Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing

Abstract

BackgroundLactobacillus represents a large genus with different implications for the human host. Specific lactobacilli are considered to maintain vaginal health and to protect from urogenital infection. The presence of Lactobacillus species in carious lesions on the other hand is associated with progressive caries. Despite their clinical significance, species-level identification of lactobacilli still poses difficulties and mostly involves a combination of different phenotypic and genotypic methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and oral Lactobacillus isolates in comparison to 16S rDNA analysis.ResultsBoth methods were used to analyze 77 vaginal and 21 oral Lactobacillus isolates. The concordance of both methods was at 96% with five samples discordantly identified. Fifteen different Lactobacillus species were found in the vaginal samples, primarily L. iners, L. crispatus, L. jensenii and L. gasseri. In the oral samples 11 different species were identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L. paracasei. Overall, the species found belonged to six different phylogenetic groups. For several samples, MALDI-TOF MS analysis only yielded scores indicating genus-level identification. However, in most cases the species found agreed with the 16S rDNA analysis result.ConclusionMALDI-TOF MS analysis proved to be a reliable and fast tool to identify lactobacilli to the species level. Even though some results were ambiguous while 16S rDNA sequencing yielded confident species identification, accuracy can be improved by extending reference databases. Thus, mass spectra analysis provides a suitable method to facilitate monitoring clinically relevant Lactobacillus species.

Identification, Classification and Screening for γ-Amino-butyric Acid Production in Lactic Acid Bacteria from Cambodian Fermented Foods

“…The remaining 28 isolates were bacilli, clostridia and staphylococci (data not shown). Our results strongly support previous findings, which stated that in some cases sequencing of the 16S rDNA has a limited discriminating and low phylogenetic power for several closely related lactobacilli and enterococcal species [24][25][26][27][28] due to substantial similarities of their 16S rDNA sequences [29][30][31][32]. Correspondingly, it was impossible to distinguish the three species Lb.…”

“…MALDI-TOF MS has been widely used for the rapid identification and taxonomic characterization of Lactobacillus spp. [15,30,[34][35][36][37][38][39][40][41][42], Enterococcus spp. [33], and Pediococcus spp.…”

Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

“…Nevertheless, with the advent of molecular biology, gene based methods were found to be more reliable, precise and consistent. Among the various genes used for identifying bacteria, rrs has been the most successful [11,12]. It has completely revolutionized the way taxonomy has developed.…”

“…REsSphI, NcoI and NheI could digest rrs, REs-DraI, EcoRI, HincII, SfuI, SspI, and VspI, and showed digestion patterns in the rrs-23S rRNA intergenic region, where as REsAvrII and HindIII digested 23S rRNA gene [28]. Matrixassisted laser desorption/ionization mass spectrometry, based on ribosomal subunit proteins as biomarkers was used to identify Lactobacillus plantarum and other species [12,31]. In order to distinguish very closely related Lactobacillus species, rpoA gene-encoding for the alpha subunit of RNA polymerase, and pheS gene-encoding for the alpha subunit of phenylalanyl-tRNA synthase were sequenced.…”

Identification of microorganisms in biofluids of individuals with periodontitis and chronic kidney disease using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

“…Oral microorganisms have usually been identified by traditional methodologies other than MALDI‐TOFMS. This technique holds the potential to provide a fast method for both genus and species identification of several microorganisms . Therefore, one important feature of this technique is that it may beneficially facilitate the monitoring of the oral ecosystem.…”