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Background  Delivery of colostrum within the first several hours after birth is vital for establishing successful passive immunity in neonatal dairy calves. However, it is unclear whether a difference in colostrum feeding strategy can affect the development of the calf gastrointestinal tract. The aim of this study was to evaluate the effect of colostrum feeding time within the first 12 h after birth on the colonic mucosal immune system in neonatal calves using a genome wide transcriptome analysis.    Results  RNA sequencing-based transcriptome analysis of colon tissues collected from 27 male Holstein calves which were randomly assigned to one of three colostrum feeding strategies – (immediately after birth (TRT0); 6 h after birth (TRT6); 12 h after birth (TRT12)) – and euthanized at 51 h of age detected 15,935 ± 210, 15,332 ± 415, and 15,539 ± 440 expressed genes in the colon under three treatments, respectively. The core transcriptome of the colon included 12,678 genes, with enriched “cellular process” and “metabolic process” as the top two biological functions with 802 of them being immune function related genes. Principal component analysis of the colon transcriptomes did not display a clear separation by colostrum feeding strategy and differential abundance analyses showed no significant difference in the expression of immune related genes among the treatments. Additionally, a weighted gene co-expression network analysis identified 4 significant (|correlation| > 0.50 and  p  ≤ 0.05) gene modules consisting of 122 immune related genes, which were positively or negatively correlated with the abundance of  Lactobacillus  and  Faecalibacterium prausnitzii  in the colon.    Conclusion  Transcriptome analysis indicates that the development of the colonic mucosal immune system in neonatal calves may be independent of the timing of initial colostrum meal within 12 h after birth. Our results also provide a molecular understanding of colonic biological function in neonatal calves and extends knowledge on how host gene expression profiles are associated with the abundance of specific bacterial groups in the colon.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5017-y) contains supplementary material, which is available to authorized users.

bmc genomics

Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves