Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species
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 gene...
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Online Access: | http://hdl.handle.net/10261/229031 https://doi.org/10.3390/microorganisms8111720 https://doi.org/10.13039/501100004770 |
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ftcsic:oai:digital.csic.es:10261/229031 2024-02-11T10:09:20+01:00 Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species Lugli, Gabriele Andrea Tarracchini, Chiara Alessandri, Giulia Milani, Christian Mancabelli, Leonardo Turroni, Francesca Neuzil-Bunesova, Vera Ruíz García, Lorena Margolles Barros, Abelardo Ventura, Marco Università degli Studi di Parma 2020-11-03 http://hdl.handle.net/10261/229031 https://doi.org/10.3390/microorganisms8111720 https://doi.org/10.13039/501100004770 unknown Multidisciplinary Digital Publishing Institute Publisher's version https://doi.org/10.3390/microorganisms8111720 Sí doi:10.3390/microorganisms8111720 issn: 2076-2607 Microorganisms 8(11): 1720 (2020) http://hdl.handle.net/10261/229031 http://dx.doi.org/10.13039/501100004770 open Bifidobacteria Genomics Pangenome Phylogeny artículo http://purl.org/coar/resource_type/c_6501 2020 ftcsic https://doi.org/10.3390/microorganisms811172010.13039/501100004770 2024-01-16T11:02:31Z 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 We thank GenProbio srl for financial support of the Laboratory of Probiogenomics. Part of this research was conducted using the High Performance Computing (HPC) facility of the University of Parma. Article in Journal/Newspaper Ursus arctos Digital.CSIC (Spanish National Research Council) Parma ENVELOPE(57.468,57.468,65.951,65.951) Microorganisms 8 11 1720 |
institution |
Open Polar |
collection |
Digital.CSIC (Spanish National Research Council) |
op_collection_id |
ftcsic |
language |
unknown |
topic |
Bifidobacteria Genomics Pangenome Phylogeny |
spellingShingle |
Bifidobacteria Genomics Pangenome Phylogeny Lugli, Gabriele Andrea Tarracchini, Chiara Alessandri, Giulia Milani, Christian Mancabelli, Leonardo Turroni, Francesca Neuzil-Bunesova, Vera Ruíz García, Lorena Margolles Barros, Abelardo Ventura, Marco Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species |
topic_facet |
Bifidobacteria Genomics Pangenome Phylogeny |
description |
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 We thank GenProbio srl for financial support of the Laboratory of Probiogenomics. Part of this research was conducted using the High Performance Computing (HPC) facility of the University of Parma. |
author2 |
Università degli Studi di Parma |
format |
Article in Journal/Newspaper |
author |
Lugli, Gabriele Andrea Tarracchini, Chiara Alessandri, Giulia Milani, Christian Mancabelli, Leonardo Turroni, Francesca Neuzil-Bunesova, Vera Ruíz García, Lorena Margolles Barros, Abelardo Ventura, Marco |
author_facet |
Lugli, Gabriele Andrea Tarracchini, Chiara Alessandri, Giulia Milani, Christian Mancabelli, Leonardo Turroni, Francesca Neuzil-Bunesova, Vera Ruíz García, Lorena Margolles Barros, Abelardo Ventura, Marco |
author_sort |
Lugli, Gabriele Andrea |
title |
Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species |
title_short |
Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species |
title_full |
Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species |
title_fullStr |
Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species |
title_full_unstemmed |
Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species |
title_sort |
decoding the genomic variability among members of the bifidobacterium dentium species |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2020 |
url |
http://hdl.handle.net/10261/229031 https://doi.org/10.3390/microorganisms8111720 https://doi.org/10.13039/501100004770 |
long_lat |
ENVELOPE(57.468,57.468,65.951,65.951) |
geographic |
Parma |
geographic_facet |
Parma |
genre |
Ursus arctos |
genre_facet |
Ursus arctos |
op_relation |
Publisher's version https://doi.org/10.3390/microorganisms8111720 Sí doi:10.3390/microorganisms8111720 issn: 2076-2607 Microorganisms 8(11): 1720 (2020) http://hdl.handle.net/10261/229031 http://dx.doi.org/10.13039/501100004770 |
op_rights |
open |
op_doi |
https://doi.org/10.3390/microorganisms811172010.13039/501100004770 |
container_title |
Microorganisms |
container_volume |
8 |
container_issue |
11 |
container_start_page |
1720 |
_version_ |
1790609178342981632 |