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Abstract

Inflammatory bowel disease (IBD) is an umbrella term for Crohn’s disease (CD) and ulcerative colitis (UC). In light of evolving epidemiology of CD, its clinical management is still complex and remains a challenge for contemporary physicians. With the advent of new diagnostic and treatment paradigms, there is a growing need for new biomarkers to guide decision-making, differential diagnosis, disease activity monitoring, as well as prognosis. However, both clinical and endoscopic scoring systems, widely utilized for disease monitoring and prognosis, have drawbacks and limitations. In recent years, biochemical peptides have become available for IBD monitoring and more frequently used as surrogate markers of gut inflammation. Emerging concepts that revolve around molecular, stem cell, epigenetic, microbial or metabolomic pathways associated with vascular and epithelial gut barrier could lead to development of new CD biomarkers. Measurement of cell-derived microvesicles (MVs) in the blood of IBD patients is another emerging concept helpful in future disease management. In this review, we discuss novel concepts of non-invasive biomarkers, which may become useful in monitoring of CD activity and prognosis. We discuss metabolomics as a new powerful tool for clinicians to guide differential IBD diagnosis. In the coming years, new developments of prognostic tools are expected, aiming for breakthroughs in the management of patients with CD.

Keywords

Crohn’s disease inflammatory bowel disease microbiota gut barrier mycobiota stem cells biomarkers disease monitoring microbiome intestinal permeability

Introduction

A number of different tests may be required to diagnose Crohn’s disease (CD). Currently endoscopy-based evaluation is the most important diagnostic tool. With an increasing number of patients with clinical symptoms mimicking CD, the detailed diagnostic evaluation is critical to proper management and prognosis in patient follow up. The diagnosis of CD still relies on clinical experience and diagnostic tools such as microbiological and biochemical testing. Advanced gastrointestinal imaging, that is, computed tomography (CT) and magnetic resonance (MRI) are also invaluable diagnostic tools. In the years to come, we envisage a single surrogate biomarker as impossible to replace endoscopic mucosal assessment in the diagnosis of CD.

In contrast, the new biomarkers could be utilized in CD monitoring and could guide physicians in differential diagnosis of inflammatory bowel disease (IBD). In this review, we focus on emerging biomarkers that may become useful in the differential diagnosis of IBD and disease monitoring. The genetic and serologic immune markers currently lack clinical accuracy, and their detailed description is beyond the scope of this review, as has been discussed elsewhere.¹ Novel diagnostic research tools, for example, metabolomics, are also briefly discussed.

Traditional management of CD has been closely related to monitoring of clinical symptoms [e.g. using the Crohn’s Disease Activity Index (CDAI), the Harvey-Bradshaw Index (HBI) or the Inflammatory Bowel Disease Questionnaire (IBDQ)], supplemented by endoscopic assessment tools [e.g. the Crohn’s Disease Endoscopic Index of Severity (CDEIS), the Simple Endoscopic Score for Crohn’s Disease (SES-CD) or the Rutgeerts Score (RS)] for postoperative recurrence to assess deep mucosal healing, and the recently developed Lehman’s score. However, these disease-activity-monitoring tools have several drawbacks and limitations. For instance, clinical scores are mostly subjective, and symptoms of irritable bowel syndrome (IBS) may confound the report of IBD patients without active bowel inflammation. Furthermore, endoscopic scores are poorly reproducible, highly dependent on the endoscopist’s experience and are of course based on invasive procedures. Therefore, all of the visual scoring systems available in clinical practice so far have limitations.²

Recently, biochemical markers (e.g. calprotectin, lactoferrin) have become widely available, thus allowing for better objective monitoring of intestinal inflammation.³ Although the aforementioned modalities are widely utilized in various combinations for disease prognosis, they cover only the tip of the iceberg of prognostic potential (Figure 1). With the advent of novel ‘–omics’ non-invasive technologies, clinicians await their practical validation and relevant correlations. Certainly, all these novel modalities should allow us to immerse in the unexplored waters around the bottom of the iceberg of ‘deep remission’. However, the boundaries of this relatively new term⁴ are not known. New definitions revolve around terms such as ‘molecular’, ‘epigenetic’, ‘microbial’ or ‘metabolomic mucosal healing’, to name a few.

Figure 1.

Current and emerging concepts in inflammatory bowel disease management.

The emerging field of microbiota research opens up new avenues for novel biomarker development in CD. Moreover, current research could fulfill this unmet need in CD management. Microbiota-based biomarkers may become useful in the differential diagnosis, as well as in monitoring and prognostication of CD. However, the field is still in its infancy and in need of continuous development from a clinical point of view.

Microbiota as a source of putative biomarkers in Crohn’s Disease

The human intestine is colonized by multiple microorganisms including bacteria, archaea, viruses, and eukaryotes; namely, gut microbiota.⁵ This microecological niche is dominated by the Firmicutes and Bacteroidetes phyla, followed by Proteobacteria and Actinobacteria and is responsible for multiple processes within the human body, such as decomposing undigested food particles to produce energy for colonocytes, synthesizing vitamins and amino acids, and increasing the bioavailability of the mineral components and lipid digestion.^6–8

Most importantly, microorganisms participate in the rapid elimination of antigens present in the intestinal lumen. Mucin synthesis protects endothelium from pathogens and toxin invasion, consequently preventing their translocation into the bloodstream and the development of systemic inflammation. By means of competitive inhibition and in the presence of antimicrobial metabolic products (bacteriocins, hydrogen ions), microbiota limits the possibility of gut colonization by pathogens.⁹ This process is done on a molecular level, by attaching pathogen-associated molecular patterns (PAMPs) to TLRs (Toll-like receptors), nucleotide-binding oligomerization domain-2 (NOD2) and Rig-I-like receptors (RLRs).¹⁰

Proper mechanisms of interaction between microbiota and gut-associated lymphoid tissue (GALT) affect tolerance to commensal bacteria and food antigens.¹¹ Since the role of innate immunity in CD pathogenesis has already been established,^12,13 it seems that the disease is propagated by a dysregulated response to the symbiotic microbiota and consequently defect in intestinal barrier integrity.¹⁴ As a reliable predictor of the disease is still lacking, it seems that microbiota-associated biomarkers being involved in the onset of inflammation and dysbiosis that is followed by relapse may be a crucial diagnostic and therapeutic target.

The clinical relevance of microbial biodiversity in Crohn’s disease

Intestinal microbial imbalance and a reduction in bacterial biodiversity, referred to as dysbiosis, has been well documented in CD.^15–18 In a pioneering study by Swidsinski and colleagues,¹⁹ the abundance of mucosal microbiota in IBD patients was found to be positively correlated with its clinical course. The expression of numerous genes were lowered in the faecal samples of IBD patients compared with healthy volunteers.²⁰ By means of culture-independent molecular techniques, it was elegantly shown that bacterial α-diversity in CD patients was lowered, and abundance of several other groups of microorganisms elevated in comparison with healthy controls (HC)^21–23 and other clinical conditions; however, the results of different studies are conflicting and may be due to the small number of cases.

Importantly, Faecalibacterium prausnitzii has been associated with an increased risk of postresection recurrence of ileal CD.²⁴ Moreover, Pascal and colleagues²⁵ discovered that other butyrate producers, that is, Christensenellaceae, Methanobrevibacter and Oscillospira were decreased in CD. Similar observations were made by Takahashi and colleagues;²⁶ the researchers found that Blautia faecis, Roseburia inulinivorans, Ruminococcus torques, Clostridium lavalense, Bacteroides uniformis, all butyrate producers, were reduced in patients with CD. He and colleagues²⁷ demonstrated that CD microbiota are clustered in two different metacommunities: (a) an increase in bacterial producers of proinflammatory hexa-acylated lipopolysaccharides; and (b) a reduction in the community able to synthesize short chain fatty acids (SCFA). In another study, the Fusobacterium level was significantly decreased in CD.²⁵ On the other hand, Enterobacteriales, predominantly adherent-invasive Escherichia coli responsible for induction of proinflammatory cytokine [i.e. tumour necrosis factor (TNF)]^25,28 synthesis were found to be increased in CD, with lesions in the ileum,^29,30 as well as Campylobacter concisus preferentially colonizing the gut of patients with CD.^31–33 Similarly, mucolytic bacteria such as Ruminococcus gnavus and Ruminococcus torques were discovered in abundance in CD patients.³⁴ Other studies delivered novel evidence of relative abundance of Faecalibacteria as a potential biomarker with high specificity in CD patients. In one of the most recent systematic reviews, Zhou and colleagues proved that lower levels of Bacteroides in the gut were associated with IBD in comparison with those in remission.³⁵

Lower level of Bacteroides in the gut microbiota is associated with inflammatory bowel disease: a meta-analysis

Recently it was demonstrated that microbial community composition was more dysbiotic at the taxonomic level in CD patients. Six-bacterial profile abundance, that is, Faecalibacterium, Peptostreptococcaceae, Anaerostipes, Christensenel-laceae, Collinsella and Methanobrevibacter were measured and found significantly decreased in CD patients.²⁵ Conversely, Escherichia and Fusobacterium richness were more pronounced when compared with HC and UC patients. Among Firmicutes and Bacteroidetes phyla, butyrate producers Faecalibacterium prausnitzii and Bacteroides fragilis respectively were previously found to be lowered in CD, species with protective effects within the gut microbiota composition.^24,36 Butyrate seems to be critical for the homeostasis within the gut. It serves as an energy source for the host and is involved in lipogenesis, gluconeogenesis, epigenetic processes, as well as suppression of inflammatory mediators. It was found that Faecalibacterium species suppressed experimental colitis via lowering nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) activation and inflammatory cytokines synthesis and by stimulating interleukin IL10 production.²⁴

Overall, fewer bacteria with anti-inflammatory properties and more bacteria with proinflammatory properties compared with healthy subjects have been identified.^30,37,38 Members of the Bacteroidetes and Firmicutes phyla were found to be reduced in CD; conversely, abundance of Enterobacteria, mostly Escherichia coli, was observed. Prosberg and colleagues,³⁹ in their systematic review and meta-analysis (5 studies; 231 patients), found lower abundance of Clostridium leptum, Faecalibacterium prausnitzii, and Bifidobacterium in patients with active CD. Zhou and Zhi,³⁵ in their meta-analysis, included 346 patients with CD, and revealed that level of Bacteroides in patients with active CD was lower than in the HC group. Bacteroides abundance was also fewer in CD patients in the remission phase than in the control group, as well as in the active phase of disease than in remission. However, obtained data were heterogenic due to different analytical methods (real-time quantitative polymerase chain reaction, fluorescence in situ hybridization, conventional culture), small sample size and ethnic differences.

Mycobiota as a potential source for novel non-invasive biomarkers in Crohn’s disease

Apart from bacterial imbalance, mycobiota diversity was found altered in CD. It was proposed that the microenvironment of CD is favourably enriched by fungi rather than bacteria. Namely, the Basidiomycota:Ascomycota ratio and the Candida albicans count were found to be increased, while Saccharomyces cerevisiae abundance decreased.^18,40,41 Other species’ numbers found elevated in CD included Gibberella moniliformis, Alternaria brassicicola and Cryptococcus neoformans. It is of interest that fungal microbiota correlated with the CD activity index and the degree of inflammation expressed by C-reactive protein (CRP) concentration.⁴²

As dysbiotic therapy was found to be effective toward the bacterial component, mycobiota abundance was expanded, highlighting that fungal composition could be further researched as a causative agent.⁴³ Importantly, from a mechanistic point of view, the antifungal inflammatory response is known to be under the control of multiple IBD risk genes.⁴¹ Moreover, ileal mucosa samples and gut lavages from CD paediatric patients were found to be enriched in Caudovirales, negatively correlated with bacterial diversity,^44,45 proving that the virome of CD should be considered when searching for a microbiota-associated biomarker.

The differential diagnosis of Crohn’s disease: the role of metabolomics

Metabolomics is the systematic study of the unique chemical fingerprints that specific cellular processes leave behind, the study of their small molecule metabolic profiles. It can give an instantaneous snapshot of the metabolic state of a cell or an organism. It uses specific technology to capture the metabolic processes. Widely used are nuclear magnetic resonance spectroscopy (NMR-S) gas chromatography–mass spectrometry (GC-MS) and liquid chromatography–mass spectrometry (LC-MS).

In CD, there have been a number of studies using these analytical techniques to identify metabolic fingerprints that could potentially be used as biomarkers to either diagnose CD or monitor disease activity. As with humans, it is not practical to study processes either on a cellular level or in vivo on the whole body. Different biological media have been studied and the results have been extrapolated to assess metabolic functions at a cellular level. Media studied include serum and plasma, urine, faecal extract and breath.⁴⁶ We will look into those four media in more detail.

Multiple clinical biomarkers of CD status have been studied so far, some of them commercially available. However, the most prevalent remain serum CRP and faecal calprotectin (FCP) concentrations.⁴⁷ Although a number of studies aimed to assess the utility of these biomarkers and to evaluate the correlation with endoscopic scores, relapse and postoperative recurrence prediction, their main value is in managing patients with CD, as reported by Mosli and colleagues.⁴⁸ Therefore, looking for a novel, accurate biomarker is a research priority.

A recent study showed that a serum profile including lipoproteins especially high-density lipoprotein cholesterol, choline, N-acetylglycoprotein and amino acids could differentiate between CD and UC but also between IBD and HC.⁴⁹ Another study showed that a plasma amino acid profile including histidine and tryptophan could differentiate CD patients from HC.⁵⁰ Furthermore, a study using GC-MS was able to separate CD from UC and controls. Metabolites included angiotensin IV, diphthamide gangliosides and combined kynurenine metabolites.⁵¹ Finally, a small study using NMR-S showed a different lipidomic profile in CD patients compared with HC.⁵² A study by Mortensten and colleagues⁵³ delivered evidence that serum extracellular matrix (ECM) components, namely degraded biglycan and citrullinated and matrix metalloprotease degraded vimentin (VICM) could serve as a biomarkers differentiating CD from UC. Also, patients with CD who are positive for anti-flagellin IgG antibodies: anti-CBir1, anti-A4-Fla2, anti-Fla-X and anti-outer-membrane porin C antibody (anti-OmpC IgA) at baseline (perioperatively), all serological biomarkers directed against gut microbial antigens, were found to be at high risk of disease recurrence at 18 months in comparison with those negative for these markers.⁵⁴ As far as serum antibodies are concerned, antiglycan, antiglycoprotein 2 (anti-GP2) antigranulocyte-macrophage-colony-stimulating factor (anti-GM-CSF) antibodies in IBD attracted attention, as all these biomarkers were found to be associated with CD pathogenesis and linked to complicated phenotypes of the disease.⁵⁵ Also, as CD genetic background was established, small noncoding ribonucleic acids (miRNA), responsible for gene expression regulation and previously found to be associated with the immune disorder pathogenesis,⁵⁶ serum mi-R223 expression was shown as elevated in CD compared with HC and positively correlated to the disease activity [CDAI; erythrocyte sedimentation rate (ESR); simple endoscopic score for CD (SES-CD)].⁵⁷ Other markers, for instance serum platelet factor 4, are promising and reliable as biomarkers for IBD.⁵⁸

Investigators of studies using urine were able to differentiate between CD and UC, and HCs. Levels of hippurate are found consistently low in CD patients.^59–61 The study by Alonso and colleagues⁵⁹ also demonstrated low levels of citrate, hydroxyisovalerate and dimethylglycine. A recent larger study which combined different IBD phenotypes showed statistically significant lower levels of acyl carnitine 4-α-hydroxyphenyl pyruvate in patients with CD phenotype compared with UC phenotype.⁶²

Two recent studies have used faecal extracts from patients with CD and produced some interesting results. One study showed significant differences in patients with CD compared with UC in aspartic acid and glutamate concentrations; branch chain amino acids lysine, alanine, phenylalanine and butyrate were also different when CD patients and controls were compared.⁶³ The other examined IBD patients and their families and showed that siblings of IBD patients can have a different metabotype and different bowel microbial species to healthy controls or IBD patients.⁶⁴ Other faecal IBD biomarkers, including S100A12 (calgranulin), high-mobility group box 1, neopterin, polymorphonuclear neutrophil elastase, human neutrophil peptides, neutrophil gelatinase-associated lipocalin, chitinase 3-like-1 and others are discussed in detail elsewhere.⁶⁵

Some studies have used more than one biofluid. Studies using both serum and urine were able to discriminate between CD and HCs but less so between CD and UC. Metabolites of interest included isoleucine, acetoacetate, hippurate, taurine, succinate, glycine, alanine and formate.^66,67 One study using terminal ileal (TI) biopsies and macrophages from affected individuals found differences in the lipidomic profile between CD patients and HCs.⁶⁸

So far, all studies conducted showed promising results but most of them were individual efforts that looked at a specific metabolic activity. Coordinated studies looking at the most promising data and building on them should be the next step.

Gut barrier and intestinal permeability: novel targets for Crohn’s disease monitoring?

Alterations in structure and function of the gut barrier play a significant role in the pathogenesis of IBD. Kiesslich and colleagues⁶⁹ in their elegant study utilizing confocal endomicroscopy documented how cell shedding and barrier loss predicted the relapse of IBD, and had the potential to serve as a diagnostic tool for the management of the disease. Chang and colleagues⁷⁰ observed how IBD patients frequently suffer from ongoing bowel symptoms of diarrhoea and abdominal pain despite mucosal healing and investigated whether impaired intestinal permeability contributed to these symptoms. The authors found that increased gut permeability correlated with increased severity of bowel symptoms beyond mucosal healing and drew the conclusion that resolution of mucosal permeability might improve outcomes of patients with IBD.⁷⁰ It is worth noting that tests measuring intestinal permeability have long been used in medical practice^71,72 (Table 1), however their clinical applicability was rather low. Endoscopic techniques, while yielding promising results, are invasive, timely, expensive and require experienced endoscopists. Microbiome research presents new views on the role of microbiota in shaping gut barrier; in parallel, new solutions for novel biomarkers emerge.

Table 1.

Approaches for measuring intestinal permeability.

Approach type	Test name	Specificity to location	Sample	Notes
Functional	Ussing chamber	Site specific	Biopsy	Invasive, ex vivo test
	Lactulose/mannitol	Small bowel	Urine	Time consuming
	Sucrose/glucose^*	Stomach	Urine	Time consuming
	Sucralose^*	Colon	Urine	Time consuming
	PEG 4000/400	Whole gut	Urine	Time consuming
	⁵¹Cr-EDTA	Whole gut	Urine	Radioactive
Bacteria related	LAL-assay	Whole gut	Plasma
	EndoCAb	Whole gut	Serum	Acute-phase specificity
Inflammation-related	Calprotectin	Whole gut	Faeces	Unspecificity
	α1-anti trypsin	Small bowel	Serum
	sIgA	Whole gut	Serum	Low specificity
	zonulin	Colon	Faeces
Epithelial damage	Citrulline	Small bowel	Plasma
	I-FABP	Site specific	Plasma	Acute-phase specificity
Histological biomarkers	Tight junction expression^**	Site specific	Biopsy	Invasive, in vivo test
	Defensins expression^**	Site specific	Biopsy	Invasive, in vivo test
	Loss of Paneth cells	Site specific	Biopsy	Invasive, in vivo test
	Shedding of epithelium	Site specific	Biopsy	Invasive, in vivo test

In combination with lactulose/mannitol test; ^**mRNA and protein level.

PEG, polyethylene glycol; 51Cr-EDTA, chromium labelled ethylenediaminetetraacetic acid; LAL, lymulus amebocyte lysate assay; EndoCAb, endogenous endotoxin-core antibody; sIgA, secretory immunoglobulin A; I-FABP, intestinal fatty-acid-binding protein; mRNA, messenger ribonucleic acid.

Dysbiosis is known to induce changes in intestinal barrier permeability.⁷³ Intestinal barrier is the physical structure present in the intestinal tract (Figure 2). The most important element of the barrier is the epithelium, primarily made up of enterocytes (80%) responsible for nutrient absorption and stimulating immune activity by secretion of cytokines and expression of immune receptors in the cell membrane. Integrity of the intestinal barrier is provided predominantly by close interlinking between intestinal epithelial cells (IECs), namely tight junctions (TJs). These are protein complexes composed of claudins, occludins, junctional adhesion molecules (JAMs) and tricellulins, which contact the cytosol with Zonula occludens (ZO) proteins, being conjugated to the cytoskeleton of the IECs. As a result of the phosphorylation of myosin light chains actin contraction occurs which relaxes the structure of the TJs and allows the luminal content to be transported paracellularly. Structural and functional homoeostasis of this structure limits the passage of pathogenic microorganisms and other harmful antigens to the blood.⁷⁴

Figure 2.

Gut-related biomarkers in inflammatory bowel disease.

Elevated intestinal permeability was established as well in quiescent IBD as first-degree relatives of CD patients.^75–82 Transepithelial electrical resistance was altered in mild and moderately active CD.⁸³ Other studies proved that increased small bowel permeability to sugar molecules or ⁵¹Cr-EDTA.⁷⁵ Moreover, studies state that in CD patients, hyperresponsiveness toward dysbiotic agents such as nonsteroidal anti-inflammatory drugs (NSAIDs) occurs as it was demonstrated that intestinal permeability is elevated even in patients with non-inflamed mucosa^84,85 that in turn may proceed to relapse for small intestinal CD⁸⁶ in humans and intestinal inflammation in animals.⁸⁷

Of note, CD patients and their relatives excrete more FCP, positively correlated with endoscopic activity and neutrophil migration towards the intestine^88,89 in comparison with HC,⁹⁰ although this biomarker is not specific to IBD. A widely studied inflammation-related biomarker called zonulin was found to be elevated in both faeces and serum during the active CD phase, but not in UC.⁹¹ Another barrier-integrity-specific molecule is Rho-A, which was found to be downregulated in IBD⁹² and Rho-associated kinase upregulated in inflamed mucosa of CD patients.⁹³ It was proved that these alterations are key mediators of chronic inflammation, cytoskeleton rearrangement and skewed cell shedding.

Since TJs are thought to be critical for intestinal barrier integrity, it was shown that in CD patients, TJs form particle-type structures with no continuity, and in the active stage of disease, the expression of claudin 3, 5, 8 and occludin was found to be decreased.^94–96 Conversely, claudin-2 abundance was proved to be increased during inflammation that in turn may lead to leak flux diarrhoea. In parallel to claudin-2 overexpression and decreased production of occludin, increased synthesis of proinflammatory molecules may initiate immune response or maintain inflammation within the intestinal wall.⁹⁷ The new CD biomarkers associated with gut barrier alterations are listed in Table 2.

Table 2.

Gut-related biomarkers in Crohn’s disease.

Biomarker	Relevance	Reference
Microbiota-related biomarkers
Adherent-invasive Escherichia coli (AIEC)	A greater pathogenic effect of AIEC (elevated TNF-α production linked to granuloma formation and lower expression of miRNA, thus decreased autophagia) typically found in chronic lesions in intestine and always present in early postoperative-recurrence lesions	Bosca-Watts et al.;⁹⁸ Barnich and Darfeuille-Michaud;⁹⁹ Nguyen et al.¹⁰⁰
Faecalibacterium sp.	The abundance is decreased in patients with CD and may predict postresection relapse; the bacteria count was found to be reduced in patients with active CD in comparison with the disease in remission	Sokol et al.;²⁴ Pascal et al.;²⁵ Prosberg et al.³⁹
Enterococcus faecalis	Decreased abundance related to clinically active CD; more richness in stool associated with ileal rather than ileocolonic CD	Pascal et al.;²⁵ Zhou et al.¹⁰¹
Bacteroides sp.	CD microbial ecosystem was found to be significantly lowered in Bacteroides sp., both in active and remission patients in comparison with HCs; the abundance was even lower in remission patients as compared with HCs and active phase of the disease	Zhou and Zhi³⁵
Clostridium leptum	Lower abundance of the species in patients with active CD in comparison with remission phase was found	Prosberg et al.³⁹
Streptococcus sp.	Percentage of the species positively correlated with the postoperative recurrence development compared with patients who stayed in remission	Pascal et al.²⁵
Anaerostipes sp.	The microbiota of CD patients is almost absent in these species when compared with HCs and UC	Pascal et al.²⁵
Methanobrevibacter sp.	Almost no abundance in CD in comparison with HCs and UC	Pascal et al.²⁵
Collinsella sp.	High abundance in CD in comparison with almost absent in HCs and UC	Pascal et al.²⁵
Fusobacterium sp.	High percentage found typically in UC, not in CD	Pascal et al.²⁵
Basidiomycota/Ascomycota ratio	The ratio was high in active CD and normal in remission	Sokol et al.¹⁸
Saccharomyces cerevisiae	Antibodies against Saccharomyces cerevisiae mannan detected in CD patients; abundance of Saccharomyces cerevisiae decreased in CD	Sokol et al.;¹⁸ Main et al.¹⁰²
Candida albicans	The abundance significantly increased in CD flare compared with disease in remission	Sokol et al.¹⁸
Short chain fatty acids (SCFAs)	CD bacterial dysbiosis reduces the community (Bifidobacterium species, Faecalibacterium prausnitzii, Alistipes shahii, and Roseburia species) able to produce SCFAs	He et al.²⁷
Gut barrier-related biomarkers
Lipopolysaccharide (LPS)	Even sixfold increase in serum LPS concentration in CD; the concentration positively correlated with disease activity	Magro et al.¹⁰³
Alpha-1-antitripsin (A-1AT)	A faecal biomarker associated with clinical relapse in patients with CD of the distal ileum; replaced with CP	Biancone et al.¹⁰⁴
Calprotectin (CP)	Positively correlated with endoscopic activity and neutrophil migration towards the intestine	Burri and Beglinger;⁸⁸ Kopylov et al.;¹⁰⁵ Egea et al.;¹⁰⁶ Sipponen et al.;¹⁰⁷ Bar-Gil Shitrit et al.¹⁰⁸
Zonulin	Faecal and serum concentration positively correlated with activity of the disease	Malíčková et al.⁹¹
Intestinal fatty acid binding protein (I-FABP)	Serum I-FABP concentration is increased parallel to the CD activity index	Sarikaya et al.¹⁰⁹
Claudins	Claudin 3, 5, 8 and 2 expression was found to be decreased and increased respectively in the active CD stage	Zeissig et al.⁹⁴
Occludin	Decreased expression during active phase of CD	Al-Sadi et al.;⁹⁵ Buschmann et al.⁹⁶
Other biomarkers
Serum
Cathelidicin (LL37)	Inverse correlation to clinical CD activity	Tran et al.¹¹⁰
CD26 (dipeptidyl peptidase IV)	Serum CD26 level lowered in both active and inactive CD when compared to controls	Magro et al.¹⁰³
Faeces
B cell-activating factor (BAFF)	Positively correlated with endoscopic inflammation in CD patients	Fu et al.¹¹¹
Lactoferrin	Negatively correlated with CD severity; paediatric CD patients with positive result of faecal occult blood test had higher concentrations of lactoferrin than the individuals with negative result of this test; however, available data show conflicting results	Sipponen et al.;¹⁰⁷ Boon et al.;¹¹² Borkowska et al.;¹¹³ Sidhu et al.¹¹⁴

CD, Crohn’s disease; HC, healthy control; TNF-α, tumour necrosis factor-alpha; UC, ulcerative colitis.

Measuring the unmeasurable: dysbiosis as a target in Crohn’s disease monitoring?

There is mounting evidence that microbiota composition in CD is altered, although the dysbiosis may be both causative and a consequence of inflammation. In paediatric cohorts,^15,41,43 the researchers found stool and mucosa dysbiosis in newly diagnosed and nontreated children, proving that microbial imbalance reflects the ongoing inflammation but may be triggered by certain environmental factors. Of note, there is also a body of evidence that microbial signature may be clinically relevant in management of CD (Table 3). On the other hand in cross-sectional studies, microbial composition differed even between IBD twins, suggesting that certain dysbiosis may be instead associated with the disease phase.^21,115 Of note, inflammation being an oxidative state induces the synthesis of particular electron acceptors for facultative anaerobes, promoting the enrichment of gut niche in pathobionts.¹¹⁶ Consequently, dysbiosis leads to an altered metabolic profile. Morgan and colleagues¹¹⁷ found that many more metabolic pathways were different between IBD and HCs than genetic clades, proving that functional alterations should be of particular interest in dysbiotic studies. It is notably important as different metabolite syntheses might induce host IBD risk factors, as seen in bile acid signalling studies^118–120 or lowered short chain fatty acids involved in immune tolerance, thus inflammation development.¹²¹ In conclusion, multiple studies highlighting certain microbiota alteration as pathogenetic factors should be taken with caution, as little prospective data exist. Different ‘-omic’ approaches may serve as a development area within mucosal homeostasis and inflammation, although not widely used in clinical practice.

Table 3.

Microbial biomarkers and their clinical relevance in management of Crohn’s disease.

Microbial biomarker	Clinical relevance	Reference
Faecalibacterium prausnitzii, Clostridium coccoides	Reduced abundance in postoperative endoscopic recurrence	Sokol et al.²⁴
F. prausnitzii, C. coccoides, Clostridium leptum, Bacteroides sp.	Reduced abundance as a predictor of endoscopic recurrence following infliximab withdrawal	Rajca et al.¹²²
F. prausnitzii, Nitrosomonas sp., Bifidobacterium sp., Desulfotomaculum thermobenzoicum, Ruminococcus flavefaciens, Desulvibrio vulgaris	Greater abundance in patients experiencing remission after surgery	de Cruz et al.¹²³
Enterococcus faecalis, unknown species of Erysipelotrichaceae	Greater abundance in patients with CD disease localised in the ileum than in the ileocolon	Pascal et al.²⁵
Bacteroides sp. (Bacteroides plebeius), Dorea sp. (Dorea longicatena), Ruminococcus sp., Dialister sp.	Increased abundance in postoperative remission patients	Mondot et al.¹²⁴
Gemmiger formicilis, Enterococcus durans, Ruminococcus lactaris	Increased abundance in postoperative recurrence patients	Mondot et al.¹²⁴
Desulvibrio longus, Streptococcus pneumoniae	Greater abundance in patients with postoperative recurrence	de Cruz et al.¹²³
Lachnospiraceae, Erysipelotrichaceae, unidentified genus within Clostridia, all members of the phylum Firmicutes	Reduced abundance in postoperative endoscopic recurrence	Dey et al.¹²⁵
Rhodobacteraceae (of class Alphaproteobacteria), an unknown Proteobacteria, Rhizobium sp. (also Alphaproteobacteria)	Greater abundance associated with postoperative recurrence	Dey et al.¹²⁵

Pluripotent progenitor and stem cells as surrogate prognostic markers of mucosal healing and clinical remission in Crohn’s disease

While stem cell therapy in Crohn’s disease has met significant scientific and clinical attention,^126,127 the usefulness of stem cells as biomarkers in IBD has been less studied. Developmentally early cells, including hematopoietic stem progenitor cells (HSPCs), mesenchymal stem cells (MSCs), endothelial progenitor cells (EPCs), and very small embryonic-like stem cells (VSELs), are mobilized in peripheral blood (PB) in response to tissue/organ injury.^128,129 The evidence is mounting that cells expressing markers for MSCs, EPCs, and small Oct-4⁺ Nanog⁺ SSEA-4⁺ CXCR4⁺ Lin⁻ CD45⁻ VSELs are mobilized into PB in patients with CD.¹³⁰ The mobilized cells express genes at the messenger RNA (mRNA) level, playing a role in development and regeneration of gastrointestinal epithelium.^131–133 Marlicz and colleagues reported an increase in the number of circulating MSCs, EPCs and small primitive cells expressing the VSEL phenotype in IBD patients with active disease.¹³⁰ The most significant increase was observed for CD105⁺/STRO-1⁺/CD45⁻ cells enriched for MSCs. The number of circulating CD34⁺/KDR⁺/CD31⁺/CD45⁻ EPCs also increased significantly. In subpopulation of cells enriched for VSELs, cells stained positive for CXCR4, CD34, CD133 and negative for lineage markers and CD45 antigen were elevated in PB of patients with CD. Of clinical importance, the highest numbers of VSELs were observed in younger patients with active ileocaecal mucosal lesions in the colon.¹³⁰

Furthermore, the authors observed that hepatocyte growth factor (HGF) and vascular endothelial growth factor (VEGF) correlated positively with advancement of mucosal lesions in the colon.¹³⁴ Active mucosal lesions were associated with higher plasma levels of HGF and VEGF in patients achieving clinical remission. Active CD was associated with strong mRNA upregulation of intestinal early differentiation markers (Lgr-5, ASCL-2, Msl-1, Bml-1, Dclk-1) in circulating PB mononuclear cells. Moreover, higher plasma C5a levels in IBD in comparison with controls were noted. The study also revealed that the number of VSELs mobilized in PB in patients remaining in clinical remission (not longer than 6 weeks since flare up) was significantly increased compared with HC.¹³⁴ The authors observed that the number of CXCR4⁺, Lin⁻, CD45⁻ cells mobilized in PB in patients in clinical remission was associated with active mucosal lesions in the colon. The significance of multifold upregulation of Lgr-5⁺ mRNA (marker of intestinal stem cells) in peripheral bone-marrow-derived mononuclear cells (BMMNCs) of Crohn’s patients with active disease awaits scientific explanation.

Evidence is mounting for endothelial impairment contributing to the onset, progression and recovery from inflammatory injury.^135,136 Of particular interest, EPCs, derived from bone marrow hematopoietic stem cells, have the capability to migrate to the site of endothelial damage through the peripheral circulation.¹³⁷ Boltin and colleagues¹³⁷ studied patients with CD in varying stages of disease activity assessed using the CDAI. Enrolled patients were being treated either with biological therapy (infliximab) or immunomodulators. The evaluation of circulating EPCs employed antibodies to the biomarkers of cluster differentiation (CD34), VEGF receptor-2, CD133, and CD45. Researchers reported a significant increase in the percentage of EPCs of the peripheral mononuclear cells in patients with CD as compared with healthy individuals. Of prognostic significance, the authors did not find the association between EPC percentages and other factors such as age, sex, CDAI, disease duration, duration of biological therapy or habits (e.g. smoking). Perhaps more advanced techniques such as tissue microarrays or RNA sequencing are needed in order to unravel such associations.¹³⁶ The current studies are seeds for the field, where enumeration of stem/progenitor cells in PB could serve as a surrogate parameter in accessing treatment efficacy in IBD. At this point, it is important to note that mobilization and activity of stem and progenitor cells could be influenced by numerous factors, such as drugs (e.g. antibiotics),¹³⁸ proton-pump inhibitors,^139,140 infection,^141,142 physical activity,^143–146 and age.¹⁴⁷

Therefore, various endogenous and environmental factors in patients with CD should be evaluated before assessing any risk factors based on biomarker measures. Moreover, intestinal microbiome could be a source of various molecules interacting with progenitor/stem cells affecting their potency. Conversely, innate immunity mechanisms could be triggered as a response to various microbial communities in the gut, for example, bone marrow expressed antimicrobial cationic-peptide-LL-37-enhanced responsiveness of hematopoietic stem progenitor cells to an SDF-1 gradient and accelerated their engraftment after transplantation.¹⁴⁸ This observation is important in light of the work by Raftery and colleagues¹⁴⁹ who report that short-term treatment with 2000 IU/day vitamin D significantly increased 25 (OH) D levels in CD patients in remission and was associated with increased LL-37 concentrations and maintenance of intestinal permeability (IP) achieving 25(OH)D ⩾ 75 ng/ml. This observation is clinically relevant, as active CD was associated with low serum 25-OH vitamin D and patients who smoked had lower 25-OH vitamin D levels than patients who did not smoke, independently of disease activity.^150,151

Blood-derived microparticles and inflammatory bowel disease

Extracellular microvesicles (ExMVs) are part of the cell secretome. Evidence is mounting that ExMVs are involved in chronic autoimmune diseases, including IBD. Ratajczak and colleagues¹⁵² demonstrated for the first time that ExMVs carry functional RNA species and proteins from one cell to another, an observation that paved up the new road to the new field of research of horizontal transfer of bioactive molecules in cell-to-cell communications.¹⁵³ This observation opened up the gates to novel concepts, in which the presence of mRNA, noncoding RNA, and miRNA in ExMVs in blood and other biological fluids gave the possibility of employing ExMVs as new biomarkers for disease conditions. Since then, ExMVs became a target for ‘liquid biopsy’ approaches. Tziatzios and colleagues found that circulating levels of platelet-derived microparticles (PDMPs) were increased in CD patients but did not correlate with disease activity. 5-ASA treatment was associated with lower levels of PDMPs, while anti-TNF-α treatment did not influence expression of ExMVs in IBD patients.¹⁵⁴ Similarly, circulating PDMPs and their counterparts in particular annexin (−) PDMPs were increased in IBD patients with active disease. Annexin (+)/(−) ratio proved to be the most reliable distinctive PDMP index between healthy individuals and IBD patients.¹⁵⁵ Of interest, Leonetti and colleagues documented that ExMVs from CD patients altered endothelial and vascular function. The authors concluded that ExMVs may play a role in CD pathophysiology and vascular-dependent intestinal damage.¹⁵⁶ Of clinical significance, our team observed that CD133⁺ cells and CD133⁺ cell-derived MVs expressed mRNAs for several antiapoptotic and proangiogenic factors, including tyrosine-protein kinase receptor (Kit) ligand, insulin growth factor-1, vascular endothelial growth factor, basic fibroblast growth factor, and interleukin-8.

More importantly, the CD133⁺ cell-derived MVs chemoattracted endothelial cells and displayed proangiogenic activity in laboratory assays.¹⁵⁷ Further Ratajczak and colleagues presented the evidence that telocytes mediate several of their biological effects in various organs by releasing ExMVs enriched in mRNA, miRNA, proteins, and several biological mediators to the target cells.¹⁵² Interestingly, Milia and colleagues delivered the evidence that in CD, the loss of telocytes might have important pathophysiological implications contributing to the architectural derangement of the intestinal wall and gut dysmotility.¹⁵⁸ Despite promising data, the field of ExMVs awaits clinical validation and practical application in the IBD clinical setting.

Targeting gut-liver axis to chase for new Crohn’s disease biomarkers

Aside the aforementioned microbial or stem-cell-related markers available for future clinical application in CD, at least two other subjects deserve discussion – the topics of incidence and prevalence of nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) among patients with IBD.¹⁵⁹ Younossi and colleagues,¹⁶⁰ in their meta-analysis (MA) that included more than eight billon individuals, found that one quarter of the adult world population might have been diagnosed with NAFLD/NASH. Of importance, gut–liver axis alterations have been implicated in the pathogenesis of NAFLD¹⁶¹ and assessment of NASH severity could serve as a marker of intestinal inflammation.¹⁶²

Reported risk factors of NASH in IBD include past small bowel surgery, obesity, use of steroids, and active disease with long duration. Moreover, a ‘trend to significance’ was found in this MA for anti-TNF-α medications as a risk factor for NAFLD and NASH.¹⁵⁹ However, the analysed data were biased and no clear conclusions could have been reached. The hypothesis of whether measuring the severity of NASH, either by means of invasive techniques (e.g. liver biopsy) or non-invasive techniques (e.g. fibroscan) could give us guidance towards severity of IBD remains to be tested.

Conclusion

New discoveries in the field of microbial and stem-cell-based biomarkers could bring new solutions to the management of patients with IBD.

Future studies could utilize small bowel endoscopic images (e.g. with capsule endoscopy) complemented by microbiological or cytologic fluid sampling of altered small bowel mucosa and further correlated with IBD progression.^69,163–165 In vivo molecular imaging of gut mucosa in IBD has prognostic potential as a personalized diagnostic tool.¹⁶⁶ Developing a simple wireless endoscopic capsule, capable of gathering confocal endomicroscopic images and sampling the intestinal fluid is not far away from realization. In fact, the intestinal gas capsule has entered the phase of human experimentation and results are awaited.¹⁶⁷ Similarly, volatile organic compounds in breath have been studied for some time now in patients with CD. None looked specifically at CD patients but rather looked at IBD as a cohort. The authors of two studies found significant differences in pentane, ethane and propane,^168,169 and of two others, claimed a unique breath fingerprint in patients with IBD.^170,171

With the advent of novel ‘-omic’ technologies, the development of new sensitive and specific biomarkers to monitor IBD is within the reach of scientists and clinicians. Despite the vast area of available data on IBD biomarkers, the ideas presented in this review offer new avenues for novel research and clinical trials in CD patients. As it is probably unlikely that a single biomarker will reliably monitor the disease, we envisage that contemporary clinicians enriched with an armamentarium of novel diagnostic and prognostic tools, would still need to rely on their experience to measure the faith of the disease. Extensive work in the field is expected to bring these new tools into everyday medical practice. Currently, it is impossible to predict their accuracy, cost and ease of use. Future clinical trials with biomarkers should compare them with hard endpoints such as surgery, hospitalization, disease complication or endoscopic deep mucosal remission. Currently, lack of these comparisons in most of putative biomarkers’ data is a general drawback of the field.

Footnotes

Funding

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

Conflict of interest statement

The authors declare that there is no conflict of interest.

ORCID iD

Wojciech Marlicz

References

Torres

Caprioli

Katsanos

et al . Predicting outcomes to optimize disease management in inflammatory bowel diseases. J Crohns Colitis 2016; 10: 1385–1394.

Rogler

Vavricka

Schoepfer

, et al. Mucosal healing and deep remission: what does it mean? World J Gastroenterol 2013; 19: 7552–7760.

Moniuszko

Gluszek

Rydzewska

Rapid fecal calprotectin test for prediction of mucosal inflammation in ulcerative colitis and Crohn disease: a prospective cohort study. Pol Arch Intern Med 2017; 127: 312–318.

Korelitz

BI.

Mucosal healing as an index of colitis activity: back to histological healing for future indices. Inflamm Bowel Dis 2010; 16: 1628–1630.

Koppel

Balskus

EP.

Exploring and understanding the biochemical diversity of the human microbiota. Cell Chem Biol 2016; 23: 18–30.

Sender

Fuchs

Milo

Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 2016; 14: e1002533.

Lynch

Pedersen

The human intestinal microbiome in health and disease. NEJM 2016; 375: 2369–2379.

Konturek

Haziri

Brzozowski

et al . Emerging role of fecal microbiota therapy in the treatment of gastrointestinal and extra-gastrointestinal diseases. J Physiol Pharmacol 2015; 66: 483–491.

Kim

Covington

Pamer

EG.

The intestinal microbiota: antibiotics, colonization resistance, and enteric pathogens. Immunol Rev 2017; 279: 90–105.

10.

Duerkop

Vaishnava

Hooper

LV.

Immune responses to the microbiota at the intestinal mucosal surface. Immunity 2009; 31: 368–376.

11.

Purchiaroni

Tortora

Gabrielli

et al . The role of intestinal microbiota and the immune system. Eur Rev Med Pharmacol Sci 2013; 17: 323–333.

12.

Hugot

J-P

Chamaillard

Zouali

et al . Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn’s disease. Nature 2001; 411: 599–603.

13.

Ogura

Bonen

Inohara

et al . A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature 2001; 411: 603–606.

14.

Øyri

Műzes

Sipos

Dysbiotic gut microbiome: a key element of Crohn’s disease. Comp Immunol Microbiol Infect Dis 2015; 43: 36–49.

15.

Gevers

Kugathasan

Denson

et al . The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 2014; 15: 382–392.

16.

Manichanh

Rigottier-Gois

Bonnaud

et al . Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 2006; 55: 205–211.

17.

Ott

Musfeldt

Wenderoth

et al . Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 2004; 53: 685–693.

18.

Sokol

Leducq

Aschard

et al . Fungal microbiota dysbiosis in IBD. Gut 2016; 1039–1048.

19.

Swidsinski

Ladhoff

Pernthaler

et al . Mucosal flora in inflammatory bowel disease. Gastroenterology 2002; 122: 44–54.

20.

Qin

Raes

et al . A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59–65.

21.

Joossens

Huys

Cnockaert

et al . Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives. Gut 2011; 60: 631–637.

22.

Varela

Manichanh

Gallart

et al . Colonisation by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis. Aliment Pharmacol Ther 2013; 38: 151–161.

23.

Wright

Kamm

Teo

et al . Recent advances in characterizing the gastrointestinal microbiome in Crohn’s disease: a systematic review. Inflamm Bowel Dis 2015; 21: 1219.

24.

Sokol

Pigneur

Watterlot

et al . Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. PNAS 2008; 105: 16731–16736.

25.

Pascal

Pozuelo

Borruel

et al . A microbial signature for Crohn’s disease. Gut 2017; 66: 813–822.

26.

Takahashi

Nishida

Fujimoto

et al . Reduced abundance of butyrate-producing bacteria species in the fecal microbial community in Crohn’s disease. Digestion 2016; 93: 59–65.

27.

Gao

Jie

et al . Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients. GigaScience 2017; 6: 1–11.

28.

Boudeau

Glasser

A-L

Masseret

et al . Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn’s disease. Infect Immun 1999; 67: 4499–4509.

29.

Darfeuille-Michaud

Neut

Barnich

et al . Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn’s disease. Gastroenterology 1998; 115: 1405–1413.

30.

Darfeuille-Michaud

Boudeau

Bulois

et al . High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology 2004; 127: 412–421.

31.

Man

Zhang

Day

et al . Campylobacter concisus and other Campylobacter species in children with newly diagnosed Crohn’s disease. Inflamm Bowel Dis 2010; 16: 1008–1016.

32.

Zhang

Man

Day

et al . Detection and isolation of Campylobacter species other than C. jejuni from children with Crohn’s disease. J Clin Microbiol 2009; 47: 453–455.

33.

Mukhopadhya

Hansen

El-Omar

et al . IBD-what role do Proteobacteria play? Nat Rev Gastroenterol Hepatol 2012; 9: 219–230.

34.

Png

Lindén

Gilshenan

et al . Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol 2010; 105: 2420–2428.

35.

Zhou

Zhi

Lower level of bacteroides in the gut microbiota is associated with inflammatory bowel disease: a meta-analysis. Biomed Res Int 2016; 2016: 5828959.

36.

Mazmanian

Round

Kasper

DL.

A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 2008; 453: 620–625.

37.

Sokol

Seksik

Furet

et al . Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 2009; 15: 1183–1189.

38.

Sokol

Seksik

Rigottier-Gois

et al . Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm Bowel Dis 2006; 12: 106–111.

39.

Prosberg

Bendtsen

Vind

et al . The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis. Scand J Gastroenterol 2016; 51: 1407–1415.

40.

Mukhopadhya

Hansen

Meharg

et al . The fungal microbiota of de-novo paediatric inflammatory bowel disease. Microbes Infect 2015; 17: 304–310.

41.

Albenberg

et al . Gut microbiota and IBD: causation or correlation? Nat Rev Gastroenterol Hepatol 2017; 14: 573–584.

42.

Wang

Tang

et al . Dysbiosis of gut fungal microbiota is associated with mucosal inflammation in Crohn’s disease. J Clin Gastroenterol 2014; 48: 513–523.

43.

Lewis

Chen

Baldassano

et al . Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe 2015; 18: 489–500.

44.

Norman

Handley

Baldridge

et al . Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 2015; 160: 447–460.

45.

Wagner

Maksimovic

Farries

et al . Bacteriophages in gut samples from pediatric Crohn’s disease patients: metagenomic analysis using 454 pyrosequencing. Inflamm Bowel Dis 2013; 19: 1598–1608.

46.

Soubières

Poullis

Emerging role of novel biomarkers in the diagnosis of inflammatory bowel disease. World J Gastrointest Pharmavol Ther 2016; 7: 41.

47.

Chang

Malter

Hudesman

Disease monitoring in inflammatory bowel disease. World J Gastroenterol 2015; 21: 11246.

48.

Mosli

Zou

Garg

et al . C-reactive protein, fecal calprotectin, and stool lactoferrin for detection of endoscopic activity in symptomatic inflammatory bowel disease patients: a systematic review and meta-analysis. Am J Gastroenterol 2015; 110: 802–819.

49.

Williams

Willsmore

Cox

et al . Serum metabolic profiling in inflammatory bowel disease. Dig Dis Sci 2012; 57: 2157–2165.

50.

Hisamatsu

Okamoto

Hashimoto

et al . Novel, objective, multivariate biomarkers composed of plasma amino acid profiles for the diagnosis and assessment of inflammatory bowel disease. PloS One 2012; 7: e31131.

51.

Yau

Leong

Shin

et al . Bimodal plasma metabolomics strategy identifies novel inflammatory metabolites in inflammatory bowel diseases. Disc Med 2014; 18: 113–124.

52.

Fathi

Oskouie

Tafazzoli

et al . Metabonomics based NMR in Crohn’s disease applying PLS-DA. Gastroenterol Hepatol Bed Bench 2013; 6(Suppl. 1): S82–S86.

53.

Mortensen

Manon-Jensen

Jensen

et al . Ulcerative colitis, Crohn’s disease, and irritable bowel syndrome have different profiles of extracellular matrix turnover, which also reflects disease activity in Crohn’s disease. PloS One 2017; 12: e0185855.

54.

Hamilton

Kamm

De Cruz

et al . Serologic antibodies in relation to outcome in postoperative Crohn’s disease. J Gastroenterol Hepatol 2017; 32: 1195–1203.

55.

Bonneau

Dumestre-Perard

Rinaudo-Gaujous

et al . Systematic review: new serological markers (anti-glycan, anti-GP2, anti-GM-CSF Ab) in the prediction of IBD patient outcomes. Autoimmun Rev 2015; 14: 231–245.

56.

Dai

Huang

Y-S

Tang

et al . Microarray analysis of microRNA expression in peripheral blood cells of systemic lupus erythematosus patients. Lupus 2007; 16: 939–946.

57.

Wang

Zhang

et al . Circulating microRNA223 is a new biomarker for inflammatory bowel disease. Medicine 2016; 95: e2703.

58.

Zhang

Y-P

et al . Serum platelet factor 4 is a reliable activity parameter in adult patients with inflammatory bowel disease: a pilot study. Medicine 2017; 96: e6323.

59.

Alonso

Julià

Vinaixa

et al . Urine metabolome profiling of immune-mediated inflammatory diseases. BMC Med 2016; 14: 133.

60.

Williams

Cox

Walker

et al . Characterization of inflammatory bowel disease with urinary metabolic profiling. Am J Gastroenterol 2009; 104: 1435–1444.

61.

Stephens

Siffledeen

et al . Urinary NMR metabolomic profiles discriminate inflammatory bowel disease from healthy. J Crohns Colitis 2013; 7: e42–e48.

62.

Martin

F-P

Ezri

Cominetti

et al . Urinary metabolic phenotyping reveals differences in the metabolic status of healthy and inflammatory bowel disease (IBD) children in relation to growth and disease activity. Int J Mol Sci 2016; 17: 1310–1325.

63.

Bjerrum

Wang

Hao

et al . Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy individuals. Metabolomics 2015; 11: 122–133.

64.

Jacobs

Goudarzi

Singh

et al . A disease-associated microbial and metabolomics state in relatives of pediatric inflammatory bowel disease patients. Cell Mol Gastroenterol Hepatol 2016; 2: 750–766.

65.

Di Ruscio

Vernia

Ciccone

et al . Surrogate fecal biomarkers in inflammatory bowel disease: rivals or complementary tools of fecal calprotectin? Inflamm Bowel Dis 2017; 24: 78–92.

66.

Schicho

Shaykhutdinov

Ngo

et al . Quantitative metabolomic profiling of serum, plasma, and urine by 1H NMR spectroscopy discriminates between patients with inflammatory bowel disease and healthy individuals. J Proteome Res 2012; 11: 3344–3357.

67.

Dawiskiba

Deja

Mulak

et al . Serum and urine metabolomic fingerprinting in diagnostics of inflammatory bowel diseases. World J Gastroenterol 2014; 20: 163–174.

68.

Sewell

Hannun

Han

et al . Lipidomic profiling in Crohn’s disease: abnormalities in phosphatidylinositols, with preservation of ceramide, phosphatidylcholine and phosphatidylserine composition. Int J Biochem Cell Biol 2012; 44: 1839–1846.

69.

Kiesslich

Duckworth

Moussata

et al . Local barrier dysfunction identified by confocal laser endomicroscopy predicts relapse in inflammatory bowel disease. Gut 2011; 1146–1153.

70.

Chang

Leong

Wasinger

et al . Impaired intestinal permeability contributes to ongoing bowel symptoms in patients with inflammatory bowel disease and mucosal healing. Gastroenterology 2017; 153: 723–731.

71.

Bischoff

Barbara

Buurman

et al . Intestinal permeability-a new target for disease prevention and therapy. BMC Gastroenterology 2014; 14: 189.

72.

Wells

Brummer

Derrien

et al . Homeostasis of the gut barrier and potential biomarkers. Am J Physiol Gastrointest Liver Physiol 2017; 312: G171–G193.

73.

Fava

Danese

Intestinal microbiota in inflammatory bowel disease: friend of foe?

World J Gastroenterol 2011; 17: 557.

74.

Salvo

Alonso

Pardo

et al . The intestinal barrier function and its involvement in digestive disease. Rev Esp Enferm Dig 2015; 107: 686–696.

75.

Laukoetter

Nava

Nusrat

Role of the intestinal barrier in inflammatory bowel disease. World J Gastroenterol 2008; 14: 401–407.

76.

Vivinus-Nébot

Frin-Mathy

Bzioueche

et al . Functional bowel symptoms in quiescent inflammatory bowel diseases: role of epithelial barrier disruption and low-grade inflammation. Gut 2014; 63: 744–752.

77.

Hollander

Vadheim

Brettholz

et al . Increased intestinal permeability in patients with Crohn’s disease and their relatives. A possible etiologic factor. Ann Intern Med 1986; 105: 883–885.

78.

May

Sutherland

Meddings

JB.

Is small intestinal permeability really increased in relatives of patients with Crohn’s disease?

Gastroenterology 1993; 104: 1627–1632.

79.

Munkholm

Langholz

Hollander

et al . Intestinal permeability in patients with Crohn’s disease and ulcerative colitis and their first degree relatives. Gut 1994; 35: 68–72.

80.

Peeters

Geypens

Claus

et al . Clustering of increased small intestinal permeability in families with Crohn’s disease. Gastroenterology 1997; 113: 802–807.

81.

Russell

Satsangi

IBD: a family affair. Best Pract Res Clin Gastroenterol 2004; 18: 525–539.

82.

Fries

Renda

Presti

MAL

et al . Intestinal permeability and genetic determinants in patients, first-degree relatives, and controls in a high-incidence area of Crohn’s disease in Southern Italy. Am J Gastroenterol 2005; 100: 2730–2736.

83.

Hering

Fromm

Schulzke

J-D.

Determinants of colonic barrier function in inflammatory bowel disease and potential therapeutics. J Physiol 2012; 590: 1035–1044.

84.

Zamora

Hilsden

Meddings

et al . Intestinal permeability before and after ibuprofen in families of children with Crohn’s disease. Can J Gastroenterol 1999; 13: 31–37.

85.

Hilsden

Meddings

Sutherland

LR.

Intestinal permeability changes in response to acetylsalicylic acid in relatives of patients with Crohn’s disease. Gastroenterology 1996; 110: 1395–1403.

86.

Wyatt

Vogelsang

Hübl

et al . Intestinal permeability and the prediction of relapse in Crohn’s disease. Lancet 1993; 341: 1437–1439.

87.

Madsen

Malfair

Gray

et al . Interleukin-10 gene-deficient mice develop a primary intestinal permeability defect in response to enteric microflora. Inflamm Bowel Dis 1999; 5: 262–270.

88.

Burri

Beglinger

The use of fecal calprotectin as a biomarker in gastrointestinal disease. Expert Rev Gastroenterol Hepatol 2014; 8: 197–210.

89.

Gisbert

McNicholl

Questions and answers on the role of faecal calprotectin as a biological marker in inflammatory bowel disease. Dig Liver Dis 2009; 41: 56–66.

90.

Thjodleifsson

Sigthorsson

Cariglia

et al . Subclinical intestinal inflammation: an inherited abnormality in Crohn’s disease relatives? Gastroenterology 2003; 124: 1728–1737.

91.

Malíčková

Francová

Lukáš

et al . Fecal zonulin is elevated in Crohn’s disease and in cigarette smokers. Pract Lab Med 2017; 9: 39–44.

92.

Lopez-Posadas

Becker

Gunther

et al . Rho-A prenylation and signaling link epithelial homeostasis to intestinal inflammation. J Clin Invest 2016; 126: 611–626.

93.

Segain

J-P

de la Bletieree

Sauzeau

et al . Rho kinase blockade prevents inflammation via nuclear factor kappa B inhibition: evidence in Crohn’s disease and experimental colitis. Gastroenterology 2003; 124: 1180–1187.

94.

Zeissig

Bürgel

Günzel

et al . Changes in expression and distribution of claudin 2, 5 and 8 lead to discontinuous tight junctions and barrier dysfunction in active Crohn’s disease. Gut 2007; 56: 61–72.

95.

Al-Sadi

Khatib

Guo

et al . Occludin regulates macromolecule flux across the intestinal epithelial tight junction barrier. Am J Physiol Gastrointest Liver Physiol 2011; 300: G1054–G1064.

96.

Buschmann

Shen

Rajapakse

et al . Occludin OCEL-domain interactions are required for maintenance and regulation of the tight junction barrier to macromolecular flux. Mol Biol Cell 2013; 24: 3056–3068.

97.

Martini

Krug

Siegmund

et al . Mend your fences: the epithelial barrier and its relationship with mucosal immunity in inflammatory bowel disease. Cell Mol Gastroenterol Hepatol 2017; 4: 33–46.

98.

Bosca-Watts

Tosca

Anton

et al . Pathogenesis of Crohn’s disease: Bug or no bug. World J Gastrointest Pathophysiol 2015; 6: 1–12.

99.

Barnich

Darfeuille-Michaud

Adherent-invasive Escherichia coli and Crohn’s disease. Curr Opin Gastroenterol 2007; 23: 16–20.

100.

Nguyen

HTT

Dalmasso

Muller

et al . Crohn’s disease-associated adherent invasive Escherichia coli modulate levels of microRNAs in intestinal epithelial cells to reduce autophagy. Gastroenterology 2014; 146: 508–519.

101.

Zhou

Chen

et al . Increased Enterococcus faecalis infection is associated with clinically active Crohn disease. Medicine 2016; 95: e5019.

102.

Main

McKenzie

Yeaman

et al . Antibody to Saccharomyces cerevisiae (bakers’ yeast) in Crohn’s disease. BMJ 1988; 297: 1105–1106.

103.

Magro

Kotze

Martinez

CAR

et al . Changes in serum levels of lipopolysaccharides and CD26 in patients with Crohn’s disease. Intest Res 2017; 15: 352–357.

104.

Biancone

Fantini

Tosti

et al . Fecal alpha-1-antitrypsin clearance as a marker of clinical relapse in patients with Crohn’s disease of the distal ileum. Eur J Gastroenterol Hepatol 2003; 15: 261–266.

105.

Kopylov

Yung

Engel

et al . Fecal calprotectin for the prediction of small-bowel Crohn’s disease by capsule endoscopy: a systematic review and meta-analysis. Eur J Gastroenterol Hepato 2016; 28: 1137–1144.

106.

Egea

Pereniguez

Perez

et al . Fecal calprotectin and C-reactive protein are associated with positive findings in capsule endoscopy in suspected small bowel Crohn’s disease. Rev Esp Enferm Dig 2016; 108: 394–400.

107.

Sipponen

Kärkkäinen

Savilahti

et al . Correlation of faecal calprotectin and lactoferrin with an endoscopic score for Crohn’s disease and histological findings. Aliment Pharmacol Ther 2008; 28: 1221–1229.

108.

Bar-Gil Shitrit

Koslowsky

Livovsky

et al . A prospective study of fecal calprotectin and lactoferrin as predictors of small bowel Crohn’s disease in patients undergoing capsule endoscopy. Scand J Gastroenterol 2017; 52: 328–333.

109.

Sarikaya

Ergul

Dogan

et al . Intestinal fatty acid binding protein (I-FABP) as a promising test for Crohn’s disease: a preliminary study. Clin Lab 2015; 61: 87–91.

110.

Tran

DH-N

Wang

et al . Circulating cathelicidin levels correlate with mucosal disease activity in ulcerative colitis, risk of intestinal stricture in Crohn’s disease, and clinical prognosis in inflammatory bowel disease. BMC Gastroenterol 2017; 17: 63.

111.

Wang

Xie

et al . Comparison of non-invasive biomarkers faecal BAFF, calprotectin and FOBT in discriminating IBS from IBD and evaluation of intestinal inflammation. Sci Rep 2017; 7: 2669.

112.

Boon

Day

Mulder

et al . Are faecal markers good indicators of mucosal healing in inflammatory bowel disease? World J Gastroenterol 2015; 21: 11469–11480.

113.

Borkowska

Liberek

Luczak

et al . Fecal lactoferrin, a marker of intestinal inflammation in children with inflammatory bowel disease. Acta Biochim Pol 2015; 62: 541–545.

114.

Sidhu

Sanders

Wilson

et al . Faecal lactoferrin, capsule endoscopy and Crohn’s disease. Is there a three way relationship? A pilot study. J Gastrointestin Liver Dis 2010; 19: 257–260.

115.

Willing

Dicksved

Halfvarson

et al . A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 2010; 139: 1844–1854.

116.

Winter

Lopez

Bäumler

AJ.

The dynamics of gut-associated microbial communities during inflammation. EMBO Rep 2013; 14: 319–327.

117.

Morgan

Tickle

Sokol

et al . Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 2012; 13: R79.

118.

Gadaleta

Van Erpecum

Oldenburg

et al . Farnesoid X receptor activation inhibits inflammation and preserves the intestinal barrier in inflammatory bowel disease. Gut 2011; 60: 463–472.

119.

Ogilvie

Jones

BV.

Dysbiosis modulates capacity for bile acid modification in the gut microbiomes of patients with inflammatory bowel disease: a mechanism and marker of disease?

Gut 2012; 61: 1642–1643.

120.

Duboc

Rajca

Rainteau

et al . Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases. Gut 2013; 62: 531–539.

121.

Smith

Howitt

Panikov

et al . The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 2013; 341: 569–573.

122.

Rajca

Grondin

Louis

et al . Alterations in the intestinal microbiome (dysbiosis) as a predictor of relapse after infliximab withdrawal in Crohn’s disease. Inflamm Bowel Dis 2014; 20: 978–986.

123.

De Cruz

Kang

Wagner

et al . Association between specific mucosa-associated microbiota in Crohn’s disease at the time of resection and subsequent disease recurrence: a pilot study. J Gastroenterol Hepatol 2015; 30: 268–278.

124.

Mondot

Lepage

Seksik

et al . Structural robustness of the gut mucosal microbiota is associated with Crohn’s disease remission after surgery. Gut 2016; 65: 954–962.

125.

Dey

Soergel

Repo

et al . Association of gut microbiota with post-operative clinical course in Crohn’s disease. BMC Gastroenterol 2013; 13: 131.

126.

Hawkey

Hematopoietic stem cell transplantation in Crohn’s disease: state-of-the-art treatment. Dig Dis 2017; 35: 107–114.

127.

Hawkey

Hommes

DW.

Is stem cell therapy ready for prime time in treatment of inflammatory bowel diseases?

Gastroenterology 2017; 152: 389–397.

128.

Zuba-Surma

Kucia

Ratajczak

et al . “Small stem cells” in adult tissues: very small embryonic-like stem cells stand up! Cytometry A 2009; 75: 4–13.

129.

Ratajczak

Zuba-Surma

Wysoczynski

et al . Very small embryonic-like stem cells: characterization, developmental origin, and biological significance. Exp Hematol 2008; 36: 742–751.

130.

Marlicz

Zuba-Surma

Kucia

et al . Various types of stem cells, including a population of very small embryonic-like stem cells, are mobilized into peripheral blood in patients with Crohn’s disease. Inflamm Bowel Dis 2012; 18: 1711–1722.

131.

Bhartiya

Stem cells to replace or regenerate the diabetic pancreas: huge potential and existing hurdles. Indian J Med Res 2016; 143: 267.

132.

Zuba-Surma

Kucia

et al . Very small embryonic-like stem cells are present in adult murine organs: ImageStream-based morphological analysis and distribution studies. Cytometry A 2008; 73: 1116–1127.

133.

Holmberg

Seidelin

Yin

et al . Culturing human intestinal stem cells for regenerative applications in the treatment of inflammatory bowel disease. EMBO Mol Med 2017; 9: 558–570.

134.

Marlicz

Zuba-Surma

Blogowski

et al . P279 mobilization of various types of pluripotent progenitor and stem cells is surrogate prognostic marker of mucosal healing in early clinical remission in Crohn’s disease. J Crohns Colitis 2012; 6: S120.

135.

Holmberg

Pedersen

Jørgensen

et al . Intestinal barrier integrity and inflammatory bowel disease: stem cell-based approaches to regenerate the barrier. J Tissue Eng Regen Med. Epub ahead of print 21 June 2017. DOI:10.1002/term.2506.

136.

Dietrich

Singh

SR.

Circulating endothelial progenitor cells in Crohn’s disease: an EPiC in the making?

Dig Dis Sci 2017; 62: 567–568.

137.

Kitagawa

Sato

Yokouchi

et al . A case of lansoprazole-associated collagenous colitis with longitudinal ulcer. J Gastrointestin Liver Dis 2013; 22: 9.

138.

Velders

van Os

Hagoort

et al . Reduced stem cell mobilization in mice receiving antibiotic modulation of the intestinal flora: involvement of endotoxins as cofactors in mobilization. Blood 2004; 103: 340–346.

139.

Yepuri

Sukhovershin

Nazari-Shafti

et al . Proton pump inhibitors accelerate endothelial senescence novelty and significance. Circ Res 2016; 118: e36–e42.

140.

Marlicz

Koulaouzidis

Loniewski

et al . Letter by Marlicz et al regarding article, “Proton Pump Inhibitors Accelerate Endothelial Senescence.” Circ Res 2016; 119: e31–e32.

141.

Spadoni

Fornasa

Rescigno

Organ-specific protection mediated by cooperation between vascular and epithelial barriers. Nat Rev Immunol 2017; 17: 761–773.

142.

Spadoni

Pietrelli

Pesole

et al . Gene expression profile of endothelial cells during perturbation of the gut vascular barrier. Gut Microbes 2016; 7: 540–548.

143.

Marycz

Mierzejewska

Smieszek

et al . Endurance exercise mobilizes developmentally early stem cells into peripheral blood and increases their number in bone marrow: implications for tissue regeneration. Stem Cells Int 2016; 2016: 5756901.

144.

Marlicz

Loniewski

The effect of exercise and diet on gut microbial diversity. Gut 2015; 64: 519–520.

145.

Mazur-Bialy

Bilski

Wojcik

et al . Beneficial effect of voluntary exercise on experimental colitis in mice fed a high-fat diet: the role of irisin, adiponectin and proinflammatory biomarkers. Nutrients 2017; 9: 410.

146.

Bilski

Mazur-Bialy

Brzozowski

et al . Can exercise affect the course of inflammatory bowel disease? Experimental and clinical evidence. Pharmacol Rep 2016; 68: 827–836.

147.

Chang

Termini

Chute

JP.

Young endothelial cells revive aging blood. J Clin Invest 2017; 127: pii: 97707.

148.

Kim

Liu

et al . The bone marrow-expressed antimicrobial cationic peptide LL-37 enhances the responsiveness of hematopoietic stem progenitor cells to an SDF-1 gradient and accelerates their engraftment after transplantation. Leukemia 2012; 26: 736–745.

149.

Raftery

Martineau

Greiller

et al . Effects of vitamin D supplementation on intestinal permeability, cathelicidin and disease markers in Crohn’s disease: results from a randomised double-blind placebo-controlled study. United European Gastroenterol J 2015; 3: 294–302.

150.

Raftery

O’Sullivan

Optimal vitamin D levels in Crohn’s disease: a review. Proc Nutr Soc 2015; 74: 56–66.

151.

Raftery

Merrick

Healy

et al . Vitamin D status is associated with intestinal inflammation as measured by fecal calprotectin in Crohn’s disease in clinical remission. Dig Dis Sci 2015; 60: 2427–2435.

152.

Ratajczak

Pedziwiatr

Extracellular microvesicles (ExMVs) in cell to cell communication: a role of telocytes. Adv Exp Med Biol 2016; 913: 41–49.

153.

Ratajczak

Horizontal transfer of RNA and proteins between cells by extracellular microvesicles: 14 years later. Clin Transl Med 2016; 5: 7.

154.

Tziatzios

Polymeros

Spathis

et al . Increased levels of circulating platelet derived microparticles in Crohn’s disease patients. Scand J Gastroenterol 2016; 51: 1184–1192.

155.

Voudoukis

Vetsika

E-K

Giannakopoulou

et al . Distinct features of circulating microparticles and their relationship with disease activity in inflammatory bowel disease. Ann Gastroenterol 2016; 29: 180–187.

156.

Leonetti

Reimund

J-M

Tesse

et al . Circulating microparticles from Crohn’s disease patients cause endothelial and vascular dysfunctions. PLoS One 2013; 8: e73088.

157.

Ratajczak

Kucia

Mierzejewska

et al . Paracrine proangiopoietic effects of human umbilical cord blood-derived purified CD133+ cells—implications for stem cell therapies in regenerative medicine. Stem Cells Dev 2012; 22: 422–430.

158.

Milia

Ruffo

Manetti

et al . Telocytes in Crohn’s disease. J Cell Mol Med 2013; 17: 1525–1536.

159.

Chao

C-Y

Battat

Al Khoury

et al . Co-existence of non-alcoholic fatty liver disease and inflammatory bowel disease: a review article. World J Gastroenterol 2016; 22: 7727–7734.

160.

Younossi

Koenig

Abdelatif

et al . Global epidemiology of nonalcoholic fatty liver disease—meta-analytic assessment of prevalence, incidence, and outcomes. Hepatology 2016; 64: 73–84.

161.

Brandl

Schnabl

Intestinal microbiota and nonalcoholic steatohepatitis. Curr Opin Gastroenterol 2017; 33: 128–133.

162.

Brandl

Schnabl

Is intestinal inflammation linking dysbiosis to gut barrier dysfunction during liver disease?

Expert Rev Gastroenterol Hepatol 2015; 9: 1069–1076.

163.

Kiesslich

Neurath

MF.

Advanced endoscopy imaging in inflammatory bowel diseases. Gastrointest Endosc 2017; 85: 496–508.

164.

East

Vleugels

Roelandt

et al . Advanced endoscopic imaging: European Society of Gastrointestinal Endoscopy (ESGE) technology review. Endoscopy 2016; 48: 1029–1045.

165.

Fritscher-Ravens

Schuppan

Ellrichmann

et al . Confocal endomicroscopy shows food-associated changes in the intestinal mucosa of patients with irritable bowel syndrome. Gastroenterology 2014; 147: 1012–1020.

166.

Atreya

Neurath

MF.

Predicting therapeutic response by in vivo molecular imaging in inflammatory bowel diseases. Dig Dis 2016; 34: 552–557.

167.

Kalantar-Zadeh

Yao

Berean

et al . Intestinal gas capsules: a proof-of-concept demonstration. Gastroenterology 2016; 150: 37–39.

168.

Pelli

Trovarelli

Capodicasa

et al . Breath alkanes determination in ulcerative colitis and Crohn’s disease. Dis Colon Rectum 1999; 42: 71–76.

169.

Dryahina

Španěl

Pospíšilová

et al . Quantification of pentane in exhaled breath, a potential biomarker of bowel disease, using selected ion flow tube mass spectrometry. Rapid Commun Mass Spectrom 2013; 27: 1983–1992.

170.

Bodelier

Smolinska

Baranska

et al . Volatile organic compounds in exhaled air as novel marker for disease activity in Crohn’s disease: a metabolomic approach. Inflamm Bowel Dis 2015; 21: 1776–1785.

171.

Patel

Alkhouri

Eng

et al . Metabolomic analysis of breath volatile organic compounds reveals unique breathprints in children with inflammatory bowel disease: a pilot study. Aliment Pharmacol Ther 2014; 40: 498–507.

Emerging concepts in non-invasive monitoring of Crohn’s disease

Abstract

Keywords

Introduction

Microbiota as a source of putative biomarkers in Crohn’s Disease

The clinical relevance of microbial biodiversity in Crohn’s disease

Lower level of Bacteroides in the gut microbiota is associated with inflammatory bowel disease: a meta-analysis

Mycobiota as a potential source for novel non-invasive biomarkers in Crohn’s disease

The differential diagnosis of Crohn’s disease: the role of metabolomics

Gut barrier and intestinal permeability: novel targets for Crohn’s disease monitoring?

Measuring the unmeasurable: dysbiosis as a target in Crohn’s disease monitoring?

Pluripotent progenitor and stem cells as surrogate prognostic markers of mucosal healing and clinical remission in Crohn’s disease

Blood-derived microparticles and inflammatory bowel disease

Targeting gut-liver axis to chase for new Crohn’s disease biomarkers

Conclusion

Footnotes

Funding

Conflict of interest statement

ORCID iD

References