Table 1.

Fluorophore set specifically accumulated by E. coli BW25113. List of fluorescent (Fluor) molecules that recorded fluorescence signals two-fold or higher (Signal strength) than the median values of autofluorescence. SMILES (Simplified Molecular Input Line Entry System [135]) Channel (as listed in Methods): Intellicyt® flow cytometer channel that registered the highest median for each fluorophore. The excitation and emission profiles of these channels should have matched the excitation and emission wavelengths for those fluorophores (Table S1). The structures of some of these fluorophores are unknown or unavailable (NA). Concentration: concentration in micromolar at which the highest median values were found for each fluorophore in the range tested. SD: standard deviation of the sample, CI95: 95% confidence interval for the data of signals from each fluorophore at the given channel. BODIPY tetra-methyl: Difluoro{2-[(3,5-dimethyl-2H-pyrrol-2-ylidene-N)methyl]-3,5-dimethyl-1H-pyrrolato-N}boron

Fluor	Channel	Mean	Concentration	Median	SD	CI95	Signal strength
2-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)−2-Deoxyglucose	BL3	10 609	2.5	11 615	3311	[9256–11 962]	4.16
2',7′-Dichlorofluorescein	BL3	16 332	3	16 550	4821	[14361–18 302]	5.93
3,6-Bis(4-chlorophenyl)−2,5-dihydropyrrolo[3,4 c]pyrrole-1,4-dione	RL1	12 552	3	12 303	1956	[11695–13 410]	2.92
3,6-Diphenyl-2,5-dihydropyrrolo[3,4 c]pyrrole-1,4-dione	RL1	10 731	3.0	9415	3065	[9388–12 074]	2.24
4-(4-(Dimethylamino)styryl-N-methylpyridinium (ASP+)-	RL1	26 815	0.3	9288	42 128	[17216–36 413]	2.21
5-Carboxyfluorescein	BL3	14 787	1.0	18 608	11 353	[11787–17 788]	6.67
7-Aminoactinomycin D	VL4	11 609	2.5	12 250	2399	[10629–12 589]	2.47
9-aminoacridine	VL1	1458	5.0	1597	426	[1349–1566]	2.83
Acridine orange	BL3	7508	10	7467	3265	[6675–8341]	2.68
Alizarin	BL3	7380	3.0	6862	3767	[6419–8341]	2.46
Amaranth	BL3	6330	5.0	6303	2604	[5665–6994]	2.26
ATTO 430LS carboxy	BL3	5203	5.0	6191	1436	[4616–5790]	2.22
ATTO 488 carboxy	BL3	19 619	1.3	19 556	5804	[18138–21 100]	7.01
ATTO 490LS carboxy	BL5	10 272	3.0	8232	7447	[8046–12 498]	9.66
ATTO 633 carboxy	RL2	20 712	3.0	18 035	11 004	[17423–24 001]	11.1
ATTO 647 carboxy	RL1	46 880	10	38 512	67 804	[29579–64 181]	9.15
ATTO Rho14 carboxy	RL1	30 855	10	12 507	37 080	[19772–41 938]	2.97
Azure A	RL1	10 631	3.0	9994	3830	[9654–11 608]	2.37
Azure B	RL1	11 507	10	10 951	3462	[10623–12 390]	2.60
Azure C	RL1	16 418	2.5	13 675	14 301	[12639–20 197]	3.25
Calcein	BL3	16 131	10	16 616	4493	[14984–17 277]	5.96
Celestine blue	RL1	14 754	10	12 252	7653	[12352–17 156]	2.91
CruzFluor 405 succinimidyl ester	BL3	15 887	10	16 691	4278	[14139–17 636]	5.98
BODIPY tetra-methyl	VL5	7969	1.0	9639	5286	[6310–9628]	2.31
DiSC3(5)	RL1	205 602	1.3	189 686	152 318	[166736–244 468]	45.1
Doxorubicin	BL3	8589	1.0	7583	4062	[7552–9625]	2.72
Ethidium bromide	BL3	11 501	10	11 246	3136	[10701–12 301]	4.03
Ethyl Red	RL1	29 928	10	18 738	25 518	[21920–37 937]	4.45
Fluorescein	BL3	16 869	5.0	17 035	3560	[15961–17 777]	6.11
H2FDA	BL1	9137	5.0	8708	4036	[8107–10 167]	3.54
Hexidium iodide	BL3	12 993	10	13 090	3819	[9250–16 735]	4.69
Methylene blue	RL1	10 259	1.0	9259	4009	[9236–11 282]	2.20
Mithramycin A	VL4	11 137	5.0	11 616	3723	[10187–12 087]	2.34
Morin	BL3	7223	3.0	7437	732	[6506–7940]	2.67
Oxazine 170	RL1	9014	3.0	10 024	3831	[8002–10 026]	2.38
Pyranine	VL4	11 124	10	11 047	6960	[9285–12 964]	2.23
Pyronin Y	BL3	11 652	1.3	9030	6434	[10011–13 294]	3.24
Rhodamine 800	RL2	13 444	1.3	8436	13 241	[9288–17 599]	5.21
Rhodamine B	BL3	7012	1.3	6580	3552	[6106–7918]	2.36
Riboflavin	BL3	7020	1.0	7254	2762	[6315–7724]	2.60
Sennoside A	VL4	9506	10	10 634	2645	[8715–10 297]	2.15
Sulphorhodamine B	BL3	9440	10	8117	4183	[8373–10 508]	2.91
SYBR Green I	BL1	16 690	2.5	8517	19 703	[11663–21 718]	3.46
SYTO13	BL1	281 386	5.0	197 317	235 885	[178007–384 765]	80.1
Thiazole orange	BL1	25 740	10	10 600	32 357	[17484–33 997]	4.30
Thionine	RL1	9878	10	10 166	5068	[8539–11 218]	2.42
Trypan Blue	RL1	19 833	5.0	15 151	16 464	[15482–24 184]	3.60