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Open AccessArticle

Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
Microbiome Research Hub, University of Parma, 43124 Parma, Italy
APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, T12 YT20 Cork, Ireland
Author to whom correspondence should be addressed.
Microorganisms 2019, 7(11), 535;
Received: 30 September 2019 / Revised: 28 October 2019 / Accepted: 4 November 2019 / Published: 6 November 2019
Bifidobacteria are among the most prevalent gut commensals in mammals, playing crucial functional roles that start from their early colonization of the infant gastrointestinal tract and last throughout the life span of their host. Metagenomic approaches have been employed to unveil the genetic features of bifidobacteria in order to understand how they participate in the correct development of a healthy microbiome. Nevertheless, their low relative abundance in many environmental samples may represent a major limitation for metagenomics approaches. To overcome this restriction, we applied an enrichment method that allows amplification of bifidobacterial DNA obtained from human or animal fecal samples for up to 26,500-fold, resulting in the metagenomic reconstruction of genomes belonging to bifidobacterial strains, present at very low abundance in collected samples. Functional predictions of the genes from these reconstructed genomes allows us to identify unique signatures among members of the same bifidobacterial species, highlighting genes correlated with the uptake of nutrients and adhesion to the intestinal mucosa. View Full-Text
Keywords: genomics; metagenomics; microbiota; Bifidobacterium genomics; metagenomics; microbiota; Bifidobacterium
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Lugli, G.A.; Duranti, S.; Milani, C.; Mancabelli, L.; Turroni, F.; Sinderen, D.; Ventura, M. Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota. Microorganisms 2019, 7, 535.

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