title: Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol.
abstract: The precise appraisal of the composition of the human gut microbiota still represents a challenging task. The advent of next generation sequencing approaches has opened new ways to dissect the microbial biodiversity of this ecosystem through the use of 16S rRNA gene-based microbiota analysis approaches. However, the detailed representation of specific groups or members of the human gut microbiota, for example Bifidobacteria, may be skewed by the PCR primers employed in the amplification step of the 16S rRNA gene-based microbial profiling pipeline and by the limited resolution of the 16S rRNA gene variable regions. Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hypervariable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus. In addition, we present an optimized protocol for ITS-based profiling utilizing qiime software, allowing accurate and subspecies-specific compositional reconstruction of the bifidobacterial community in the human gut.
authors.affiliation: Department of Life Sciences, Laboratory of Probiogenomics, University of Parma, Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.forename: Gabriele A
authors.initials: GA
authors.lastname: Lugli
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mancabelli
authors.forename: Sabrina
authors.initials: S
authors.lastname: Duranti
authors.forename: Alice
authors.initials: A
authors.lastname: Viappiani
authors.forename: Marta
authors.initials: M
authors.lastname: Mangifesta
authors.forename: Nicola
authors.initials: N
authors.lastname: Segata
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
mesh_terms: D000328:Adult; D001644:Bifidobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D004269:DNA, Bacterial / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer; D012336:RNA, Ribosomal, 16S
keywords: Bifidobacteria; ITS; Ion Torrent; biodiversity; protocols