Evaluation of bacterial biomarkers to aid in challenging inflammatory bowel diseases diagnostics and subtype classification

Mireia Lopez-Siles* (Corresponding Author), Xavier Aldeguer, Miriam Sabat-Mir, Mariona Serra-Pagès, Sylvia H Duncan, Harry J. Flint, L Jesús Garcia-Gil, Margarita Martinez-Medina

*Corresponding author for this work

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The challenges for inflammatory bowel disease (IBD) diagnostics are to discriminate it from gut conditions with similar symptoms such as irritable bowel syndrome (IBS), to distinguish IBD subtypes, to predict disease progression, and to establish the risk to develop colorectal cancer (CRC). Alterations in gut microbiota have been proposed as a source of information to assist in IBD diagnostics. Faecalibacterium prausnitzii (F. prausnitzii), its phylogroups, and Escherichia coli (E. coli) have been reported as potential biomarkers, but their performance in challenging IBD diagnostic situations remains elusive. We hypothesize that bacterial biomarkers based in these species may help to discriminate these conditions of complex diagnostics.

To evaluate the usefulness of indices calculated from the quantification of these species as biomarkers to aid in IBD diagnostics.

A retrospective study of 131 patients (31 controls (H), 45 Crohn’s disease (CD), 25 ulcerative colitis (UC), 10 IBS, and 20 CRC subjects) was performed to assess the usefulness of bacterial biomarkers in biopsies. Further, the performance of biomarkers in faeces was studied in 29 stool samples (19 CD, 10 UC). Relative abundances of F. prausnitzii, its phylogroups (PHGI and PHGII), and E. coli quantification were determined by qPCR. Loads were combined to calculate the FP-E index, the PHGI–E index and the PHGII-E index. Biomarkers accuracy to discriminate among conditions was measured by the area under the receiver operating characteristic curve (AUC).

In biopsies, FP-E index was good for discriminating IBS from CD (AUC = 0.752) while PHGII-E index was suitable for discriminating IBS from UC (AUC = 0.632). The FP-E index would be the choice to discriminate IBD from CRC, especially from all UC subtypes (AUC ≥ 0.875), regardless of the activity status of the patient. Discrimination between UC patients that had the longest disease duration and those with CRC featured slightly lower AUC values. Concerning differentiation in IBD with shared location, PHGI-E index can establish progression from proctitis and left-sided colitis to ulcerative pancolitis (AUC ≥ 0.800). PHG I-E index analysis in tissue would be the choice to discriminate within IBD subtypes of shared location (AUC ≥ 0.712), while in non-invasive faecal samples FP or PHGI could be good indicators (AUC ≥ 0.833).

F. prausnitzii phylogroups combined with E. coli offer potential to discriminate between IBD and CRC patients and can assist in IBD subtypes classification, which may help in solving IBD diagnostics challenges.
Original languageEnglish
Pages (from-to)64-77
Number of pages14
JournalWorld Journal of Gastrointestinal Pathophysiology
Issue number3
Early online date12 May 2020
Publication statusPublished - 12 May 2020

Bibliographical note

Supported by the Spanish Ministry of Education and Science, No. SAF2010-15896, No. SAF2013-43284-P and No. SAF2017-82261-P.


  • Crohn’s disease
  • ulcerative colitis
  • inflammatory bowel disease
  • diagnostic tests
  • Faecalibacterium prausnitzii
  • Escherichia coli
  • irritable bowel syndrome
  • colorectal cancer


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