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Pathog Immun. 2018;3(2):164-180. doi: 10.20411/pai.v3i2.250. Epub 2018 Sep 12.

Fecal Host Transcriptomics for Non-Invasive Human Mucosal Immune Profiling: Proof of Concept in Clostridium Difficile Infection.

Author information

Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah.
ARUP Laboratories, Salt Lake City, Utah.
Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, Utah.
Division of Infectious Diseases and Clinical Epidemiology, Intermountain Medical Center, Murray, Utah.
Contributed equally



Host factors play an important role in pathogenesis and disease outcome in Clostridium difficile infection (CDI), and characterization of these responses could uncover potential host biomarkers to complement existing microbe-based diagnostics.


We extracted RNA from fecal samples of patients with CDI and profiled human mRNA using amplicon-based next-generation sequencing (NGS). We compared the fecal host mRNA transcript expression profiles of patients with CDI to controls with non-CDI diarrhea.


We found that the ratio of human actin gamma 1 (ACTG1) to 16S ribosomal RNA (rRNA) was highly correlated with NGS quality as measured by percentage of reads on target. Patients with CDI could be differentiated from those with non-CDI diarrhea based on their fecal mRNA expression profiles using principal component analysis. Among the most differentially expressed genes were ones related to immune response (IL23A, IL34) and actin-cytoskeleton function (TNNT1, MYL4, SMTN, MYBPC3, all adjusted P-values < 1 × 10-3).


In this proof-of-concept study, we used host fecal transcriptomics for non-invasive profiling of the mucosal immune response in CDI. We identified differentially expressed genes with biological plausibility based on animal and cell culture models. This demonstrates the potential of fecal transcriptomics to uncover host-based biomarkers for enteric infections.


Clostridium difficile; actin-cytoskeleton; fecal transcriptomics; host transcriptomics; mucosal immune response

Conflict of interest statement

CONFLICTS OF INTEREST R.S. is a coinventor on a patent application pending for Taxonomer, which has been licensed by IDbyDNA from the University of Utah. He owns equity in and consults for IDbyDNA. B.K.L. has received research support from OpGen, travel support for a speaking engagement from Luminex, and is a member of the scientific advisory board of Merck. All other authors report no potential conflicts of interest.

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