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. 2015 Apr 20:6:148.
doi: 10.3389/fgene.2015.00148. eCollection 2015.

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

Stefanía Magnúsdóttir  1 , Dmitry Ravcheev  1 , Valérie de Crécy-Lagard  2 , Ines Thiele  1
Affiliations

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

Stefanía Magnúsdóttir et al. Front Genet. .

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.

Keywords: B-vitamin biosynthesis; PubSEED; genome annotation; gut microbiota; subsystem.

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Figures

Figure 1
Figure 1
Biotin biosynthesis. The biotin biosynthesis subsystem contains 9 functional roles (Supplementary Table 2) and 10 metabolites. Functional roles are represented by rectangles. The major biosynthesis routes are colored green, alternative routes are blue, salvage routes are red, and known transporters are yellow. Metabolites are represented by circles, and yellow circles represent metabolites that can be salvaged from the environment in some cases. Only the core metabolites of the biosynthesis pathway are listed. Each bar graph represents the percentage of organisms in each phylum that contain the functional role.
Figure 2
Figure 2
Cobalamin biosynthesis. The cobalamin biosynthesis subsystem contains 17 functional roles (Supplementary Table 2) and 15 metabolites. Refer to Figure 1 for figure descriptions. Note that we show only CbiD since none of the HGM genomes contained CobF. The “* or **” text in the first green box on the top left corner of the figure refer to two functional roles “*CbiKX” and “**CysG”. The corresponding bar charts for the two functional roles are shown below the green box, just above the “Abbr./Metabolites” table.
Figure 3
Figure 3
Folate biosynthesis. The folate biosynthesis subsystem contains 11 functional roles (Supplementary Table 2) and 14 metabolites. Refer to Figure 1 for figure descriptions.
Figure 4
Figure 4
Niacin biosynthesis. The niacin biosynthesis subsystem contains 14 functional roles (Supplementary Table 2) and 10 metabolites. Refer to Figure 1 for figure descriptions.
Figure 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.
Figure 6
Figure 6
Pyridoxine biosynthesis. The pyridoxine biosynthesis subsystem contains 11 functional roles (Supplementary Table 2) and 16 metabolites. Refer to Figure 1 for figure descriptions.
Figure 7
Figure 7
Riboflavin biosynthesis. The riboflavin biosynthesis subsystem contains 10 functional roles (Supplementary Table 2) and 11 metabolites. Refer to Figure 1 for figure explanations.
Figure 8
Figure 8
Thiamin biosynthesis. The thiamin biosynthesis subsystem contains 9 functional roles (Supplementary Table 2) and 10 metabolites. One functional role, sulfur carrier protein This, is drawn as a metabolite because it is combined with other metabolites and recycled in the pathway. Refer to Figure 1 for figure explanations.
Figure 9
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).
Figure 10
Figure 10
Inversed pattern pairs of HGM and non-HGM genomes. The HGM genomes showed ten pairs of inversed patters, whereas the non-HGM contained 5 pairs.
See this image and copyright information in PMC

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