GNPS - Bifidobacterium type strains grown anaerobically in MRS medium, glucose and l-cysteine
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ABSTRACT: Bifidobacterium type strains were grown anaerobically in MRS medium (containing 2% (w/v) glucose and supplemented with 0.05 % (w/v) l-cysteine) at 37 C for 72 h, after which optical density OD600nm was measured and the culture supernatants were extracted as previously published (Laursen et al. 2021; Nature Microbiology) and analysed by LC-MS (DDA acquisition).
Project description:Bifidobacterium type strains were grown anaerobically in MRS medium (containing 2% (w/v) glucose and supplemented with 0.05 % (w/v) l-cysteine) at 37 C for 72 h, after which optical density OD600nm was measured and the culture supernatants were extracted as previously published (Laursen et al. 2021; Nature Microbiology) and analysed by LC-MS (DDA acquisition).
Project description:A continuous culture of Bifidobacterium longum NCC2705 was carried out in a 2.5-l reactor (Bioengineering AG, Wald, Switzerland), equipped with a Biospectra control system (Biospectra AG, Schlieren, Switzerland) and containing 2 l of MRS, added of 0.05% cysteine, inoculated with 2 % (v/v) preculture. The temperature was maintained at 37°C and the pH at 6.0 by addition of 5 M NaOH. The culture was stirred constantly at 250 rpm using two rushton type propellers. Anaerobic conditions were maintained by flushing the headspace of the reactor with CO2. After 8 h in batch mode the culture was run in continuous mode at a dilution rate of 0.1 h-1. Fresh medium was added using a peristaltic pump (Alitea, Bioengineering AG, Wald, Switzerland), and fermented broth harvested with a second peristaltic pump (Alitea, Bioengineering AG, Wald, Switzerland) set at a slightly higher flow rate. A stabilization period of 90 h (corresponding to nine reactor volume changes) was operated prior culture monitoring (t=0). Aliquots of 2 ml taken at t=31, 134 and 211 h were centrifuged (4,000 g, 1 min, room temperature) for transcriptomic analysis. Supernatants were discarded and cell pellets snap frozen in liquid nitrogen and stored at -80ºC until RNA-extraction. Keywords: Time course of Bifidobacterium longum in continuous culture
Project description:B. pertussis mid-log phase cultures were diluted in modified Stainer-Scholte medium to a starting optical density at 600 nm of 0.03 to 0.05, then grown at 37 C with shaking until three hours beyond the log to stationary phase transition.
Project description:We previously observed in mice that Bacteroides thetaiotaomicron (B. theta) significantly increased in abundance in the gut microbiome of mice when mice were fed egg and yeast dietary protein sources. We also observed that B. theta was expressing proteins previously connected to growth on mucin glycans when mice were fed an egg-white diet. To confirm that the bacterium were actually responding to the protein sources, we grew it in vitro using a defined medium, where the sole carbon source was dietary protein, mucin, or glucose. Our controls were glucose and mucin, and our experimental protein sources were soy protein, egg-white protein, and Torula yeast protein. We grew four B. theta cultures per carbon source statically at 37°C in a Coy anaerobic chamber (2.5 % H2 /10 % CO2 /88.5 % N2) in minimal medium (100 mM KH2PO4, 8.5 mM [NH2]4SO4, 15 mM NaCl, 5.8 μM vitamin K3, 1.44 μM FeSO4⋅7H2O, 1 mM MgCl2, 1.9 μM hematin, 0.2 mM L-histidine, 3.69 nM vitamin B12, 208 μM L-cysteine, and 7.2 μM CaCl2⋅2H2O) with one of the above mentioned nutrients added at 0.5% (wt/v) concentration. In order to aid the solubilization of the dietary proteins, we pre-prepared the proteins in 200 mM NaOH at 37°C for four days, the glucose control was also dissolved in 200 mM NaOH. After 8 hours, we enumerated CFUs to confirm growth, and we pelleted cells by centrifuging at 4,000 g for 10 minutes. We then removed the supernatant and froze the pellets at -80°C within 30 minutes.
Project description:The purpose of this project was to determine the whole transcriptome response of Bifidobacterium longum subsp. infantis to human milk urea compared to complex nitrogen and L-cysteine.
Project description:This project provides tandem mass spectrometry data of Bacillus cereus AH187 strain. The strain was grown on liquid MOD medium supplemented with glucose and harvested at three growth stages.
Project description:A continuous culture of Bifidobacterium longum NCC2705 was carried out in a 2.5-l reactor (Bioengineering AG, Wald, Switzerland), equipped with a Biospectra control system (Biospectra AG, Schlieren, Switzerland) and containing 2 l of MRS, added of 0.05% cysteine, inoculated with 2 % (v/v) preculture. The temperature was maintained at 37°C and the pH at 6.0 by addition of 5 M NaOH. The culture was stirred constantly at 250 rpm using two rushton type propellers. Anaerobic conditions were maintained by flushing the headspace of the reactor with CO2. After 8 h in batch mode the culture was run in continuous mode at a dilution rate of 0.1 h-1. Fresh medium was added using a peristaltic pump (Alitea, Bioengineering AG, Wald, Switzerland), and fermented broth harvested with a second peristaltic pump (Alitea, Bioengineering AG, Wald, Switzerland) set at a slightly higher flow rate. A stabilization period of 90 h (corresponding to nine reactor volume changes) was operated prior culture monitoring (t=0). Aliquots of 2 ml taken at t=31, 134 and 211 h were centrifuged (4,000 g, 1 min, room temperature) for transcriptomic analysis. Supernatants were discarded and cell pellets snap frozen in liquid nitrogen and stored at -80ºC until RNA-extraction. Keywords: Time course of Bifidobacterium longum in continuous culture Bifidobacterium longum NCC2705 at time 31 versus time 134 h and versus time 211 h in continuous culture. Two technical replicares with dyes swaps
Project description:This project provides tandem mass spectrometry data of Bacillus cereus AH187 strain. The strain was grown on liquid MOD medium supplemented with glucose and harvested at three growth stages.
Project description:B. cenocepacia J2315 was grown to mid-stationary phase in basal salt medium with two different substrates: 20 mM glucose or 40 mM glycerol. Cells were harvested after 30 hours incubation at 37 degrees centigrade. <br>The expression profile was compared to cells grown on the same medium and harvested in mid-log phase.
Project description:The aim of this RNA-sequencing study is to measure differential gene expression in 8 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bifidobacterium adolescentis, Bifidobacterium catenulatum, Subdoligranulum variabile and Roseburia intestinalis, Agathobacter rectalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidota species and referred to as polysaccharide utilization loci. In Bacillota and Actinomycetota species, these loci are not so clear-cut, athough the GP-PUL concept has already been proposed. Here we compare the differential gene expression in minimal culture medium supplemented with a complex carbohydrate with a minimal culture medium supplemented with glucose. This differential analysis reveals a source-specific genetic response and a coordinated expression of genes involved in carbohydrate transport, carbohydrate degradation and transcriptional activation of these complex enzymatic machineries.