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Campylobacter jejuni   is a major human pathogen and a leading cause of bacterial derived gastroenteritis worldwide.   C. jejuni   regulates gene expression under various environmental conditions and stresses, indicative of its ability to survive in diverse niches. Despite this ability to highly regulate gene transcription,   C. jejuni   encodes few transcription factors and its genome lacks many canonical transcriptional regulators. High throughput deep sequencing of mRNA transcripts (termed RNAseq) has been used to study the transcriptome of many different organisms, including   C. jejuni  ; however, this technology has yet to be applied to defining the transcriptome of   C. jejuni   during  in vivo  colonization of its natural host, the chicken. In addition to its use in profiling the abundance of annotated genes, RNAseq is a powerful tool for identifying and quantifying, as-of-yet, unknown transcripts including non-coding regulatory RNAs, 5’ untranslated regulatory elements, and anti-sense transcripts. Here we report the complete transcriptome of   C. jejuni   during colonization of the chicken cecum and in two different  in vitro  growth phases using strand-specific RNAseq. Through this study, we identified over 250 genes differentially expressed  in vivo  in addition to numerous putative regulatory RNAs, including trans-acting non-coding RNAs and anti-sense transcripts. These latter potential regulatory elements were not identified in two prior studies using ORF-based microarrays, highlighting the power and value of the RNAseq approach. Our results provide new insights into how   C. jejuni   responds and adapts to the cecal environment and reveals new functions involved in colonization of its natural host.

The Complete Campylobacter jejuni Transcriptome during Colonization of a Natural Host Determined by RNAseq