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9 protocols using yeast extract

1

Microbial Growth Media Preparation

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Glucose medium (w/v): Glucose (Aladdin, Shanghai, China) 10%, peptone (Oxoid, UK) 2%, yeast extract (Oxoid, UK) 1%.
Sugarcane molasses medium: Sugarcane molasses (Zhongfuxin, Guangxi, China) 20 BX°, (NH4)2SO4 (Macklin, Shanghai, China) 0.1%, KH2PO4 (Macklin, Shanghai, China) 0.1%, MgSO4 (Macklin, Shanghai, China) 0.04% (w/v).
Nitrogen-rich medium (w/v): Soybean meal (Macklin, Shanghai, China) 5%, peptone 2%, yeast extract 1%.
YEPD medium (w/v): Glucose 2%, peptone 2%, yeast extract 1%.
GPYM medium (w/v): Glucose 4%, peptone 0.5%, yeast extract 0.5%, MgSO4·7 H2O 0.1%, malt extract (Solarbio, Beijing, China) 0.5%.
About 100 mL of Glucose medium, sugarcane molasses medium, and nitrogen-rich medium were prepared, respectively, in 250 mL conical flask, and 10% (v/v) yeast seed liquids were inoculated, respectively, and cultivated at 28°C, 150 rpm for 3 days.
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2

Oral Biofilm Formation: An In Vitro Study

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Streptococcus mutans UA159 (S. mutans), Streptococcus sanguis (S. sanguis), and Actinomyces viscosus (A. viscosus) were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). Training typodonts and typodont teeth were purchased from Liyue Model Technology Co., Ltd. (Dongguan, China). Brain–heart infusion (BHI) broth was purchased from Oxoid (Basingstoke, England). Sucrose, yeast extract, crystal violet, and the Sucrose content test kit were purchased from Solarbio (Beijing, China). All other chemicals used were of analytical grade or better. The Beizhi P50 water flosser was provided by Shanghai Feixiang Technology Co., Ltd. (Shanghai, China).
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3

Cultivation of Pseudomonas sp. M30-35

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Luria broth (LB) (5 g/L yeast extract (Solarbio, Beijing, China), 10 g/L peptone (Solarbio, Beijing, China), 10 g/L sodium chloride (Guangfu, Tianjin, China), PH 7.2) were used for bacterial culture. Pseudomonas sp. strain M30-35 (obtained from the State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China; the strain is deposited in the Marine Culture Collection of China with preservation number 1k03247.) was incubated, in the dark, at 28 °C, with shaking at 220 rpm (YiHeng, THZ-98AB, ShangHai, China), for 24 h. Bacteria were harvested at an OD600 between 0.9 and 1.0, then diluted to 109 colony forming units (CFU) mL−1, as measured by optical density and serial dilutions (Zhao et al., 2016 (link)).
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4

Riboflavin Biosynthesis Evaluation

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Fermentation was
performed as follows: to test the riboflavin biosynthesis
ability of the constructed strains, 20 μL of a cryopreservation
stock stored at −80 °C was mixed with 100 μL of
sterile ddH2O, spread on an agar plate, and incubated at
37 °C for 24 h. After that, the colonies on the plate were scraped
and suspended in 1 mL of the fermentation medium to acquire the seed
suspension, which was used to inoculate 500 mL baffled shake flasks
containing 80 mL of the fermentation medium, adjusting the initial
OD600 to 0.1. The fermentation medium contained 40 g/L
sucrose, 16.5 g/L corn steep powder (Solarbio, Beijing, China), 5
g/L (NH4)2SO4, 5 g/L yeast extract
(Solarbio, Beijing, China), 0.5 g/L MgSO4, 3 g/L K2HPO4, 1 g/L KH2PO4, and corresponding
antibiotics. The fermentation was conducted at 37 °C and 180
rpm for 48 h, during which samples were drawn at 12, 18, 24, 36, 42,
and 48 h to measure the cell growth and the titer of riboflavin. Cell
growth was monitored by measuring the optical density at 600 nm, and
the riboflavin concentration was determined as follows: culture samples
were diluted with 0.01 M NaOH to the linear range of the spectrophotometer.
After dissolving for 20 min, 1 mL of samples was centrifuged at 10,000g for 2 min to remove the cell debris, and the absorption
at 444 nm (A444) was measured immediately.7 (link)
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5

Extraction and Analysis of Dry Tubers

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Dry B. striata tubers were bought from Hubei Zexi Traditional Chinese Medicine Technology Co., Ltd. (Qichun, Hubei, China). The authenticity of medicinal materials was identified by Dr. Xiongjie Sun of Hubei University of Chinese Medicine. Vitamins, yeast extract, peptone, bacterial DNA extraction kit, bile salts, and L-cysteine were obtained from Beijing Solarbio Science & Technology Co., Ltd. (Beijing, China). Pepsin, α-amylase, pancreatin, trypsin, and SCFAs standards (Acetic acid, propionic acid, butyric acid, pentanoic acid, and indole) were bought from Shanghai Aladdin Biochemical Technology Co., Ltd (Shanghai, China). All materials were of standard analytical grades.
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6

Construction of Engineered Yarrowia lipolytica Strains

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Luria broth (LB), agar, yeast extract, ampicillin, kanamycin, and peptone were obtained from Solarbio, China. The standards of acetyl-CoA, malonyl-CoA, orcinol, OG, and TAL were obtained from Weikeqi, China. Escherichia coli cells were cultured at 37°C in LB, supplemented with appropriate antibiotics, such as ampicillin or kanamycin, at a final concentration of 100 mg/L. The wild-type Y. lipolytica strain W29 (ATCC No. 20460) obtained from the ARS Culture Collection (NRRL), which was used as the starting strain for the construction of all the engineered strains. Y. lipolytica strains were grown in YNB or YPD medium at 30°C and 220 rpm. The gRNA plasmid pCfB6627 was obtained from Addgene (https://www.addgene.org/), article number #106159. Composition of media are listed in S5 Text.
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7

Biopolymer-Based Microcapsule Synthesis

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Petroleum ether (PE), sodium
carbonate (Na2CO3), anhydrous ethanol, sodium
chloride (NaCl), and isopropyl alcohol were obtained from Sinopharm.
Lithium bromide (LiBr) and Span-80 were purchased from Aladdin. Branched
polyethylenimine (PEI, Mw ∼ 25,000) was acquired from Sigma-Aldrich.
Polyethylene glycol 8000 (PEG-8000), vancomycin, yeast extract, tryptone,
agar power, DNase I, phosphate-buffered saline (PBS), penicillin/streptomycin,
and a CCK-8 assay kit (CA1210) were purchased from Solarbio. A live/dead
staining kit (L34951) was obtained from Thermo Fisher Scientific.
FITC and rhodamine B were purchased from Macklin.
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8

Anaerobic Isolation and Cultivation of P. gulae

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The collected GCF samples were vortex shaken and isolated using disposable loops (Biologix, Shandong, China) on 10% brain-heart infusion (BHI) sheep blood plates (Solarbio, Beijing, China) containing 5 μg/mL hemoglobin chloride, 1 μg/mL vitamin K1 (VK1), 0.4 mg/mL L-cysteine hydrochloride and 5 mg/mL yeast extract (Solarbio, Beijing, China). The incubation took place at 37°C with 80% humidity under anaerobic conditions (10% CO2, 10% H2, and 80% N2) within an anaerobic culture vessel (YY-s Plus, LongFuJia Biotechnology, Beijing, China) for a culture period of 7–15 days. Single colonies were meticulously chosen and subjected to purification once more. The resulting single colonies were inoculated with a 5% fetal bovine serum (FBS) BHI liquid medium containing hemoglobin chloride and VK1 to be enriched and stored at −80°C. American Type Culture Collection (ATCC) 51700 P. gulae was purchased as a quality control bacterium.
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9

Analytical Techniques for Fungal Research

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Unless otherwise noted, all the chemical reagents and solvents were purchased from commercial suppliers Maclin Biochemical Co., Ltd. (Shanghai, China) and Kermel Chemical Reagent Co., Ltd. (Tianjin, China) and used without further refinement. Pepton, yeast extract, and agar were purchased from Solarbio Science & Technology Co., Ltd. (Beijing, China). BiGGY (bismuth sulfite glucose glycine yeast) agar medium was obtained from Hope Bio-Technology Co., Ltd. (Qingdao, China).
1H-NMR and 13C-NMR spectra of synthesized products were measured on a Bruker-600 spectrometer (Bruker, Madison, WI, USA), using tetramethylsilane (TMS) as an internal standard. High-resolution mass spectra (HRMS) of synthesized products were measured using an AB SciexX500r TOF mass spectrometer (AB SCIEX, Framingham, MA, USA). The fluorescence microscopic images of fungal cells were obtained using a confocal microscope (Leica, Wetzlar, Germany). The fluorescence images of fungous colonies on agar plates were recorded using a fluorescence image analyzer (Amersham Typhoon, Tokyo, Japan). The bioassay solutions in 96-well plates were also analyzed using an microplate reader (Tecan, Männedorf, Switzerland). All pH measurements were taken using a pHS-3C pH meter (INESA, Shanghai, China).
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