Ackermann M (2015) A functional perspective on phenotypic heterogeneity in microorganisms. Nat Rev Microbiol 13:497–508. https://doi.org/10.1038/nrmicro3491

Article  CAS  PubMed  Google Scholar 

Afroz T, Biliouris K, Kaznessis Y, Beisel CL (2014) Bacterial sugar utilization gives rise to distinct single-cell behaviours. Mol Microbiol 93. https://doi.org/10.1111/mmi.12695

Andersen JB, Sternberg C, Poulsen LK, Bjørn SP, Givskov M, Molin S (1998) New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol 64. https://doi.org/10.1128/aem.64.6.2240-2246.1998

Anderson CJ, Clark DE, Adli M, Kendall MM (2015) Ethanolamine signaling promotes Salmonella niche recognition and adaptation during infection. PLoS Pathog 11. https://doi.org/10.1371/journal.ppat.1005278

Avery SV (2006) Microbial cell individuality and the underlying sources of heterogeneity. Nat Rev Microbiol 4

Blander JM (2016) Death in the intestinal epithelium—basic biology and implications for inflammatory bowel disease. FEBS J 283:2720–2730

Article  CAS  PubMed  PubMed Central  Google Scholar 

Burton NA, Schürmann N, Casse O, Steeb AK, Claudi B, Zankl J, Schmidt A, Bumann D (2014) Disparate impact of oxidative host defenses determines the fate of Salmonella during systemic infection in mice. Cell Host Microbe 15. https://doi.org/10.1016/j.chom.2013.12.006

Bury-Moné S, Sclavi B (2017) Stochasticity of gene expression as a motor of epigenetics in bacteria: from individual to collective behaviors. Res Microbiol 168:503–514

Article  PubMed  Google Scholar 

Campbell-Valois FX, Sansonetti PJ (2014) Tracking bacterial pathogens with genetically-encoded reporters. FEBS Lett 588:2428–2436. https://doi.org/10.1016/j.febslet.2014.05.022

Article  CAS  PubMed  Google Scholar 

Cayron J, Lesterlin C (2019) Multi-scale analysis of bacterial growth under stress treatments. J Vis Exp. https://doi.org/10.3791/60576

Conway T, Krogfelt KA, Cohen PS (2004) The life of commensal Escherichia coli in the mammalian intestine. EcoSal Plus 1. https://doi.org/10.1128/ecosalplus.8.3.1.2

Crepin S, Harel J, Dozois CM (2012) Chromosomal complementation using Tn7 transposon vectors in enterobacteriaceae. Appl Environ Microbiol 78. https://doi.org/10.1128/AEM.00986-12

Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640–6645. https://doi.org/10.1073/pnas.120163297

Article  CAS  PubMed  PubMed Central  Google Scholar 

Davis KM, Mohammadi S, Isberg RR (2015) Community behavior and spatial regulation within a bacterial microcolony in deep tissue sites serves to protect against host Attack. Cell Host Microbe 17. https://doi.org/10.1016/j.chom.2014.11.008

Gardette M, Daniel J, Loukiadis E, Jubelin G (2020) Role of the nitric oxide reductase NorVW in the survival and virulence of enterohaemorrhagic Escherichia coli during infection. Pathogens 9:1–14. https://doi.org/10.3390/pathogens9090683

Article  CAS  Google Scholar 

Garsin DA (2010) Ethanolamine utilization in bacterial pathogens: roles and regulation. Nat Rev Microbiol 8:290–295

Article  CAS  PubMed  PubMed Central  Google Scholar 

Garsin DA (2012) Ethanolamine: a signal to commence a host-associated lifestyle? MBio 3:10–1128. https://doi.org/10.1128/mbio.00172-12

Article  Google Scholar 

Hennessy RC, Christiansen L, Olsson S, Stougaard P (2018) A broad-host range dual-fluorescence reporter system for gene expression analysis in gram-negative bacteria. J Microbiol Methods 144. https://doi.org/10.1016/j.mimet.2017.11.024

Kaval KG, Garsin DA (2018) Ethanolamine utilization in bacteria. MBio 9. https://doi.org/10.1128/mBio.00066-18

Kendall MM, Gruber CC, Parker CT, Sperandio V (2012) Ethanolamine controls expression of genes encoding components involved in interkingdom signaling and virulence in enterohemorrhagic Escherichia coli O157:H7. MBio 3. https://doi.org/10.1128/mBio.00050-12

Kim JM, Garcia-Alcala M, Balleza E, Cluzel P (2020) Stochastic transcriptional pulses orchestrate flagellar biosynthesis in Escherichia coli. Sci Adv 6. https://doi.org/10.1126/sciadv.aax0947

Kiviet DJ, Nghe P, Walker N, Boulineau S, Sunderlikova V, Tans SJ (2014) Stochasticity of metabolism and growth at the single-cell level. Nature 514. https://doi.org/10.1038/nature13582

Lasaro M, Liu Z, Bishar R, Kelly K, Chattopadhyay S, Paul S, Sokurenko E, Zhu J, Goulian M (2014) Escherichia coli isolate for studying colonization of the mouse intestine and its application to two-component signaling knockouts. J Bacteriol 196. https://doi.org/10.1128/JB.01296-13

Lauren DM, Shailab S, RJ W, Pola K, Maria K, Carolina AF, Aimee S (2022) Development of a dual-fluorescent-reporter system in Clostridioides difficile reveals a division of labor between virulence and transmission Gene Expression. mSphere 7:e00132-22. https://doi.org/10.1128/msphere.00132-22

Article  CAS  Google Scholar 

Li J, Claudi B, Fanous J, Chicherova N, Cianfanelli FR, Campbell RAA, Bumann D (2021) Tissue compartmentalization enables Salmonella persistence during chemotherapy. Proc Natl Acad Sci U S A 118. https://doi.org/10.1073/pnas.2113951118

Lim HN, van Oudenaarden A (2007) A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet 39:269–275. https://doi.org/10.1038/ng1956

Article  CAS  PubMed  Google Scholar 

Maltby R, Leatham-Jensen MP, Gibson T, Cohen PS, Conway T (2013) Nutritional basis for colonization resistance by human commensal Escherichia coli strains HS and Nissle 1917 against E. coli O157:H7 in the mouse intestine. PLoS One 8. https://doi.org/10.1371/journal.pone.0053957

Martin CS, Jubelin G, Darsonval M, Leroy S, Leneveu‐Jenvrin C, Hmidene G, Omhover L, Stahl V, Guillier L, Briandet R, Desvaux M (2022) Genetic, physiological, and cellular heterogeneities of bacterial pathogens in food matrices: Consequences for food safety. Compr Rev food Sci food Saf. https://doi.org/10.1111/1541-4337.13020

Miller WG, Leveau JHJ, Lindow SE (2000) Improved gfp and inaZ broad-host-range promoter-probe vectors. Mol Plant-Microbe Interact 13. https://doi.org/10.1094/MPMI.2000.13.11.1243

Moreira de Gouveia MI, Daniel J, Garrivier A, Bernalier-Donadille A, Jubelin G (2022) Diversity of ethanolamine utilization by human commensal Escherichia coli. Res Microbiol:103989. https://doi.org/10.1016/j.resmic.2022.103989

Nielsen AT, Dolganov NA, Rasmussen T, Otto G, Miller MC, Felt SA, Torreilles S, Schoolnik GK (2010) A bistable switch and anatomical site control Vibrio cholerae virulence gene expression in the intestine. PLoS Pathog 6. https://doi.org/10.1371/journal.ppat.1001102

Nuss AM, Schuster F, Roselius L, Klein J, Bücker R, Herbst K, Heroven AK, Pisano F, Wittmann C, Münch R, Müller J, Jahn D, Dersch P (2016) A precise temperature-responsive bistable switch controlling Yersinia virulence. PLoS Pathog 12. https://doi.org/10.1371/journal.ppat.1006091

Packer D (2021) The history of the antibody as a tool. Acta Histochem 123

Patange O, Schwall C, Jones M, Villava C, Griffith DA, Phillips A, Locke JCW (2018) Escherichia coli can survive stress by noisy growth modulation. Nat Commun 9. https://doi.org/10.1038/s41467-018-07702-z

Payros D, Secher T, Boury M, Brehin C, Ménard S, Salvadorcartier C, Cuevas-Ramos G, Watrin C, Marcq I, Nougayrède JP, Dubois D, Bedu A, Garnier F, Clermont O, Denamur E, Plaisancié P, Theodorou V, Fioramonti J, Olier M, Oswald E (2014) Maternally acquired genotoxic Escherichia coli alters offspring’s intestinal homeostasis. Gut Microbes 5. https://doi.org/10.4161/gmic.28932

Peñate-Medina O, Tower RJ, Peñate-Medina T, Will O, Saris PEJ, Suojanen J, Sorsa T, Huuskonen L, Hiippala K, Satokari R, Glüer CC, de Vos WM, Reunanen J (2019) Universal membrane-labeling combined with expression of Katushka far-red fluorescent protein enables non-invasive dynamic and longitudinal quantitative 3D dual-color fluorescent imaging of multiple bacterial strains in mouse intestine. BMC Microbiol 19. https://doi.org/10.1186/s12866-019-1538-z

Rosochacki SJ, Matejczyk M (2002) Green fluorescent protein as a molecular marker in microbiology. Acta Microbiol Pol 51:205–216

CAS  PubMed  Google Scholar 

Rowley CA, Sauder AB, Kendall MM (2020) The ethanolamine-sensing transcription factor EutR promotes virulence and transmission during Citrobacter rodentium intestinal infection. Infect Immun 88. https://doi.org/10.1128/IAI.00137-20

Sampaio NMV, Blassick CM, Andreani V, Lugagne JB, Dunlop MJ (2022) Dynamic gene expression and growth underlie cell-to-cell heterogeneity in Escherichia coli stress response. Proc Natl Acad Sci U S A 119. https://doi.org/10.1073/pnas.2115032119

Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682. https://doi.org/10.1038/nmeth.2019

Article  CAS  PubMed  Google Scholar 

Schulte M, Olschewski K, Hensel M (2021) Fluorescent protein-based reporters reveal stress response of intracellular Salmonella enterica at level of single bacterial cells. Cell Microbiol 23. https://doi.org/10.1111/cmi.13293

Sharma V (2018) ImageJ plugin HyperStackReg V5.6. https://doi.org/10.5281/zenodo.2252521

Striednig B, Lanner U, Niggli S, Katic A, Vormittag S, Brülisauer S, Hochstrasser R, Kaech A, Welin A, Flieger A, Ziegler U, Schmidt A, Hilbi H, Personnic N (2021) Quorum sensing governs a transmissive Legionella subpopulation at the pathogen vacuole periphery. EMBO Rep 22. https://doi.org/10.15252/embr.202152972

Takhaveev V, Heinemann M (2018) Metabolic heterogeneity in clonal microbial populations. Curr Opin Microbiol 45

Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Coppée JY, Lecuit M, Johansson J, Cossart P (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459. https://doi.org/10.1038/nature08080

Yang C, Ren C, Zhou J, Liu J, Zhang Y, Huang F, Ding D, Xu B, Liu J (2017) Dual fluorescent- and isotopic-labelled self-assembling vancomycin for in vivo imaging of bacterial infections. Angew Chemie - Int Ed 56:2356–2360. https://doi.org/10.1002/anie.201610926

Article  CAS  Google Scholar 

Yoon SA, Park SY, Cha Y, Gopala L, Lee MH (2021) Strategies of detecting bacteria using fluorescence-based dyes. Front Chem 9:743923. https://doi.org/10.3389/fchem.2021.743923

Article  CAS  PubMed  PubMed Central  Google Scholar