Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis

Abstract

Various diseases have been linked to the human microbiota, but the underlying molecular mechanisms of the microbiota in disease pathogenesis are often poorly understood. Using acne as a disease model, we aimed to understand the molecular response of the skin microbiota to host metabolite signaling in disease pathogenesis. Metatranscriptomic analysis revealed that the transcriptional profiles of the skin microbiota separated acne patients from healthy individuals. The vitamin B12 biosynthesis pathway in the skin bacterium Propionibacterium acnes was significantly down-regulated in acne patients. We hypothesized that host vitamin B12 modulates the activities of the skin microbiota and contributes to acne pathogenesis. To test this hypothesis, we analyzed the skin microbiota in healthy subjects supplemented with vitamin B12. We found that the supplementation repressed the expression of vitamin B12 biosynthesis genes in P. acnes and altered the transcriptome of the skin microbiota. One of the 10 subjects studied developed acne 1 week after vitamin B12 supplementation. To further understand the molecular mechanism, we revealed that vitamin B12 supplementation in P. acnes cultures promoted the production of porphyrins, which have been shown to induce inflammation in acne. Our findings suggest a new bacterial pathogenesis pathway in acne and provide one molecular explanation for the long-standing clinical observation that vitamin B12 supplementation leads to acne development in a subset of individuals. Our study discovered that vitamin B12, an essential nutrient in humans, modulates the transcriptional activities of skin bacteria, and provided evidence that metabolite-mediated interactions between the host and the skin microbiota play essential roles in disease development.

Conflict of interest statement

Competing interests: The Regents of the University of California is the owner of a patent application (US application No. 62/078,275, titled “New acne treatment targets”) related to the role of vitamin B12 in acne, which names D.K., B.S., N.C., and H.L. as inventors. The other author declares no competing interests.

Copyright © 2015, American Association for the Advancement of Science.

Figures

Fig. 1.. The gene expression profiles of P. acnes in the skin microbiota were distinct between acne patients and healthy individuals.

(A) Based on the gene expression of P. acnes in the skin microbiota, acne patients (labeled in red, “Acne”) formed a separate cluster from healthy individuals (labeled in green, “Healthy”) in an unsupervised hierarchical clustering analysis. (B) 136 differentially expressed P. acnes OGUs were identified between acne patients and healthy individuals. Among them, 109 OGUs were up-regulated and 27 OGUs were down-regulated in acne patients. The OGU names are listed in table S2.

Fig. 2.. A schematic of the metabolic pathways in P. acnes illustrating the observed differentially expressed OGUs in acne patients compared to healthy individuals.

Genes encoding sugar transport and sugar metabolism pathways were up-regulated in acne patients. Genes in the vitamin B12 biosynthesis and fatty acid biosynthesis pathways were down-regulated. FC: fold change. The full gene names are listed in table S3.

Fig. 3.. Vitamin B12 biosynthesis genes were down-regulated in the skin microbiota of acne patients compared to healthy individuals.

Down-regulation of the genes in P. acnes vitamin B12 biosynthesis pathway was validated in a separate cohort of acne patients (n=9) and healthy individuals (n=15). Consistent with the RNA-Seq data, cysG+cbiX and cbiL were significantly down-regulated, and btuR showed a lower average expression level in acne patients compared to healthy individuals. Significance was determined by Student’s t-test. The mean of the expression levels of each gene is indicated by a black bar. The gene expression data are listed in table S4.

Fig. 4.. Vitamin B12 supplementation in healthy subjects repressed P. acnes cob/cbi operons.

The gene expression levels of cbiL, cysG+cbiX, and btuR in P. acnes vitamin B12 biosynthesis pathway were significantly repressed in the healthy subjects (n=10) on day 14 after vitamin B12 supplementation, to a level similar to those observed in the acne patients (n=9). Without vitamin B12 supplementation, the expression levels of these genes did not change significantly on day 2 and day 14 compared to day 0 (n=9). The expression levels, quantified by qRT-PCR, for each gene on day 0, day 2, and day 14 are shown. Data from healthy subjects with vitamin B12 supplementation are shown in purple and without supplementation are shown in green. As a comparison, data from the acne patients are shown in red. The mean of the expression levels of each gene is indicated by a black bar. Significance was determined by Student’s t-test. The gene expression data are listed in tables S5A and S5B.

Fig. 5.. Vitamin B12 supplementation in the host altered the transcriptome of P. acnes in the skin microbiota.

(A) The differentially expressed P. acnes OGUs between the Day0 samples and Day14 samples from the healthy subjects supplemented with vitamin B12. The red and green colors represent the fold change of the OGUs. Red indicates up-regulation after vitamin B12 supplementation and green indicates down-regulation. The functional categories of the OGUs are labeled by the color bars next to the OGUs’ names. (B) The P. acnes gene expression profile of subject HL414 on day 14 after vitamin B12 supplementation (HL414-Day14) was similar to those from the acne patients and clustered together. The Day0 sample from subject HL414 (“HL414_Day0”, healthy skin, before vitamin B12 supplementation) was similar to the samples from other healthy subjects. Samples from the acne patients were labeled in red (“Acne”), and samples from the healthy subjects were labeled in green (“Healthy”, “Day0”, “Day14”), except for HL414-Day14.

Fig. 6.. Vitamin B12 supplementation repressed the expression of cob/cbi operons in the vitamin B12 biosynthesis pathway and promoted porphyrin production in P. acnes cultures.

(A) The expression levels of cbiL, cysG+cbiX, and btuR were significantly repressed on day 2, day 8, and day 14 after vitamin B12 supplementation in P. acnes cultures. The experiments were repeated three times independently. Each dot represents the average gene expression level of two to three technical replicates in each independent experiment. The dotted lines indicate the changes between the P. acnes cultures in medium only (black) and the cultures in medium with vitamin B12 supplementation (red). The mean of the gene expression levels from the three independent experiments is shown as a black bar. Significance was determined by Student’s t-test. The gene expression data are listed in table S7. (B) Porphyrin production in P. acnes cultures on day 8 and day 14 after vitamin B12 supplementation was significantly increased. Significance was determined by Student’s t-test. Data are presented as the mean ± standard deviation. The experiments were repeated three times independently with three to four biological replicates each time. The porphyrin levels are listed in table S8.

Fig. 7.. A model of vitamin B12 modulating the transcriptional and metabolic activities of the skin bacterium P. acnes in acne pathogenesis.

In healthy skin, when the host vitamin B12 level is normal, the vitamin B12 biosynthesis pathway in P. acnes is expressed and porphyrins are produced at a low level. When the host vitamin B12 level is elevated, it signals transcriptional changes in P. acnes. The levels of 2-oxoglutarate and L-glutamate are increased, and the vitamin B12 biosynthesis in P. acnes is repressed. The metabolic flow of L-glutamate is shunted toward the porphyrin biosynthesis pathway, leading to an over-production of porphyrins by P. acnes in the follicle. The overproduced porphyrins, secreted by P. acnes, induce an inflammatory response in the host cells leading to acne development in a subset of individuals. 2-OG: 2-oxoglutarate. L-Glu: L-glutamate.