Microbial diversity and composition in IBD

There seem to be a general acquiescence as regards to IBD patients having an altered microbial composition and a reduced diversity compared to healthy controls, both in fecal and mucosal

samples. (Berry & Reinisch 2013) (Sheehan et al. 2015) This is referred to as a dysbiotic microbiota which also tend to exhibit a lower stability than the microbiota of a healthy adult. (Satokari 2015) The microbial dysbiosis is most noticeable when the inflammation is active. (Biedermann & Rogler 2015) Research have shown that diversity can vary between non-inflamed and inflamed areas of the intestines of the same individual, with the latter displaying less alpha-diversity. (Sepehri et al. 2007) Interestingly, it has also been shown that inflammations of the colon might lead to depletion of bacteria in the feces, whilst simultaneously giving increased bacterial concentrations in the crypts.

(Swidsinski et al. 2005) Based on findings of the microbiota of UC patients presenting itself with a lower diversity than that of CD patients, as well as different prevalence of certain bacteria, it has been suggested that the bacterial diversity of IBD is disease specific. (Ott et al. 2004) (Swidsinski et al. 2009) The possibility that disease phenotype might exert an influence on the microbial

composition and diversity in IBD patients has also been proposed based on findings in a study by Willing et al (2010), showing that the microbial profile of patients with ileal CD differs from patients with colonic CD. Regarding the other microbial residents of the gut, it has been independently shown that CD patients carry an increased fungal diversity (Ott et al. 2008) and higher phage numbers compared to healthy counterparts. (Lepage et al. 2008)

Spatial arrangement of gut bacteria in IBD patients

The microbiota of the mucosa and lumen might be expected to differ. (Frank et al. 2007) According to a study by Gevers et al (2014), some microbial differences between CD patients and healthy controls only became evident when mucosal samples were analyzed as compared to fecal samples.

This included a reduction in Bifidobacteriaceae, and an increase in Fusobacteriaceae and Enterobacteriaceae. These observations led to proposals of mucosal bacterias being of greater significance for the aetiology of the disease (Baumgart & Carding 2007) and that IBD to a smaller extent affect the luminal microbiota. (Sheehan et al. 2015)

On a phylum level, the mucosal microbiota of IBD patients in general present itself with a

decreased abundance of Firmicutes and Bacteroidetes an increased abundance of Actinobacteria and Proteobacteria. (Frank et al. 2007) Increased levels of the latter phyla includes Desulfovibrio in mucosa of UC patients (Rowan et al. 2010) and mucosa associated Escherichia coli. Increased

abundance of AIEC are particularly evident in CD patients where it has the potential to invade epithelial cells and replicate intracellularly. (Rolhion & Darfeuille-Michaud 2007) AIEC has further been suggested to be enriched in inflamed tissue in ileal CD as opposed to in normal tissue.

(Baumgart et al. 2007) In addition, Clostridium (cluster XIV, XVIII, IV) which in a cooperative manner are able to stimulate T-reg cells, (Atarashi et al. 2013) are found to be depleted in IBD patients. (Kabeerdoss et al. 2015) These clusters include several important producers of SCFA such as C. leptum (cluster XIVa), C. coccoides, Roseburia hominis and Faecalibacterium prausnitzii (cluster IV) which are considered to be of great importance to the preservation of immunological balance and gut homeostasis. (Lopetuso et al. 2013) (Satokari 2015)

An impoverished detection of mucosal SCFA-producing bacteria in IBD patients was also revealed in a study by Frank et al (2007) and Willings et al (2010), with the latter study presenting decreased levels of Faecallibacterium and Roseburia and increased levels of E.coli and R.gnavus from the Enterobacteriace in patients with ileal CD. CD but not UC patients have further been proposed to have increased amounts of Mycobacterium avium subspecies paratuberculosis (MAP), although these findings seem to vary between projects. (Feller et al. 2007) Depletion of lactic acid bacteria within Lactobacillus (phylum Firmicutes) has also been detected in IBD patients. (Ott et al. 2004) Bacteroides should normally be found mainly in feces, but adhesive and infiltrating bacteria of this genus has been found in inflamed mucosal tissues of the colon of IBD patients. (Swidsinski et al.

2005) Samples of both colon and small intestine of IBD patients have also proven to be deficient of the Lachnospiraceae family compared to healthy subjects. (Frank et al. 2007) When comparing biofilm-formation and bacterial density of the IBD mucosa to healthy counterparts, this is found to be significantly increased, with B. fragilis being responsible for the majority of the biofilm.

(Swidsinski et al. 2005) Concentration of mucosal bacteria also seem to be positively correlated with disease severity, in both inflamed and non-inflamed colonic tissue. (Swidsinski et al. 2002)

Analysis of fecal microbiota in UC patients has also unveiled a reduced abundance of bacteria involved in SCFA-metabolism such as R. bromii, Roseburia sp, and A. municiphila. Bacteria of increased prevalence in UC patients included Fusobacterium sp. (Rajilic-Stojanovic et al. 2013) where certain strains of this genus possess invasive and proinflammatory properties. (Strauss et al.

2011) Increased numbers of Helicobacter sp. and Campylobacter sp. has also been found (Rajilic-Stojanovic et al. 2013) Other proteobacteria of exaggerated numbers in feces of IBD patients include the genera Desulfovibrio (Loubinoux et al. 2002) which possess toxigenic properties due to its ability to produce pro-inflammatory hydrogen sulphide. (Cammarota et al. 2015)

Microbiome of the IBD microbiota

As opposed to the extensive research that has been conducted on the taxonomic characteristics of the gut microbiota in IBD, research performed with respect to the microbiome are still scarce.

However, a study by Morgan et al (2012) seeking to unveil functional perturbations of the IBD microbiome, found shifts in oxidative stress pathways, and a decreased expression of genes related to synthesis of SCFA and amino acids. Several genes involved in pathological processes, most notably adherence invasion and type 2 secretion systems were also found to be increased in patients with ileal CD. They also found an increase in cysteine metabolism along with increased

N-acetylgalactosamine transporters, which potentially could indicate an abundance of bacteria metabolizing mucin. (Morgan et al. 2012)

It has been proposed that microbial anomalies observed in IBD could serve as useful biological markers for inflammation activity (Berry & Reinisch 2013) and diagnostic tests for microbial

dysbiosis based on deviations from a healthy gut microbiota have already been developed. (Casen et al. 2015) Albeit the linkage between IBD and microbial dysbiosis has been known for long, the question of whether the aberrant microbiota is a cause or consequence of IBD remains unknown.

(Baumgart & Carding 2007) (Maynard et al. 2012) (Mukhopadhya et al. 2012) (Sartor et al, 2015)

Figure 1.1: The figure gives a simplified illustration of layers of the gut mucosa and the interplay between a subset of the immunological, and microbial factors implicated to contribute in the development of IBD. Picture from (Sartor 2015)