Comparative genomics of the Bifidobacterium brevetaxon View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-03-01

AUTHORS

Francesca Bottacini, Mary O’Connell Motherway, Justin Kuczynski, Kerry Joan O’Connell, Fausta Serafini, Sabrina Duranti, Christian Milani, Francesca Turroni, Gabriele Andrea Lugli, Aldert Zomer, Daria Zhurina, Christian Riedel, Marco Ventura, Douwe van Sinderen

ABSTRACT

BackgroundBifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host’s health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina.ResultsIn silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol.ConclusionsGenome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve. More... »

PAGES

170

Journal

TITLE

BMC Genomics

ISSUE

1

VOLUME

15

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-15-170

DOI

http://dx.doi.org/10.1186/1471-2164-15-170

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1014252423

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24581150


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27 schema:description BackgroundBifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host’s health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina.ResultsIn silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol.ConclusionsGenome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.
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33 schema:keywords B. breve
34 B. breve species
35 B. breve strains
36 Bifidobacterium breve
37 DNA
38 Matching Analysis
39 ResultsIn silico analysis
40 adaptation
41 analysis
42 biosynthetic machinery
43 breve
44 broad range
45 capability
46 carbohydrate fermentation
47 clear correlation
48 close trend
49 clusters
50 colonization
51 comparative genomics
52 components
53 correlation
54 different environments
55 different strains
56 elements
57 environment
58 exopolysaccharide production
59 explanation
60 fermentation
61 foreign DNA
62 gastrointestinal tract
63 gene cluster
64 gene-trait matching analysis
65 genes
66 genetic explanation
67 genetic variability
68 genome
69 genome sequence
70 genomics
71 gut colonization
72 gut microbiota
73 health status
74 host
75 host environment
76 host health status
77 human gut microbiota
78 human milk
79 hypothetical genes
80 identification
81 invasion
82 latter genes
83 machinery
84 metabolic capabilities
85 microbiota
86 milk
87 mobile elements
88 number
89 pan-genome
90 part
91 phenotype
92 pili
93 presence
94 production
95 protection
96 range
97 reasons
98 representatives
99 sequence
100 silico analysis
101 sorbitol
102 sortase-dependent pili
103 species
104 status
105 strains
106 study
107 tract
108 trends
109 utilization
110 utilization phenotype
111 vagina
112 variability
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