Sampling methods for NMR-based metabolomics of Staphylococcus aureus.
To select an appropriate sampling method for comparison of metabolite profiles between planktonic and biofilm Staphylococcus aureus using NMR techniques, we evaluated three methods: quenching-centrifugation (QC), filtration-quenching (FQ) and filtration-quenching-lyophilization (FQL). We found differences in metabolite loss, yield, reproducibility and metabolite profile. QC caused severe metabolite leakage and possible decomposition of nucleotides. FQ achieved high yields and reproducibility, although it had the disadvantages of long filtration and rinse times before quenching. FQL resulted in a loss of a few metabolites and a lower yield due to lyophilization. Although the biomarkers discovered by each method were nearly the same and seemed insensitive to technical variances, we conclude that FQ is the most appropriate sampling method because of its high yield and reproducibility.
Wu
Xiao-He
XH
College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
Yu
Hai-Long
HL
Ba
Zhao-Yong
ZY
Chen
Jing-Yu
JY
Sun
Hong-Gang
HG
Han
Bei-Zhong
BZ
D000465:Algorithms; D001426:Bacterial Proteins / Q000378:metabolism*; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D055442:Metabolome / Q000502:physiology*; D020543:Proteome / Q000378:metabolism*; D013048:Specimen Handling / Q000379:methods; D013211:Staphylococcus aureus / Q000378:metabolism*; D014462:Ultrafiltration / Q000379:methods
D001426:Bacterial Proteins; D020543:Proteome