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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

Pantothenate biosynthesis. The pantothenate biosynthesis subsystem contains 10 functional roles (Supplementary Table 2) and 12 metabolites. Refer to Figure 1 for figure descriptions.
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Figure 5: Pantothenate biosynthesis. The pantothenate biosynthesis subsystem contains 10 functional roles (Supplementary Table 2) and 12 metabolites. Refer to Figure 1 for figure descriptions.

Mentions: Pantothenate is a precursor for coenzyme A (CoA) and it can be synthesized de novo from 2-dihydropantoate and β-alanine (Figure 5). Because CoA is the active form of pantothenate, we considered the de novo pantothenate biosynthesis pathway to be complete when a genome contained the functional roles needed for CoA biosynthesis. Although this pathway is well defined, it caused many uncertainties in our analysis. Many of the analyzed genomes were missing the roles KPHMT or ASPDC. When a genome was missing a single enzyme in the branched pathway, the organisms were still predicted to be a pantothenate producer. Some genomes were lacking the role PBAL, which is the final step of pantothenate biosynthesis. Hence, the absence of PBAL always resulted in a non-producer prediction.


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)

Pantothenate biosynthesis. The pantothenate biosynthesis subsystem contains 10 functional roles (Supplementary Table 2) and 12 metabolites. Refer to Figure 1 for figure descriptions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Pantothenate biosynthesis. The pantothenate biosynthesis subsystem contains 10 functional roles (Supplementary Table 2) and 12 metabolites. Refer to Figure 1 for figure descriptions.
Mentions: Pantothenate is a precursor for coenzyme A (CoA) and it can be synthesized de novo from 2-dihydropantoate and β-alanine (Figure 5). Because CoA is the active form of pantothenate, we considered the de novo pantothenate biosynthesis pathway to be complete when a genome contained the functional roles needed for CoA biosynthesis. Although this pathway is well defined, it caused many uncertainties in our analysis. Many of the analyzed genomes were missing the roles KPHMT or ASPDC. When a genome was missing a single enzyme in the branched pathway, the organisms were still predicted to be a pantothenate producer. Some genomes were lacking the role PBAL, which is the final step of pantothenate biosynthesis. Hence, the absence of PBAL always resulted in a non-producer prediction.

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