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Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes.

Magnúsdóttir S, Ravcheev D, de Crécy-Lagard V, Thiele I - Front Genet (2015)

Bottom Line: We compared our predictions to experimental data from 16 organisms and found 88% of our predictions to be in agreement with published data.In addition, we identified several pairs of organisms whose vitamin synthesis pathway pattern complemented those of other organisms.This result indicates the co-evolution of the gut microbes in the human gut environment.

View Article: PubMed Central - PubMed

Affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg.

ABSTRACT
The human gut microbiota supplies its host with essential nutrients, including B-vitamins. Using the PubSEED platform, we systematically assessed the genomes of 256 common human gut bacteria for the presence of biosynthesis pathways for eight B-vitamins: biotin, cobalamin, folate, niacin, pantothenate, pyridoxine, riboflavin, and thiamin. On the basis of the presence and absence of genome annotations, we predicted that each of the eight vitamins was produced by 40-65% of the 256 human gut microbes. The distribution of synthesis pathways was diverse; some genomes had all eight biosynthesis pathways, whereas others contained no de novo synthesis pathways. We compared our predictions to experimental data from 16 organisms and found 88% of our predictions to be in agreement with published data. In addition, we identified several pairs of organisms whose vitamin synthesis pathway pattern complemented those of other organisms. This analysis suggests that human gut bacteria actively exchange B-vitamins among each other, thereby enabling the survival of organisms that do not synthesize any of these essential cofactors. This result indicates the co-evolution of the gut microbes in the human gut environment. Our work presents the first comprehensive assessment of the B-vitamin synthesis capabilities of the human gut microbiota. We propose that in addition to diet, the gut microbiota is an important source of B-vitamins, and that changes in the gut microbiota composition can severely affect our dietary B-vitamin requirements.

No MeSH data available.


Related in: MedlinePlus

NCBI based taxonomic trees and the presence or absence of the eight B-vitamin biosynthesis pathways. The two taxonomic trees show the (A) 256 HGM genomes and (B) the 257 non-HGM genomes, along with heatmaps showing the presence (green) or absence (black) of each vitamin pathway. The taxonomic trees were produced using PhyloT: a tree generator (http://phylot.biobyte.de/index.html), and visualized through iTOL (http://itol.embl.de/) (Letunic and Bork, 2007, 2011).
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Figure 9: NCBI based taxonomic trees and the presence or absence of the eight B-vitamin biosynthesis pathways. The two taxonomic trees show the (A) 256 HGM genomes and (B) the 257 non-HGM genomes, along with heatmaps showing the presence (green) or absence (black) of each vitamin pathway. The taxonomic trees were produced using PhyloT: a tree generator (http://phylot.biobyte.de/index.html), and visualized through iTOL (http://itol.embl.de/) (Letunic and Bork, 2007, 2011).

Mentions: Examining the variation of the different synthesis pathways in our former analysis, we wondered how the combinations of the vitamins synthesized varied across the HGM genomes. Our data consist of binary information regarding the distribution of pathways in 256 HGM and 257 non-HGM genomes, i.e., the presence or absence of a vitamin biosynthesis pathway in a genome (Figure 9). We investigated the 28 = 256 possible patterns of the eight studied pathways. Only 68 (27%) of the 256 possible pathway patterns were found in the 256 HGM genomes (Supplementary Table 1), suggesting that the occurrences of these B-vitamin pathways may not be independent.


Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes.

Magnúsdóttir S, Ravcheev D, de Crécy-Lagard V, Thiele I - Front Genet (2015)

NCBI based taxonomic trees and the presence or absence of the eight B-vitamin biosynthesis pathways. The two taxonomic trees show the (A) 256 HGM genomes and (B) the 257 non-HGM genomes, along with heatmaps showing the presence (green) or absence (black) of each vitamin pathway. The taxonomic trees were produced using PhyloT: a tree generator (http://phylot.biobyte.de/index.html), and visualized through iTOL (http://itol.embl.de/) (Letunic and Bork, 2007, 2011).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403557&req=5

Figure 9: NCBI based taxonomic trees and the presence or absence of the eight B-vitamin biosynthesis pathways. The two taxonomic trees show the (A) 256 HGM genomes and (B) the 257 non-HGM genomes, along with heatmaps showing the presence (green) or absence (black) of each vitamin pathway. The taxonomic trees were produced using PhyloT: a tree generator (http://phylot.biobyte.de/index.html), and visualized through iTOL (http://itol.embl.de/) (Letunic and Bork, 2007, 2011).
Mentions: Examining the variation of the different synthesis pathways in our former analysis, we wondered how the combinations of the vitamins synthesized varied across the HGM genomes. Our data consist of binary information regarding the distribution of pathways in 256 HGM and 257 non-HGM genomes, i.e., the presence or absence of a vitamin biosynthesis pathway in a genome (Figure 9). We investigated the 28 = 256 possible patterns of the eight studied pathways. Only 68 (27%) of the 256 possible pathway patterns were found in the 256 HGM genomes (Supplementary Table 1), suggesting that the occurrences of these B-vitamin pathways may not be independent.

Bottom Line: We compared our predictions to experimental data from 16 organisms and found 88% of our predictions to be in agreement with published data.In addition, we identified several pairs of organisms whose vitamin synthesis pathway pattern complemented those of other organisms.This result indicates the co-evolution of the gut microbes in the human gut environment.

View Article: PubMed Central - PubMed

Affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg.

ABSTRACT
The human gut microbiota supplies its host with essential nutrients, including B-vitamins. Using the PubSEED platform, we systematically assessed the genomes of 256 common human gut bacteria for the presence of biosynthesis pathways for eight B-vitamins: biotin, cobalamin, folate, niacin, pantothenate, pyridoxine, riboflavin, and thiamin. On the basis of the presence and absence of genome annotations, we predicted that each of the eight vitamins was produced by 40-65% of the 256 human gut microbes. The distribution of synthesis pathways was diverse; some genomes had all eight biosynthesis pathways, whereas others contained no de novo synthesis pathways. We compared our predictions to experimental data from 16 organisms and found 88% of our predictions to be in agreement with published data. In addition, we identified several pairs of organisms whose vitamin synthesis pathway pattern complemented those of other organisms. This analysis suggests that human gut bacteria actively exchange B-vitamins among each other, thereby enabling the survival of organisms that do not synthesize any of these essential cofactors. This result indicates the co-evolution of the gut microbes in the human gut environment. Our work presents the first comprehensive assessment of the B-vitamin synthesis capabilities of the human gut microbiota. We propose that in addition to diet, the gut microbiota is an important source of B-vitamins, and that changes in the gut microbiota composition can severely affect our dietary B-vitamin requirements.

No MeSH data available.


Related in: MedlinePlus