Technique(s) Biological target Labelling method Live/fixed Organism Reference
cell wall cell wall cell wall cell wall cell wall cell wall
3D STORM (dual-color imaging) Membrane N-acetylglucosamineprotein A enterotoxin B nile red WGA (AF647) Indirect immunofluorescence staining (AF647) Indirect immunofluorescence staining (AF647)
fixed
Staphylococcus aureus
10.1186/s12915-022-01472-3
dSTORM peptidoglycan azido-D-Ala-D-Ala probe linked to AF647 fixed Streptococcus pneumoniae 10.1016/j.xpro.2021.101006
dSTORM/ 3D-SIM penicillin-binding proteins glycan strands CephCy5 azide N-acetylmuramic acid (AzNAM)
fixed
Staphylococcus aureus
10.1021/acschembio.2c00741
STED/SIM
peptidoglycan
Fluorescein/OregonGreen488/ TAMARA-labelled d-amino acids
fixed
Staphylococcus aureus Streptococcus mutans Bacillus subtilis Escherichia coli Zymomonas mobilis
10.1099/mic.0.000996
3D-SIM Z-ring (SepF and FtsZ) indirect immunofluorescence staining (AF555 and AF488) fixed Methanobrevibacter smithii 10.1038/s41467-021-23099-8
3D-SIM bactofilin (CcmA) HaloTag (JF549) fixed Helicobacter pylori 10.7554/eLife.80111
SIM teixobactin fluorescent teixobactin analogues (fluorescein, Cy3 and Cy5) fixed Bacillus subtilis 10.1039/d2sc01388f
DNA DNA DNA DNA DNA DNA
PALM (SMT)
DNA methyltransferase (DnmA)
PAmCherry
live
Bacillus subtilis
10.1128/mbio.03185-22
PALM (SMT) translesion synthesis polymerases (Pol IV) single-stranded DNA-binding protein (SSB)
PAmCherry, mYPet
live
Escherichia coli
10.1073/pnas.2208875119
PALM (imaging/ SMT) PAINT two-component system SsrB, SsrA membranes PAmCherry Nile red
fixed/live
Salmonella enterica
10.7554/eLife.45311
PALM (imaging/ SMT) 3D-SIM RNA polymerase Nucleoid PAmCherry HU-mCherry
fixed/live
Escherichia coli
10.1073/pnas.1507592112
PALM (imaging/ SMT) DNA polymerase I ligase
PamCherry
fixed/live
Escherichia coli
10.1073/pnas.1301804110
SIM
extracellular polysaccharides eDNA fluorescein isothiocyanate-labeled concanavalin A propidium iodide
fixed
Bacillus subtilis Brevundimonas diminuta
10.1007/s11356-022-21645-5
secretion systems secretion systems secretion systems secretion systems secretion systems secretion systems
2D/3D-MINFLUX/ STORM/ STED T3SS translocon (YopD) T3SS basal body (YscD) ALFA-Tag/NbALFA based labelling (AbberiorSTAR635P, AF647) Halo-Tag (AF647)
fixed
Yersinia enterocolitica
10.1088/2050-6120/aca880
PALM (SMT) T3SS basal body (YscD) PAmCherry live Yersinia enerocolitica 10.1038/s41467-021-21863-4
PALM (imaging/ SMT) SecYEG translocon ATPase (SecA)
Ypet/mEos3.2
fixed/ live
Escherichia coli
10.1038/s41598-021-81081-2
2D/3D-PALM (dual-color imaging) T3SS PrgH, SpaO, OrgA, OrgB, InvC, InvI, InvA SipD mEos3.2 indirect immunofluorescence staining (flag-tag, AF647)
fixed
Salmonella enterica
10.1073/pnas.1705823114
dSTORM (dual-color imaging/ SMT) flagellar basal body complex (FliN) T1SS ATPase subunit (SiiF) T1SS Secretin (SiiC) T3SS export aparatus (SpaS) T3SS ATPase (InvC) Halo (TMR, Atto6) SNAP (TMR-Star) fixed/ live
Salmonella enterica
10.1038/srep31601
2D/3D-STED (dual-color imaging)/ SIM T3SS translocon (YopB, YopD, LcrV) T3SS basal body YscD indirect immunofluoescence staining (AbberiorSTARRed and AF594) GFP
fixed
Yersinia enterocolitica
10.1371/journal.ppat.1007527
2D/3D-STED
T3SS translocon (YopD)
ALFA-Tag/NbALFA based labelling (AF647, AbberiorSTAR635P)
fixed
Yersinia enterocolitica
10.1371/journal.ppat.1010251
2D/3D-SIM
T6SS proteins (TssB,TssA) Type six secretion dynamic localization protein A (TslA) sfGFP/mCherry2/mNeonGreen indirect immunofluorescence staining (AF594)
fixed/live
Acinetobacter spp. Burkholderia thailandensis
10.15252/embj.2021108595
SIM
T9SS components (GldL and GldM) Adhesin (SprB)
indirect immunofluoescence staining (AF488, AF561)
fixed
Flavobacterium johnsoniae
10.1371/journal.pbio.3001443
SIM T4SS protein (VirB6a) sfGFP fixed Agrobacterium tumefaciens 10.1074/jbc.RA118.002751
adhesins, virulence factors adhesins, virulence factors adhesins, virulence factors adhesins, virulence factors adhesins, virulence factors adhesins, virulence factors
DNA-PAINT fibronectin binding proteins (FnBPA and FnBPB) Fn conjugated to a DNA-PAINT docking sequence, Cy3B-labeled complementary imager strands fixed Staphylococcus aureus 10.1021/acsnano.2c00630
PAINT/ dSTORM (dual-color imaging) listeriolysin S membrane Direct immunofluoescence staining (HA-tag, AF647) Nile red
fixed
Listeria monocytogenes
10.1073/pnas.2108155118
PALM, dSTORM; dSTORM/PALM (dual-color imaging) F-type ATPase (F1-like-X0) protease (MIP0582) mEos3.2 indirect immunofluoescence staining (HA-tag, AF 647)
fixed
Mycoplasma spp.
10.1128/spectrum.00645-22
SIM hemolysin A (HlyA) eGFP/ Indirect immunofluoescence staining (Cy3 or AbberiorStar635P) fixed Escherichia coli 10.1128/AEM.01896-21