BackgroundLimited research has focused on the effect of Lactobacillus on the intestinal toxicity of deoxynivalenol (DON). The present study was conducted to investigate the role of Lactobacillus plantarum (L. plantarum) JM113 in protecting against the intestinal toxicity caused by DON.MethodsA total of 144 one-day-old healthy Arbor Acres broilers were randomly distributed into 3 treatments, including the CON (basal diet), the DON (extra 10 mg/kg deoxynivalenol), and the DL (extra 1 × 109 CFU/ kg L. plantarum JM113 based on DON group) treatments. The growth performance, organ indexes, intestinal morphology, pancreatic digestive enzymes, intestinal secreted immunoglobulin A (sIgA), jejunal transcriptome, and intestinal microbiota were evaluated.ResultsCompared with the CON and DL groups, the DON supplementation altered intestinal morphology, especially in duodenum and jejunum, where villi were shorter and crypts were deeper (P < 0.05). Meanwhile, the significantly decreased mRNA expression of jejunal claudin-1 and occludin (P < 0.05), ileal rBAT and jejunal GLUT1 of 21-day-old broilers (P < 0.05), as well as duodenal PepT1 and ileal rBAT of 42-day-old broilers were identified in the DON group. Moreover, supplementation with L. plantarum JM113 could increase duodenal expression of IL-10 and IL-12 of 21-day-old broilers, ileal sIgA of 42-day-old broilers, and the bursa of Fabricius index of 21-day-old broilers. Further jejunal transcriptome proved that the genes related to the intestinal absorption and metabolism were significantly reduced in the DON group but a significant increase when supplemented with extra L. plantarum JM113. Furthermore, the bacteria related to nutrient utilization, including the Proteobacteria, Escherichia, Cc-115 (P < 0.05), Lactobacillus and Prevotella (P < 0.1) were all decreased in the DON group. By contrast, supplementation with L. plantarum JM113 increased the relative abundance of beneficial bacterium, including the Bacteroidetes, Roseburia, Anaerofustis, Anaerostipe, and Ruminococcus bromii (P < 0.05). Specifically, the increased abundance of bacteria in the DL group could be proved by the significantly increased caecal content of propionic acid, n-Butyric acid, and total short-chain fatty acid.ConclusionsL. plantarum JM113 enhanced the digestion, absorption, and metabolic functions of the gut when challenged with DON by reducing the injury to intestinal barriers and by increasing the abundance of beneficial bacterium.Electronic supplementary materialThe online version of this article (10.1186/s40104-018-0286-5) contains supplementary material, which is available to authorized users.