title: Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR.
abstract: Lactobacilli represent a wide range of bacterial species with several implications for the human host. They play a crucial role in maintaining the ecological equilibrium of different biological niches and are essential for fermented food production and probiotic formulation. Despite the consensus about the 'health-promoting' significance of Lactobacillus genus, its genotypic and phenotypic characterization still poses several difficulties. The aim of this study was to assess the integration of different approaches, genotypic (16S rRNA gene sequencing), proteomic (MALDI-TOF MS) and metabolomic (1H-NMR), for the taxonomic and metabolic characterization of Lactobacillus species. For this purpose we analyzed 40 strains of various origin (intestinal, vaginal, food, probiotics), belonging to different species. The high discriminatory power of MALDI-TOF for species identification was underlined by the excellent agreement with the genotypic analysis. Indeed, MALDI-TOF allowed to correctly identify 39 out of 40 Lactobacillus strains at the species level, with an overall concordance of 97.5%. In the perspective to simplify the MALDI TOF sample preparation, especially for routine practice, we demonstrated the perfect agreement of the colony-picking from agar plates with the protein extraction protocol. 1H-NMR analysis, applied to both culture supernatants and bacterial lysates, identified a panel of metabolites whose variations in concentration were associated with the taxonomy, but also revealed a high intra-species variability that did not allow a species-level identification. Therefore, despite not suitable for mere taxonomic purposes, metabolomics can be useful to correlate particular biological activities with taxonomy and to understand the mechanisms related to the antimicrobial effect shown by some Lactobacillus species.
authors.affiliation: Microbiology, DIMES, University of Bologna, Bologna, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Foschi
authors.affiliation: Centre of Foodomics, Department of Agro-Food Science and Technology, University of Bologna, Bologna, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Laghi
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
authors.forename: Carola
authors.initials: C
authors.lastname: Parolin
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
authors.forename: Barbara
authors.initials: B
authors.lastname: Giordani
authors.affiliation: Microbiology, DIMES, University of Bologna, Bologna, Italy.
authors.forename: Monica
authors.initials: M
authors.lastname: Compri
authors.affiliation: Microbiology, DIMES, University of Bologna, Bologna, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Cevenini
authors.affiliation: Microbiology, DIMES, University of Bologna, Bologna, Italy.
authors.forename: Antonella
authors.identifier: http://orcid.org/0000-0002-7397-6560
authors.initials: A
authors.lastname: Marangoni
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
authors.forename: Beatrice
authors.initials: B
authors.lastname: Vitali
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics*; D005243:Feces / Q000382:microbiology; D005260:Female; D006801:Humans; D007422:Intestines / Q000382:microbiology; D007778:Lactobacillus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D055442:Metabolome; D010802:Phylogeny; D019936:Probiotics / Q000032:analysis*; D040901:Proteomics; D066244:Proton Magnetic Resonance Spectroscopy / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D014621:Vagina / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S