Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences
Bifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of specie...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-05-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00657/full |
| _version_ | 1819096727748083712 |
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| author | Katelyn eBrandt Katelyn eBrandt Rodolphe eBarrangou Rodolphe eBarrangou |
| author_facet | Katelyn eBrandt Katelyn eBrandt Rodolphe eBarrangou Rodolphe eBarrangou |
| author_sort | Katelyn eBrandt |
| collection | DOAJ |
| description | Bifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of species and subspecies that encode a broad range of proteins implicated in complex and non-digestible carbohydrate uptake and catabolism, ranging from human breast milk oligosaccharides, to plant fibers. Recent genomic studies have created a need to properly place Bifidobacterium species in a phylogenetic tree. Current approaches, based on core-genome analyses come at the cost of intensive sequencing and demanding analytical processes. Here, we propose a typing method based on sequences of glycolysis genes and the proteins they encode, to provide insights into diversity, typing, and phylogeny in this complex and broad genus. We show that glycolysis genes occur broadly in these genomes, to encode the machinery necessary for the biochemical spine of the cell, and provide a robust phylogenetic marker. Furthermore, glycolytic sequences-based trees are congruent with both the classical 16S rRNA phylogeny, and core genome-based strain clustering. Furthermore, these glycolysis markers can also be used to provide insights into the adaptive evolution of this genus, especially with regards to trends towards a high GC content. This streamlined method may open new avenues for phylogenetic studies on a broad scale, given the widespread occurrence of the glycolysis pathway in bacteria, and the diversity of the sequences they encode. |
| first_indexed | 2024-12-22T00:03:48Z |
| format | Article |
| id | doaj.art-9323c76a1c264193af038fa52f2476a5 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-22T00:03:48Z |
| publishDate | 2016-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-9323c76a1c264193af038fa52f2476a52022-12-21T18:45:38ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2016-05-01710.3389/fmicb.2016.00657195501Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequencesKatelyn eBrandt0Katelyn eBrandt1Rodolphe eBarrangou2Rodolphe eBarrangou3North Carolina State UniversityNorth Carolina State UniversityNorth Carolina State UniversityNorth Carolina State UniversityBifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of species and subspecies that encode a broad range of proteins implicated in complex and non-digestible carbohydrate uptake and catabolism, ranging from human breast milk oligosaccharides, to plant fibers. Recent genomic studies have created a need to properly place Bifidobacterium species in a phylogenetic tree. Current approaches, based on core-genome analyses come at the cost of intensive sequencing and demanding analytical processes. Here, we propose a typing method based on sequences of glycolysis genes and the proteins they encode, to provide insights into diversity, typing, and phylogeny in this complex and broad genus. We show that glycolysis genes occur broadly in these genomes, to encode the machinery necessary for the biochemical spine of the cell, and provide a robust phylogenetic marker. Furthermore, glycolytic sequences-based trees are congruent with both the classical 16S rRNA phylogeny, and core genome-based strain clustering. Furthermore, these glycolysis markers can also be used to provide insights into the adaptive evolution of this genus, especially with regards to trends towards a high GC content. This streamlined method may open new avenues for phylogenetic studies on a broad scale, given the widespread occurrence of the glycolysis pathway in bacteria, and the diversity of the sequences they encode.http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00657/fullBifidobacteriumGlycolysisevolutionphylogenyprobiotic |
| spellingShingle | Katelyn eBrandt Katelyn eBrandt Rodolphe eBarrangou Rodolphe eBarrangou Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences Frontiers in Microbiology Bifidobacterium Glycolysis evolution phylogeny probiotic |
| title | Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences |
| title_full | Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences |
| title_fullStr | Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences |
| title_full_unstemmed | Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences |
| title_short | Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences |
| title_sort | phylogenetic analysis of the bifidobacterium genus using glycolysis enzyme sequences |
| topic | Bifidobacterium Glycolysis evolution phylogeny probiotic |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00657/full |
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