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Decoding the Genomic Variability among Members of the Bifidobacteriumdentium Species

GA. Lugli, C. Tarracchini, G. Alessandri, C. Milani, L. Mancabelli, F. Turroni, V. Neuzil-Bunesova, L. Ruiz, A. Margolles, M. Ventura,

. 2020 ; 8 (11) : . [pub] 20201103

Jazyk angličtina Země Švýcarsko

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/bmc21001832

Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR-Cas and restriction-modification systems may be responsible for the high genome synteny identified among members of this taxon.

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$a Lugli, Gabriele Andrea $u Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
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$a Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR-Cas and restriction-modification systems may be responsible for the high genome synteny identified among members of this taxon.
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$a Tarracchini, Chiara $u Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
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$a Alessandri, Giulia $u Department of Veterinary Medical Science, University of Parma, 43126 Parma, Italy.
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$a Mancabelli, Leonardo $u Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
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$a Turroni, Francesca $u Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
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$a Neuzil-Bunesova, Vera $u Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic.
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$a Ruiz, Lorena $u Department of Microbiology and Biochemistry, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares s/n, Villaviciosa, 33300 Asturias, Spain. MicroHealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain.
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$a Ventura, Marco $u Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy. Microbiome Research Hub, University of Parma, 13121 Parma, Italy.
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