Yeast extract

D-glucose (Panreac, Barcelona, Spain), peptone (Condra, Barcelona, Spain), tryptone (Condra, Barcelona, Spain), and yeast extract (Helicon, Moscow, Russia) were applied as nutrients for biofilm cultivation. Graphite powder (Fluka, Berlin, Germany), paraffin oil (Fluka, Berlin, Germany), ferrocene (Dia-m, Moscow, Russia), and a dialysis membrane with a transmission limit of 14 kDa (Roth, Dautphetal, Germany) were used for working graphite paste electrode (GPE) formation. Sodium–potassium phosphate buffer solution, pH = 6.8, was prepared from 33 mM KH₂PO₄ and 33 mM Na₂HPO₄ (Dia-m, Moscow, Russia).

Glycol chitosan 72 kDa (GlycChit, the degree of deacetylation is 92), mannan (46 kDa), polyethyleneimine 1.8 kDa (PEI1.8), Et₂O, DMF, DMSO, HBr, (HOCH2CH2)3N, 2-hydroxypropyl-β-cyclodextrin (HPCD), 4-toluenesulfonyl chloride (TsCl), genipin, 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC), N-hydroxysuccinimide (NHS), N-acetylcysteine, limonene were purchased from Sigma Aldrich (St. Louis, MI, USA). Mannotriose-di-(N-acetyl-D-glucosamine) (triMan-GlcNAc2) was obtained from Dayang Chem (Hangzhou, China) Co., Ltd.
Using CD spectroscopy (Jasco J-815 CD Spectrometer, JASCO Corp., Tokyo, Japan), the degree of deacylation in glycol chitosan samples was determined by the peak at 215 nm corresponding to the absorption of the amide bond and was 92%.
Moxifloxacin hydrochloride (MF) was obtained by Canon Pharma (Moscow, Russia).
Linalool was purchased from Carl Roth GmbH (Karlsruhe, Germany). Eugenol at the highest commercial quality was purchased from Acros Organics (Geel, Belgium). Apiol with 98–99% purity was obtained by high-efficiency distillation using a pilot plant device at N.D. Zelinsky Institute of Organic Chemistry RAS (Moscow, Russia) [42 (link)].
The components of the LB medium were bactotrypton, agarose and yeast extract (Helicon, Russia).

The M. hominis H34 strain was grown on Brain Heart Infusion medium (DIFCO, USA) supplemented with 10% horse serum (Biolot, Russia), 1% yeast extract (Helicon, Russia), and penicillin (Sintez, Russia) with a final concentration of 500 units/mL with the addition of 1% arginine or 20 mM thymidine as a carbon source. The cultures were incubated at 37 °C in aerobic condition. The growth curves were monitored through total amount of genomic DNA. The R package Growthcurver was used to fit the growth curve data to the logistic equation (Sprouffske and Wagner, 2016 (link)). The value of arguments (r, the growth rate) were extracted (Supplementary Table S1). The 0.002% (w/v) phenol red (Sigma-Aldrich, USA) was added in the culture medium to indirect detect of metabolic activity. A color change of medium was monitored using the OD at 560 nm (Cummings and McCormack, 1990 (link)).

The reagents of chemical grade qualifications were obtained from Merck (Munchen, Germany), Sigma (Sigma-Aldrich Rus LLC, Moscow, Russia), and Helicon (Moscow, Russia). The molecular biology kits for restriction, ligation, Taq polymerase, and oligonucleotides were from Evrogen (Moscow, Russia) and Thermo Fisher Scientific RU (Moscow, Khimki, Russia); kanamycin was from Sintez (Moscow, Russia). Yeast extract, bactoagar, tripton, and pepton were from Helicon and Dia-M (Moscow, Russia). DNA and protein molecular weight markers were from BioRad (California, USA).

The ability of zinc chelated compounds to reduce the formation of biofilms in E. coli BL 21 culture was studied on the example of five zinc complexes with Gly, Ala, Met, Val, Phe [63 (link),64 ,65 ]. After filtration (0.22 µm, Millipore, Burlington, MA, USA), 0.25 mL of an aqueous solution of Zn(AA)₂ (8 mmol/L) was introduced into 2 mL of LB culture medium, thus the concentration of Zn(AA)₂ in the culture medium was 1 mmol/L. The culture medium was used as a control: 10 g of tryptone (Pronadisa, Madrid, Spain), 5 g of yeast extract (Helicon, Moscow, Russian Federation), 10 g of sodium chloride were dissolved in 800 mL of highly purified water and then diluted to 1 L with the same solvent. Control and test samples were prepared in 3 repetitions. The test and control solutions were inoculated with 10 µL of overnight culture (18 to 24 h at 37 °C and 100 rpm) of E. coli BL 21 and then incubated at 37 °C for 12 h and 100 rpm. Before the measurements test and control solutions were diluted with culture medium in 1.5 and 12 times, respectively. The formation of biofilms in E. coli culture was evaluated by the number and size of dispersed phase particles using low-angle laser light scattering method.

Ferrocene (Dia-m, Moscow, Russia) was used as an electron transport mediator. Nutrient medium was prepared using D-glucose (Panreac, Barcelona, Spain), peptone (Conda, Madrid, Spain), tryptone (Conda, Madrid, Spain), and yeast extract (Helicon, Moscow, Russia). Graphite powder with a particle size of 75 μm with a high frequency of 99.997% (Fluka, Darmstadt, Germany), paraffin oil (Fluka, Germany), carbon nanotubes of the “Taunit” («NanoTechCenter», Tambov, Russia) series with an outer diameter of 10–30 nm, length ≥ 2 μm, and amount of impurities ≤ 1%, and a dialysis membrane with a transmission limit of 14 kDa (Roth, Germany) were taken to create a working graphite paste electrode. Biosensor measurements were performed using a sodium-potassium phosphate buffer solution pH = 6.8 (33 mM KH₂PO₄ + 33 mM Na₂HPO₄, Dia-m, Moscow, Russia).