Ciprofloxacin

B. fragilis (ATCC, USA) was expanded in liquid brain–heart infusion (BHI; BD Bioscience, USA) medium at 37°C under anaerobic condition. The mice were treated with metronidazole (100 mg/kg; Solarbio, China) by oral gavage every day and ciprofloxacin dissolved in drinking water (0.625 mg/mL; Solarbio, China) for 7 days. Two days after the cessation of antibiotics treatment, Mmp7^+/+ and Mmp7^−/−mice were orally administrated with a single inoculum of 1 × 10⁸ colony-forming units (CFUs) of B. fragilis. One day after gavage, the mice were sacrificed for determination of bacteria.

Tylosin, tilmicosin, doxycycline, ciprofloxacin, and L-methionine (L-met) were purchased from Solarbio (Beijing, China). L-met was prepared with ddH₂O amino acid stock solution (500 mM). After filtering the stock solution with a sterile hydrophilic PVDF with a membrane pore size of 0.22 µm (Biosharp, China), it was stored at –20°C. The drugs were diluted to the required concentration.

The homology and similarity of the Spgillcin sequence was performed using the NCBI website (http://www.ncbi.nlm.nih.gov). The signal peptide of Spgillcin was predicted with SignalP 5.0 Server (http://www.cbs.dtu.dk/services/SignalP/), and the functional domain was predicted using SMART (http://smart.embl-heidelberg.de/). Network Protein Sequence@ website (http://www.prabi.fr) was used to predict the second structure of the Spgillcin mature peptide, and the physicochemical properties including molecular weight, hydrophobicity, net positive charge, and theoretical isoelectric point were predicted by ProtParam tool (https://web.expasy.org/protparam/).
The truncated peptide Spgillcin_177–189 (KKRRCFFRHIYVA) was analyzed using antimicrobial peptide database CAMP_R.3 (http://www.camp3.bicnirrh.res.in), and the physicochemical parameters of Spgillcin_177–189 were predicted as mentioned above. This peptide was synthesized by Genscript (Naijing, China) and verified by high-performance liquid chromatography and mass spectrometry. AMP LL-37 was purchased from GL bioChem (Shanghai, China). The antibiotics including vancomycin, ceftazidime, ciprofloxacin, and polymyxin B were purchased from Solarbio company (Beijing, China), and rifampicin was purchased from Topscience company (Shanghai, China).

The standard of berberine (C₂₀H₁₈NO₄, molecular weight: 235.324 kD) was obtained from Solarbio Biotechnology Co., Ltd. (Beijing, China). Dextran sulfate sodium (DSS molecular weight: 36000-50000kD), ciprofloxacin, metronidazole, Phorbol 12-myristate (PMA), ionomycin, and Bravertin A were also obtained from Solarbio Biotechnology Co., Ltd. (Beijing, China). Total DNA extraction kit, total RNA extraction kit, first-stand cDNA reverse transcription kit, polymerase chain reaction kit, and primers were obtained from TianGen Biotechnology Co., Ltd. (Beijing, China). Mouse IL-10 and IL-17 ELISA kits were obtained from Multi Science Biotechnology Co., Ltd. (Hangzhou, China). APC anti-CD4, FITC anti-IL17A, PE anti-CD25, and Alexa Fluor 488 anti-Foxp3 antibodies for flow cytometry were purchased from BD bioscience Co., Ltd. (Franklin Lakes, NJ, United States). BCA, alanine aminotransferase (ALT), aspartate aminotransferase (AST), blood urea nitrogen (BUN), and creatinine (Cr) test kit were purchased from Nanjing Jiancheng Biological Engineering Institute (Nanjing, China).

First, E. coli K12 (MG1655) was been sequenced (Shanghai Majorbio Bio-pharm Technology Co., Ltd), which was designated as the original wild type strain (Table 1). Activating E. coli from storage tube with glycerol stock which stored in − 80 °C, expanding propagating on a Luria Bertani (LB) agar plates, cultured at 37 °C for 16 h. The selected seed strain was cultured in LB broth at 37 °C for 12 h for following selected experiments (Li et al. 2016 (link)).Table 1

The MIC of each antibiotic to wild-type E. coli K12

No	Antibiotics	Abbreviation	Classification	Stock solution (mg/L)	MIC (mg/L)
1	ciprofloxacin	Cip	Quinolones	200	0.2
2	tetracycline	Tet	tetracyclines	10	2.34
3	Gentamicin	Gen	Aminoglycosides	10	8.75
4	polymyxin B	Pol	Polypeptides	10	0.94
5	erythromycin	Ery	Macrolides	6.4	15
6	chloramphenicol	Chl	chloramphenicols	30	4.69

The involved antibiotics: chloramphenicol (Chl), ciprofloxacin (Cip), erythromycin (Ery), gentamycin (Gen), tetracycline (Tet), and polymyxin B (Pol) and cupric (CuSO4·5H2O) were get from Solarbio, Inc. (Shanghai, China). 90% inhibition of growth was regarded as the MIC of each antibiotic, which was determined as Additional file 1: Test S1 described, and the MIC of copper ions was also investigated with the same method. The detailed accounts are displayed in Additional file 1: Text S1. The tetracycline resistant cultures were kept from light so as not to degrade the antibiotic.