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

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.

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

“…We used the results of two previous studies on respiratory reductases 58 and B-vitamin synthesis pathways 59 . We extended the previous analyses to the 612 of our 773 organisms that were available in PubSEED 60 .…”

Effects of dietary nitrogen levels and carbohydrate sources on apparent ruminal synthesis of some B vitamins in dairy cows

“…This hypothesis is supported by the negative correlation between riboflavin ARS and NDF and ADF intakes, as well as with NDF ruminally digested (kg/d; Table 4). As recently performed for the human gut microbiota (Magnúsdóttir et al, 2015), a genome assessment of the B-vitamin biosynthetic pathway among rumen microbes would help to validate this hypothesis and to understand the effect of the microbiota composition (in line with the diet composition) on B-vitamin synthesis. Riboflavin ARS was strongly negatively correlated with ruminal protein balance and had a high positive correlation with microbial synthesis efficiency, whether in the liquid-associated bacteria fraction or in the mixed bacteria fraction, which contained both solid-and liquid-associated bacteria.…”

Cross-feeding interactions of gut symbionts driven by human milk oligosaccharidesand mucins

“…Genomic prediction of B vitamins biosynthesis (presence = 1 and absence = 0) based on the combination of essential functional roles by Magnusdottir et al (Magnusdottir et al 2015). …”

“…The gut microbiota exhibits close cooperation in B-vitamins biosynthesis (Magnusdottir et al 2015). Vitamin B12 is an essential co-factor for the synthesis of propionate (Takahashi-Iniguez et al 2012) and amino acids including folate, ubiquinone, and methionine (Romine et al 2017).…”