2.3. Identification of Bacteria by MALDI-TOF MS Biotyper

Bacterial strains from the fecal microbiota of male and female rats, before and after restriction, were isolated on Luria-Bertani medium and identified by analysis of the total proteome using an Autoflex III Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight mass spectrometer (MALDI-TOF MS) (Bruker, Marcy-l’Etoile, France) coupled to the MALDI-Biotyper 3.1 system, as previously described [12,13]. Formic acid was used on the bacterial spots as a quick extraction procedure [14], then the MALDI target plate was introduced in the mass spectrometer for measurement and data acquisition. For each sample, 600 spectra were pooled, and the generated spectra were compared with the MALDI-Biotyper 3.1 database. A score was calculated based on the matching between the reference spectrum and the unknown spectrum. A score of ≥2.0 allows species identification [15].