title: Enhanced microbial diversity in the saliva microbiome induced by short-term probiotic intake revealed by 16S rRNA sequencing on the IonTorrent PGM platform.
abstract: Microbial communities populating several human body habitats are important determinants of human health. Cultivation-free community-wide approaches like bacterial 16S rRNA sequencing recently revolutionized the study of such human-associated microbial diversity, and the continuously decreasing cost/throughput ratio of current sequencing platforms is further enhancing the availability and effectiveness of microbiome research. The IonTorrent PGM platform is among the latest available commercial high-throughput sequencing tools, but it is just starting to be used for 16S rRNA surveys with only episodic assessments of its performance. We present here the first IonTorrent profiling of the human saliva microbiome collected from 12 healthy individuals. In this cohort, a subset of the volunteers was asked to assume a probiotic product, in order to investigate its impact on the composition and the structure of the saliva microbiome. Analysis of the generated dataset suggests the suitability of the IonTorrent platform for 16S rRNA surveys, even though some platform-specific choices are required to optimize the consistency of the obtained bacterial profiles. Interestingly, we found a marked and statistically significant increase of the overall bacterial diversity in the saliva of individuals who received the probiotic product compared to the control group, suggesting a short-term effect of probiotic product administration on oral microbiome composition.
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Erik
authors.initials: E
authors.lastname: Dassi
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Annalisa
authors.initials: A
authors.lastname: Ballarini
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Covello
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Quattrone
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jousson
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy; NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Veronica
authors.initials: V
authors.lastname: De Sanctis
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy; NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Bertorelli
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Michela Alessandra
authors.initials: MA
authors.lastname: Denti
authors.affiliation: Centre for Integrative Biology, University of Trento, Italy. Electronic address: nicola.segata@unitn.it.
authors.forename: Nicola
authors.initials: N
authors.lastname: Segata
mesh_terms: D000328:Adult; D001419:Bacteria / Q000145:classification / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D064307:Microbiota / Q000235:genetics*; D019936:Probiotics / Q000008:administration & dosage*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012463:Saliva / Q000382:microbiology*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA; IonTorrent; Metagenomics; Probiotics; Saliva microbiome