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We tested the hypothesis that pigmentation abnormalities are an overt signal of more generalised modifications in tissue structure and function, using as a model the Senegalese sole and two important innate immune barriers, the skin and intestine, and their microbiomes. Stereological analyses in pseudo-albino sole revealed a significantly increased mucous cell number in skin (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.001) and a significantly thicker muscle layer and <jats:italic>lamina propria<\/jats:italic> in gut (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.001). RNA-seq transcriptome analysis of the skin and gut identified 573 differentially expressed transcripts (DETs, FDR\u2009&lt;\u20090.05) between pseudo-albino and pigmented soles (one pool\/tissue from 4 individuals\/phenotype). DETs were mainly linked to pigment production, skin structure and regeneration and smooth muscle contraction. The microbiome (16\u2009S rRNA analysis) was highly diverse in pigmented and pseudo-albino skin but in gut had low complexity and diverged between the two pigmentation phenotypes. Quantitative PCR revealed significantly lower loads of <jats:italic>Mycoplasma<\/jats:italic> (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.05) and <jats:italic>Vibrio<\/jats:italic> bacteria (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.01) in pseudo-albino compared to the control. The study revealed that pseudo-albinism in addition to pigmentation changes was associated with generalised changes in the skin and gut structure and a modification in the gut microbiome.<\/jats:p>","DOI":"10.1038\/s41598-019-49501-6","type":"journal-article","created":{"date-parts":[[2019,9,20]],"date-time":"2019-09-20T10:15:48Z","timestamp":1568974548000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Understanding pseudo-albinism in sole (Solea senegalensis): a transcriptomics and metagenomics approach"],"prefix":"10.1038","volume":"9","author":[{"given":"Patricia I. 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