High purity SCFA standards for gas chromatography (GC) analysis, including acetic acid, propionic acid and butyric acid, were purchased from Sigma Aldrich Chemical Co. (St Louis, MO, USA). l -Cysteine hydrochloride monohydrate, bile salts, tryptone, yeast extract, glucose and other chemicals were obtained from Sangon Biotech (Shanghai, China). Media used in this study included: brain heart infusion (BHI) media (Solarbio, Beijing, China), gut microbiota medium (GMM) without agar (Goodman et al. 2011 (link)), fastidious anaerobe broth (FAB, Solarbio, Beijing, China), bacterial growth media (BGM) (Mcdonald et al. 2013 (link)). All media were prepared following the manufacturer’s instructions.
Tryptone
Manufactured by Sangon
Sourced in China
Tryptone is a nutritional component used in culture media for the growth of microorganisms. It is a complex mixture of peptides and amino acids derived from the enzymatic digestion of casein.
Automatically generated - may contain errors
Lab products found in correlation
Yeast extract, by Sangon (14 mentions)
Peptone, by Sangon (7 mentions)
Kanamycin, by Sangon (3 mentions)
Sodium chloride (nacl), by Sangon (2 mentions)
Isopropyl β d 1 thiogalactopyranoside (iptg), by Tsingke (2 mentions)
Taq plus dna polymerase, by Tsingke (2 mentions)
Ampicillin, by Sangon (2 mentions)
Streptomycin, by Sangon (2 mentions)
Beef extract, by Sangon (2 mentions)
Yeast powder, by Sangon (2 mentions)
L sodium glutamate l msg, by Sangon (2 mentions)
Polyvinyl alcohol (pva), by Sinopharm (2 mentions)
Acetic acid, by Sinopharm (2 mentions)
Sodium alginate, by Sinopharm (2 mentions)
Tetrahydrofuran, by Sinopharm (2 mentions)
Sodium acetate, by Sinopharm (2 mentions)
Calcium chloride, by Sinopharm (2 mentions)
Boric acid, by Sinopharm (2 mentions)
Dna gel extraction kit, by Takara Bio (2 mentions)
Butyric acid, by Merck Group (1 mentions)
22 protocols using tryptone
1
Optimized GC Analysis of SCFAs
2
Biochemical Reagents for Microbial Culture
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Glycerol, NAD+, NADH, and ethylenediaminetetraacetic acid (EDTA) were purchased from Sigma Chem. Co. (Beijing, China). The media (Tryptone, yeast extract, nutrient broth) were purchased from Sangon Biotech Co. Ltd. (Shanghai, China). All other chemicals used were analytical grade and were purchased from either Sigma or Merck (Beijing, China).
3
Recombinant Protein Expression and Purification
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Tris–HCl, tryptone, yeast extract, isopropyl-D-thiogalactoside (IPTG), bovine serum albumin (BSA), MgCl2, NaCl, Ethylene diamine tetraacetic acid (EDTA), dithiothreitol (DTT), guanosine monophosphate (GMP), adenosine triphosphate (ATP), CTP, GTP and UTP were purchased from Sangon Biotech (Shanghai, China). 3M sodium acetate (NaAc) solution (pH 5.2) were purchased from Sigma-Aldrich Co. LLC (St Louis, MO, USA). DNA fragment rapid purification and plasmid extraction kits were purchased from Yuanpinghao Biotech (Tianjing, China). KOD-plus mutagenesis kit and KOD-plus-neo Kit were from TOYOBO (Osaka, Japan). T4 DNA ligase, and all restriction endonucleases were obtained from Thermo Scientific (Waltham, MA, USA). [3H] L-leucine were purchased from Perkin Elmer Inc. (Waltham, MA, USA). Oligonucleotide primers were synthesized by Biosune (Shanghai, China). Escherichia coli Rosetta (DE3) cells were purchased from TIANGEN (Beijing, China). Nickel-nitrilotriacetic (Ni-NTA) Superflow resin was purchased from Qiagen, Inc. (Hilden, Germany). The Superdex™ 200 increase (10/300 GL) and Superose 6 increase (10/300 GL) were purchased from GE Healthcare (Fairfield, CT, USA). Crystallization kits were from Hampton research (Aliso Viejo, CA, USA). T7 RNA polymerase was purified from an overproduction strain in our laboratory (45 (link)).
4
Enzymatic Synthesis of Valuable Compounds
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l -Phenylalanine (l -PA), trans-cinnamic acid, styrene, (S)-1-phenyl-1, 2-ethanediol, styrene oxide, 2-hydroxyacetophenone (2-HAP), (±)-phenylglycinol, (R)-phenylglycinol, (S)-phenylglycinol, l -alanine (l -Ala), n-dodecane, pyridoxal-5′-phosphate (PLP) and (R)-α-methylbenzylamine (R-MBA) were from Energy Chemical and Titan Scientific (Shanghai, China). Yeast extract, tryptone and antibiotics (kanamycin, ampicillin and streptomycin) were from Sangon Biotech (Shanghai, China). T4 DNA ligase and restriction enzymes were from New England Biolabs (NEB, Beijing, China). Isopropyl β-d -1-thiogalactopyranoside (IPTG) and Taq plus DNA polymerase were purchased from Tsingke (Beijing, China). All other chemical reagents were obtained from commercial sources.
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5
Culturing Xanthomonas campestris pv. campestris
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Xcc wild type strains XC1, 8004 and their derivatives were described previously40 (link). Xcc strains were routinely grown at 30 °C in the media shown in Supplementary Table 1 with 25 μg ml−1 of rifampicin. For media preparation (Supplementary Table 2 ), tryptone, peptone and yeast extract were purchased from Sangon Biotech (China). Escherichia coli strains were grown at 37 °C in LB medium. Bacterial growth was determined by measuring optical density at 600 nm.
6
Plasmid-based Recombinant Protein Production
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Plasmid pET22 was used as the vector for gene cloning and expression. E. coli strain DH5α (Transgen, China) was used as the host for cloning, and E. coli strain BL21 (DE3) plysS (Transgen, China) was used as protein expression. E. coli cells were grown at 37°C in LB medium containing 10g NaCl, 10g tryptone, and 5g yeast extract (Sangon Biotech, China) per liter at pH 7.0, and LB agar medium was added with 1.5–2.0% (w/v) agar.
7
Bacterial Cultivation Protocols for E. coli and X. citri
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Strains and plasmids used in this study are listed in Supplementary Table 1 . E. coli strains were grown in Luria-Bertani medium (10 g L–1 Tryptone, 5 g L–1 yeast extract, 10 g L–1 NaCl, pH 7.0) at 37°C. X. citri strains were grown at 28°C in NYG medium (5 g L–1 peptone, 3 g L–1 yeast extract, 20 g L–1 glycerol, pH 7.0) and YEB medium (10 g L–1 peptone, 5 g L–1 yeast extract, 10 g L–1 NaCl, 5 g L–1 sucrose, 0.5 g L–1 MgSO4 pH 7.5). Tryptone, peptone, beef extract, and yeast extract were purchased from Sangon Biotech (Shanghai, China) to prepare culture medium. Antibiotics such as sodium ampicillin (100 μg/mL), kanamycin sulfate (30 μg/mL), and gentamycin (30 μg/mL) were added for E. coli and X. citri, if required. Bacterial growth in a liquid medium was determined by measuring optical density at 600 nm (OD600) using a Bioscreen-C Automated Growth Curves Analysis System (Oy Growth Curves FP-1100-C, Helsinki, Finland).
8
Cultivation of E. coli and L. enzymogenes
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The strains and plasmids used in this study are shown in Table 2 . E. coli strains were grown in Luria-Bertani medium (10 g/liter tryptone, 5 g/liter yeast extract, and 10 g/liter NaCl [pH 7.0]) at 37°C. L. enzymogenes strains were grown at 28°C in Luria-Bertani medium and 10% TSB. M813 modified medium (4 g glucose, 3 g K2HPO4, 1.2 g NaH2PO4, 1 g NH4Cl, 0.3 g MgSO4, 0.15 g KCl, 10 mg CaCl2, and 2.8 mg FeSO4·7H2O, per liter) was used for the growth of L. enzymogenes OH11 (32 (link)). For the preparation of culture medium, tryptone, peptone, beef extract, and yeast extract were purchased from Sangon Biotech (Shanghai, China). When required, antibiotics were added (100 μg/ml sodium ampicillin, 30 μg/ml kanamycin sulfate, and 50 μg/ml gentamicin) to the E. coli or L. enzymogenes cultures. The bacterial growth in liquid medium was determined by measuring the optical density at 600 nm (OD600) using a Bioscreen-C automated growth curves analysis system (Oy Growth Curves, Helsinki, Finland).
9
Fluorescence Probes for Cell Imaging
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FDAA probes were bought from Chinese Peptide Company (Hangzhou, China). FISH probes used in this study were synthesized and labeled at the 5′ ends with FAM (carboxyfluorescein) by Sangon Biotech (Shanghai, China). Tryptone, peptone, calf brain infusion, beef heart infusion, yeast extract, glucose, L-cysteine, vitamin K1, vitamin K3, paraformaldehyde (PFA) and phosphate buffer saline (PBS) were purchased from Sangon Biotech (Shanghai, China). Other chemicals, not noted above, were from Sigma–Aldrich (St. Louis, MO, USA).
10
Bacterial Growth Characterization Protocol
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The strains and plasmids used in this study are shown in Supplementary Table 1. E. coli strains were grown in Luria-Bertani medium (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.0) at 37 °C. L. enzymogenes strains were grown at 28 °C in Luria-Bertani medium and 10% TSB. For the preparation of culture media, tryptone, peptone, beef extract, and yeast extract were purchased from Sangon Biotech (Shanghai, China). When required, antibiotics were added (30 μg/mL kanamycin sulfate, 50 μg/mL gentamycin) to the E. coli or L. enzymogenes cultures. The bacterial growth in liquid medium was determined by measuring the optical density at 600 nm (OD600) using a Bioscreen-C Automated Growth Curves Analysis System (OY Growth Curves FP-1100-C, Helsinki, Finland).
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