree - Bernoulli (Jan. 2015)
M. Doumic , M. Hoffmann , N. Krell , L. Robert
  URL Full text PDF Bibtex doi:10.3150/14-BEJ623

2014

⊞ Division in Escherichia coli is triggered by a size-sensing rather than a timing mechanism - BMC Biology (Feb. 2014)
L. Robert , M. Hoffmann , N. Krell , S. Aymerich , M. Doumic
  URL Full text PDF Bibtex doi:10.1186/1741-7007-12-17