Intestinal microbiota in inflammatory bowel disease: Friend of foe?

Serine proteases at the cutting edge of IBD: Focus on gastrointestinal inflammation

Serine proteases have been long recognized to coordinate many physiological processes and play key roles in regulating the inflammatory response. Accordingly, their dysregulation has been regularly associated with several inflammatory disorders and suggested as a central mechanism in the pathophysiology of digestive inflammation. So far, studies addressing the proteolytic homeostasis in the gut have mainly focused on host serine proteases as candidates of interest, while largely ignoring the potential contribution of their bacterial counterparts. The human gut microbiota comprises a complex ecosystem that contributes to host health and disease. Yet, our understanding of microbially produced serine proteases and investigation of whether they are causally linked to IBD is still in its infancy. In this review, we highlight recent advances in the emerging roles of host and bacterial serine proteases in digestive inflammation. We also discuss the application of available tools in the gut to monitor disease-related serine proteases. An exhaustive representation and understanding of such functional potential would help in closing existing gaps in mechanistic knowledge.

Gut Microbiome, Intestinal Permeability, and Tissue Bacteria in Metabolic Disease: Perpetrators or Bystanders?

The emerging evidence on the interconnectedness between the gut microbiome and host metabolism has led to a paradigm shift in the study of metabolic diseases such as obesity and type 2 diabetes with implications on both underlying pathophysiology and potential treatment. Mounting preclinical and clinical evidence of gut microbiota shifts, increased intestinal permeability in metabolic disease, and the critical positioning of the intestinal barrier at the interface between environment and internal milieu have led to the rekindling of the "leaky gut" concept. Although increased circulation of surrogate markers and directly measurable intestinal permeability have been linked to increased systemic inflammation in metabolic disease, mechanistic models behind this phenomenon are underdeveloped. Given repeated observations of microorganisms in several tissues with congruent phylogenetic findings, we review current evidence on these unanticipated niches, focusing specifically on the interaction between gut permeability and intestinal as well as extra-intestinal bacteria and their joint contributions to systemic inflammation and metabolism. We further address limitations of current studies and suggest strategies drawing on standard techniques for permeability measurement, recent advancements in microbial culture independent techniques and computational methodologies to robustly develop these concepts, which may be of considerable value for the development of prevention and treatment strategies.

Immune modulatory capacity of probiotic lactic acid bacteria and applications in vaccine development

Vaccination is one of the most important prevention tools providing protection against infectious diseases especially in children below the age of five. According to estimates, more than 5 million lives are saved annually by the implementation of six standard vaccines, including diphtheria, hepatitis B, Haemophilus influenza type b, polio, tetanus and yellow fever. Despite these efforts, we are faced with challenges in developing countries where increasing population and increasing disease burden and difficulties in vaccine coverage and delivery cause significant morbidity and mortality. Additionally, the high cost of these vaccines is also one of the causes for inappropriate and inadequate vaccinations in these regions. Thus, developing cost-effective vaccine strategies that could provide a stronger immune response with reduced vaccination schedules and maximum coverage is of critical importance. In last decade, different approaches have been investigated; among which live bacterial vaccines have been the focus of attention. In this regard, probiotic lactic acid bacteria have been extensively studied as safe and effective vaccine candidates. These microorganisms represent the largest group of probiotic bacteria in the intestine and are generally recognised as safe (GRAS) bacteria. They have also attracted attention due to their immunomodulatory actions and their effective role as novel vaccine adjuvants. A significant property of these bacteria is their ability to mimic natural infections, while intrinsically possessing mucosal adjuvant properties. Additionally, as live bacterial vaccines are administered orally or nasally, they have higher acceptance and better safety, but also avoid the risk of contamination due to needles and syringes. In this review, we emphasise the role of probiotic Lactobacillus strains as putative oral vaccine carriers and novel vaccine adjuvants.

Extracellular Vesicles with Possible Roles in Gut Intestinal Tract Homeostasis and IBD

The intestinal tract consists of various types of cells, such as epithelial cells, Paneth cells, macrophages, and lymphocytes, which constitute the intestinal immune system and play a significant role in maintaining intestinal homeostasis by producing antimicrobial materials and controlling the host-commensal balance. Various studies have found that the dysfunction of intestinal homeostasis contributes to the pathogenesis of inflammatory bowel disease (IBD). As a novel mediator, extracellular vesicles (EVs) have been recognized as effective communicators, not only between cells but also between cells and the organism. In recent years, EVs have been regarded as vital characters for dysregulated homeostasis and IBD in either the etiology or the pathology of intestinal inflammation. Here, we review recent studies on EVs associated with intestinal homeostasis and IBD and discuss their source, cargo, and origin, as well as their therapeutic effects on IBD, which mainly include artificial nanoparticles and EVs derived from microorganisms.

The Macrophages and Intestinal Symbiosis

The human intestinal tract is inhabited by trillions of microorganisms and houses the largest pool of macrophages in the human body. Being a part of the innate immune system, the macrophages, the professional phagocytes, vigorously respond to the microbial and dietary antigens present in the intestine. Because such a robust immune response poses the danger to the survival of the non-harmful and beneficial gut microbiota, the macrophages developed mechanisms of recognition and hyposensitivity toward the non-harmful/beneficial inhabitants of the gut. We will discuss the evolution and identity of some of these mechanisms in the following chapter.

Phycocyanin Ameliorates Radiation-Induced Acute Intestinal Toxicity by Regulating the Effect of the Gut Microbiota on the TLR4/Myd88/NF-κB Pathway

BACKGROUND

Radiation-induced gastrointestinal syndrome, including nausea, diarrhea, and dehydration, contributes to morbidity and mortality after medical or industrial radiation exposure, which seriously affects patient quality of life after treatment. No safe and effective radiation countermeasure has been approved for clinical therapy. In this study, we aimed to investigate the potential protective effects of phycocyanin (PC) against radiation-induced acute intestinal injury.

MATERIALS AND METHODS

C57BL/6 mice were orally administered 50 mg/kg PC once per day for 1 month before exposure to total-abdominal x-ray irradiation at a single dose of 12 Gy. The effects of PC on intestinal histopathology and integrity, gut microbiota, lipopolysaccharides (LPS), inflammatory cytokines, and Toll-like receptor 4 (TLR4)/myeloid differentiation factor 88 (Myd88)/nuclear factor κB (NF-κB) signaling were evaluated.

RESULTS

Severe histopathological damage, such as intestinal mucosal epithelial cell apoptosis, necrosis, and nuclear rupture, was most clearly observed 24 hours after total-abdominal x-ray irradiation. Intestinal integrity was damaged by irradiation, which manifested in reduced levels of the tight-junction proteins Claudin-1, Occludin, and zonula occludens-1(ZO-1). PC pretreatment significantly ameliorated radiation-induced intestinal injury. PC also modulated the gut microbiota composition, increasing the proportion of beneficial bacteria and decreasing that of harmful bacteria, which in turn lowered LPS levels and suppressed TLR4/Myd88/NF-κB pathway activation. Finally, levels of corresponding inflammatory cytokines, including tumor necrosis factor α and interleukin-6, were also downregulated.

CONCLUSION

PC protects against mouse intestinal injury from high-dose radiation by regulating the effect of the gut microbiota on the TLR4/Myd88/NF-κB pathway, suggesting PC as a promising natural radiation countermeasure.

Looking like the locals - gut microbiome changes post-release in an endangered species

BACKGROUND

Captivity presents extreme lifestyle changes relative to the wild, and evidence of microbiome dysbiosis in captive animals is growing. The gut microbiome plays a crucial role in host health. Whilst captive breeding and subsequent reintroduction to the wild is important for conservation, such efforts often have limited success. Post-release monitoring is essential for assessing translocation success, but changes to the microbiome of released individuals are poorly understood. The Tasmanian devil was previously shown to exhibit loss of microbiome diversity as a result of intense captive management. This current study examines changes in the devil gut microbiome in response to translocation and aims to determine if perturbations from captivity are permanent or reversible.

METHODS

Using 16S rRNA amplicon sequencing, we conducted temporal monitoring of the gut microbiome of released devils during two translocation events, captive-to-wild and wild-to-wild. To investigate whether the microbiome of the released devils changed following translocation, we characterized their microbiome at multiple time points during the translocation process over the course of 6-12 months and compared them to the microbiome of wild incumbent devils (resident wild-born devils at the respective release sites).

RESULTS

We showed that the pre-release microbiome was significantly different to the microbiome of wild incumbent animals, but that the microbiomes of animals post-release (as early as 3 to 4 weeks post-release) were similar to wild incumbents. The gut microbiome of released animals showed significant compositional shifts toward the wild incumbent microbiome of both translocation events.

CONCLUSION

Our results suggest that the devil gut microbiome is dynamic and that loss of microbiome diversity in captivity can be restored following release to the wild. We recommend the broader application of microbiome monitoring in wildlife translocation programs to assess the impacts of translocation on animal microbiomes.

Anti-diarrhea effects and identification of Musca domestica larvae low molecular weight peptides (LMWP)

Musca domestica larvae have been used clinically to cure children malnutritional stagnation and low molecular weight peptides (LMWP) of Musca domestica larvae showed more useful bioactivities. But there is no report on anti-diarrhea effects and identification of the LWMP. The purposes of this study were clarifying the anti-diarrhea effects by regulating intestinal microecology and identification of LMWP. In anti-diarrhea test, diarrhea mice were administered LMWP by oral gavage. Then rectal stool indicator bacteria were counted also the identification of rectal stool bacteria were determined by PCR-DGGE. In LMWP identification test, GFC and RP-HPLC were used to separate the peptide. Then the single polypeptide was tested by MALDI TOF and N-terminal sequence analysis. The results of anti-diarrhea showed that LMWP was effective in the inhibition diarrhea in mice. And microbial diversity indices showed that LMWP treatment group exhibited a higher number of bands. The identification test showed that LMWP had four main components (10-30KD, S1, S2, S3), and there were 5, 7 and 4 peaks in S1, S2 and S3, respectively. The the molecular weight of S2-5, S3-2 and S3-3 was 877.053D, 877.0631D and 1069.4391D, respectively. And S3-3 was determined as Chain A, Carboxypeptidase G2. So the hypothesis that intestinal microbiological regulation might be one of the potential anti-diarrhea mechanisms of Musca domestica larvae LMWP which had four main components and one of the single polypeptide was identified could be drawn.

Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome

Inflammatory bowel disease (IBD) is a chronic complex inflammatory gut pathological condition, examples of which include Crohn’s disease (CD) and ulcerative colitis (UC), which is associated with significant morbidity. Although the etiology of IBD is unknown, gut microbiota alteration (dysbiosis) is considered a novel factor involved in the pathogenesis of IBD. The gut microbiota acts as a metabolic organ and contributes to human health by performing various physiological functions; deviation in the gut flora composition is involved in various disease pathologies, including IBD. This review aims to summarize the current knowledge of gut microbiota alteration in IBD and how this contributes to intestinal inflammation, as well as explore the potential role of gut microbiota-based treatment approaches for the prevention and treatment of IBD. The current literature has clearly demonstrated a perturbation of the gut microbiota in IBD patients and mice colitis models, but a clear causal link of cause and effect has not yet been presented. In addition, gut microbiota-based therapeutic approaches have also shown good evidence of their effects in the amelioration of colitis in animal models (mice) and IBD patients, which indicates that gut flora might be a new promising therapeutic target for the treatment of IBD. However, insufficient data and confusing results from previous studies have led to a failure to define a core microbiome associated with IBD and the hidden mechanism of pathogenesis, which suggests that well-designed randomized control trials and mouse models are required for further research. In addition, a better understanding of this ecosystem will also determine the role of prebiotics and probiotics as therapeutic agents in the management of IBD.

Smoking and microbiome in oral, airway, gut and some systemic diseases

The human microbiome harbors a diverse array of microbes which establishes a mutually beneficial relation with the host in healthy conditions, however, the dynamic homeostasis is influenced by both host and environmental factors. Smoking contributes to modifications of the oral, lung and gut microbiome, leading to various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn’s disease, ulcerative colitis and cancers. However, the exact causal relationship between smoking and microbiome alteration remains to be further explored.

Immunoglobulin G4-related immune responses to common food antigens in patients with ulcerative colitis and Crohn's disease

BACKGROUND/AIMS

It is unclear whether IgG4-related immune responses to food can play a role in the pathogenesis of inflammatory bowel disease (IBD). The aim of the present study was to investigate the serum levels of IgG4 to common food antigens in patients with ulcerative colitis (UC), Crohn's disease (CD), and healthy controls.

MATERIALS AND METHODS

Thirty-six patients with CD (n=12) or UC (n=24) and 36 sex- and age-matched healthy individuals (mean age, 49 years) participated in the study. Serum levels of IgG4 to 90 common food antigens were measured. The number of subjects with positivity, defined by cut-off values ≥0.7 U/mL, was compared.

RESULTS

Serum titers of IgG4 to salmon, onion, shrimp, cuttlefish, eel, millet, gluten, soybean, and coconut in patients with IBD were significantly or tended to be higher than those in the control group. Serum levels of IgG4 to salmon, millet, and onion in patients with CD were significantly or tended to be higher than those in the control group. Serum titers of IgG4 to cuttlefish and onion in patients with UC tended to be higher than those in the control group. The number of subjects with positivity to cod, tuna, mackerel, oat, pea, peanut, and coconut was significantly higher in patients with CD than in healthy controls. The number of subjects with positivity to kiwi and cuttlefish was significantly higher in patients with UC than in controls.

CONCLUSION

Patients with IBD shows higher serum levels of IgG4 to diverse food antigens. Patients with CD present IgG4-related immune reactions to more foods than patients with UC.

SYNBIOTIC ADDITIVES IN THE WAFFLES TECHNOLOGY

The problems considered in the paper are the incidence of dysbiosis in the Ukrainian people, the reasons for it, and the methods of improving the diet of those suffering from microfloral disorders. Useful properties and effects of the microorganisms Bifidobacterium and Lactobacillus, and of inulin and lactulose have been studied as well as the ways in which they help to restore a person’s normobiocoenosis. After a research in vitro, with the conditions imitating the human gastrointestinal tract, the survival rate of encapsulated cells of bifidobacteria and lactobacilli in an unfavourable environment has been determined. It has been grounded how necessary microencapsulated forms of microorganisms are in the production of confectionery – firstly, to ‘protect’ them against physiological and technological factors, and secondly, to help them reach the lower regions of the small intestine where their capsules are destroyed and the bacteria are released. The reasons have been given why fatty filling for waffles, as an object to be enriched with useful ingredients, should be preferred when developing healthy and wholesome confectionery. It has been shown how promising probiotics and prebiotics are if used in confectionery technology. The two synbiotic complexes SC 1 and SC 2 have been developed, and such parameters have been determined as the optimum weight fractions of inulin and lactulose in the formulation of the filling, and the number of probiotic microorganisms. It has been established that lactulose can reduce sugar in the formulation of the filling, and using inulin results in replacement of an equivalent amount of fat. To prove how practical it is to add synbiotics to waffles, and to determine the product’s consumer appeal, a tasting assessment of the new types of waffle products has been made. It has been proved that adding synbiotic complexes to the formulations of waffles will result in the consistent high quality of the products, and in their better sensory characteristics. Besides, it can contribute to making the people of Ukraine healthier and fitter for work.

Escherichia coli Pathobionts Associated with Inflammatory Bowel Disease

Gut bacteria play a key role in initiating and maintaining the inflammatory process in the gut tissues of inflammatory bowel disease (IBD) patients, by supplying antigens or other stimulatory factors that trigger immune cell activation. Changes in the composition of the intestinal microbiota in IBD patients compared to that in healthy controls and a reduced diversity of intestinal microbial species are linked to the pathogenesis of IBD. Adherent invasive Escherichia coli (AIEC) has been linked to Crohn's disease (CD) patients, while diffusely adherent E. coli (DAEC) has been associated with ulcerative colitis (UC). Bacteriological analysis of intestinal biopsy specimens and fecal samples from IBD patients shows an increased number of E. coli strains belonging to the B2 phylogenetic group, which are typically known as extraintestinal pathogenic E. coli (ExPEC). Results from studies of both cell cultures and animal models reveal pathogenic features of these E. coli pathobionts, which may link them to IBD pathogenesis. This suggests that IBD-associated E. coli strains play a facilitative role during IBD flares. In this review, we explain IBD-associated E. coli and its role in IBD pathogenesis.

Mucosa-associated microbiota drives pathogenic functions in IBD-derived intestinal iNKT cells

Inflammatory bowel disease (IBD) pathogenesis has been linked to the aberrant activation of the Gut-associated lymphoid tissues against components of the intestinal microbiota. Although the contribution of CD4⁺ T helper cells to inflammatory processes is being increasingly acknowledged, the functional engagement of human invariant natural killer T (iNKT) cells is still poorly defined. Here, we evaluated the functional characteristics of intestinal iNKT cells during IBD pathogenesis and to exploit the role of mucosa-associated microbiota recognition in triggering iNKT cells' pro-inflammatory responses in vivo. Lamina propria iNKT cells, isolated from surgical specimens of active ulcerative colitis and Crohn's disease patients and non-IBD donors, were phenotypically and functionally analyzed ex vivo, and stable cell lines and clones were generated for in vitro functional assays. iNKT cells expressing a pro-inflammatory cytokine profile were enriched in the lamina propria of IBD patients, and their exposure to the mucosa-associated microbiota drives pro-inflammatory activation, inducing direct pathogenic activities against the epithelial barrier integrity. These observations suggest that iNKT cell pro-inflammatory functions may contribute to the fuelling of intestinal inflammation in IBD patients.

Disease-Specific Enteric Microbiome Dysbiosis in Inflammatory Bowel Disease

Inflammatory Bowel disease (IBD) is traditionally divided into Crohn's disease (CD) and ulcerative colitis (UC). UC is a relapsing non-transmural inflammatory disease that is restricted to the colon and is characterized by flare-ups of bloody diarrhea. CD is a chronic, segmental localized granulomatous disease that can affect any part of the entire gastrointestinal tract. Ileo-anal pouch is a procedure restoring functionality of the rectum after a colectomy. IBD is a multifactorial disease and flares of IBD are probably triggered by changes in the intestinal microbiota followed by an abnormal immune response. In this study, we aim to analyze the intestinal bacterial diversity in IBD patients during various stages of disease compared with healthy controls. Permission for human experiments and recruitment of participants was obtained from the Ethic Committee for Copenhagen County hospitals (Permission no. KA-03019, Permission no. KA-20060159). Stools from 26 healthy controls, 42 CD, 38 UC and 18 pouch patients were collected. Stool DNA extraction was performed using Qiagen, DNA mini stool kit Denmark. DGGE-PCR amplifying the V2-V3 region of 16S-rDNA gene of the bacteria was amplified by universal primers HDA1 and HDA2. Analysis of DGGE was performed blinded using BioNumerics version 7.5. After normalization, a DGGE gel band matching was performed. The similarities between profiles were calculated with a ranked Pearson correlation coefficient based on the band matching results using band intensities. Simpson's index of diversity and Pielou's species evenness were calculated. Based on the Shannon Diversity Index, UC patients had lower species diversity and bacterial evenness in comparison to healthy persons, p < 0.05. However, only CD and disease pouch patients had lower species diversity compared to those with inactive disease and healthy controls. Well-functioning pouch patients had decreased species evenness in comparison to diseased pouch patients and control group. During the active disease stage in CD and pouch, the patients have a low bacterial diversity in their gut when compared to the inactive stage. In UC patients, a generally low diversity was observed at all stages of the disease compared to healthy controls.

Contribution of sulfate-reducing bacteria to homeostasis disruption during intestinal inflammation

Alteration in microbial populations and metabolism are key events associated with disruption of intestinal homeostasis and immune tolerance during intestinal inflammation. A substantial imbalance in bacterial populations in the intestine and their relationships with the host have been observed in patients with inflammatory bowel disease (IBD), believed to be part of an intricate mechanism of triggering and progression of intestinal inflammation. Because elevated numbers of sulfate-reducing bacteria (SRB) have been found in the intestines of patients with IBD, the study of their interaction with intestinal cells and their potential involvement in IBD has been the focus of investigation to better understand the intestinal pathology during IBD, as well as to find new ways to treat the disease. SRB not only directly interact with intestinal epithelial cells during intestinal inflammation but may also promote intestinal damage through generation of hydrogen sulfide at high levels. Herein we review the literature to discuss the various aspects of SRB interaction with host intestinal tissue, focusing on their interaction with intestinal epithelial and immune cells during intestinal inflammation.

The influence of vitamin D on M1 and M2 macrophages in patients with Crohn's disease

Defective bacterial clearance by macrophages plays an important role in Crohn's disease (CD). Phenotypes and functions of inflammatory M1 and anti-inflammatory M2 have not been studied in CD. Vitamin D supplementation reduces the severity of CD by unclear mechanisms. We studied macrophage characteristics in CD and controls and the effects of 1,25 vitamin D (1,25D). PBMC were isolated from CD patients and controls. M1 and M2 were generated by culturing of monocytes with GM-CSF and M-CSF, respectively. CD M1 and M2 showed normal phagocytosis and chemotaxis to CCL2 and fMLP. LPS-induced production of TNF-α, IL-12p40 and IL-10 was comparable between groups. Phagocytosis was unaltered with 1,25D; migration only increased marginally. M1 produced more IL-12p40 and TNF-α; IL-10 was greater in M2. 1,25D markedly decreased IL-12p40 by M1 and M2. 1,25D decreased TNF-α in CD M1; IL-10 levels were unaffected. M2 express F13A1, PTGS2, CD163, CXCL10, CD14 and MMP2, whereas TGF-β, CCL1 and CYP27B1 expression was higher in M1. Marker expression was similar between CD and controls. M1 and M2 markers were not differentially modulated by 1,25D. CD macrophages are not functionally or phenotypically different vs.

CONTROLS

1,25D markedly decreased pro-inflammatory M1 cytokines but did not modulate polarization to anti-inflammatory M2 phenotype.

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

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.

Phytochemicals That Influence Gut Microbiota as Prophylactics and for the Treatment of Obesity and Inflammatory Diseases

Gut microbiota (GM) plays several crucial roles in host physiology and influences several relevant functions. In more than one respect, it can be said that you “feed your microbiota and are fed by it.” GM diversity is affected by diet and influences metabolic and immune functions of the host's physiology. Consequently, an imbalance of GM, or dysbiosis, may be the cause or at least may lead to the progression of various pathologies such as infectious diseases, gastrointestinal cancers, inflammatory bowel disease, and even obesity and diabetes. Therefore, GM is an appropriate target for nutritional interventions to improve health. For this reason, phytochemicals that can influence GM have recently been studied as adjuvants for the treatment of obesity and inflammatory diseases. Phytochemicals include prebiotics and probiotics, as well as several chemical compounds such as polyphenols and derivatives, carotenoids, and thiosulfates. The largest group of these comprises polyphenols, which can be subclassified into four main groups: flavonoids (including eight subgroups), phenolic acids (such as curcumin), stilbenoids (such as resveratrol), and lignans. Consequently, in this review, we will present, organize, and discuss the most recent evidence indicating a relationship between the effects of different phytochemicals on GM that affect obesity and/or inflammation, focusing on the effect of approximately 40 different phytochemical compounds that have been chemically identified and that constitute some natural reservoir, such as potential prophylactics, as candidates for the treatment of obesity and inflammatory diseases.

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes and metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn's disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study's results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.

Lack of Adrenomedullin Aggravates Acute TNBS-Induced Colitis Symptoms in Mice, Especially in Females

Adrenomedullin (AM) is a biologically active peptide which has been tested as a new therapy for inflammatory bowel disease (IBD) in animal models and in patients with severe ulcerative colitis. We used an inducible knockout (KO) mouse model for AM to evaluate the effects of endogenous levels of this peptide on the development and degree of pathogenesis of IBD. Acute colitis was induced in mice of both sexes by rectal instillation of 3 mg 2,4,6-trinitrobenzenesulfonic acid (TNBS) in 100 μL of 50% ethanol. Control mice received the same volume of saline in 50% ethanol. During the following 5 days, the weight and the disease severity index of all animals were recorded. After sacrifice, the inflammatory response was macroscopically assessed by analyzing the weight of the colon; by histomorphometrical analysis on histological sections; and by qRT-PCR determination of different inflammatory, adhesion, and regeneration molecules. TNBS administration caused a significantly more severe colitis in KO mice, and especially in females, when compared to wild type (WT) animals. Abrogation of the AM gene caused more severe diarrhea, accompanied by rectal bleeding, anorexia, and a significant increase of colon weight. Histological analysis of TNBS-treated KO mice showed large areas of lymphocyte infiltrates in the mucosa and submucosa, with loss of tissue architecture. No alterations were observed in the expression levels of inflammatory cytokines at the time of sacrifice; meanwhile lack of AM resulted in lower levels of some adhesion molecules and regeneration markers. Taken together, these results support the protective role of endogenous AM against the development of acute colitis, and that its effects are particularly beneficial on females.

Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health

The role of gut microbiota in early life and its impact on gut health and subsequent diseases remain unclear. There is a lack of research and awareness in this area, especially in the Asia-Pacific region, including Malaysia. This paper reports the position of a Malaysian Working Group on some key issues surrounding gut microbiota in early life and its role in gut health and diseases, as well as experts' stand on probiotics and prebiotics. The group reached a consensus that certain factors, including elective caesarean; premature deliveries; complementary feeding; use of antibiotics, prebiotics and/or probiotics; and exposure to the external environmental, have an impact on gut microbiota in early life. However, as evidence is lacking, especially from the Asia-Pacific region, further studies are needed to understand how gut microbiota in early life affects subsequent diseases, including allergy, inflammatory bowel disease, obesity and infantile colic. Lastly, although beneficial in acute diarrhoeal disease and probably allergic eczema, probiotics (and/or prebiotics) should be used cautiously in other gut dysbiotic conditions until more data are available.

Recipe for IBD: can we use food to control inflammatory bowel disease?

The mucosal immune system and the microbiota in the intestinal tract have recently been shown to play a key role in the pathogenesis of inflammatory bowel disease (IBD). Both of these can be influenced by food. Thus, we propose dietary intervention as a therapeutic option for IBD. In this review, we discuss the interaction of the intestinal mucosal immune system and the intestinal microbiota in the context of IBD. In addition, we discuss the impact of food components on immune responses in IBD. Finally, we address the current evidence of how this interaction (i.e., immune system-microbiota) can be modulated by food components, pre/probiotics, and fecal microbiota transplantation (FMT) and how these approaches can support intestinal homeostasis. By gathering the vast amount of literature available on the impact of food on IBD, we aim to distinguish between scientifically sound data and theories, which have not been included in this review.

Update on intestinal microbiota in Crohn's disease 2017: Mechanisms, clinical application, adverse reactions, and outlook

The pathogenesis of Crohn's disease (CD) is complex, and it is thought to be associated with the environment, immune, hereditary, microbe, and other factors. If the balance between the host and the intestinal microbes in CD patients was broken, immune-inflammatory response of susceptible individuals might be triggered. Probiotics could improve the intestinal microbial flora balance and treat human effectively. There are several new mechanisms that might explain the role of probiotics. Fecal microbiota transplantation (FMT) is becoming more and more attractive in treating a large amount of digestive system diseases that are related to the dysbiosis of intestinal microbiota. FMT has been widely used in recurrent Clostridium difficile infection. More and more attention has been paid on the clinical application of FMT in CD, while the exact mechanism is still a mystery. So in this review, we explore the mechanism, clinical application, and adverse reactions of intestinal microbiota in CD so that we can use the tool to cure more diseases. Enteric microbiota leads to new therapeutic strategies for CD.

The potential role of fecal microbiota transplantation in the treatment of inflammatory Bowel disease

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of an unknown etiology. Its pathogenesis involves an interplay of infectious, genetic, environmental, and immunological factors. The current therapeutic options have various limitations in terms of cost, side effect profile, and the development of drug resistance and dependence. Therefore, there is a need to develop future therapeutic options which are safe and effective to control the inflammatory process. This review focuses in a method for the administration of fecal matters (which contains a mixture of various commensals) from a healthy donor to the inflamed colon called fecal microbiota transplantation (FMT) aiming to correct the underlying dysbiosis in the gut as one of the major driving force for the inflammatory process. IBD patients have reduced number of protective (e.g., clostridia and bacteroids) and increased number of pathogenic (e.g., adhesive invasive E. coli and mycobacterium avium paratuberculosis) commensals, and this method is aimed to shift these changes in the gut. Recent studies from animal models and clinical trials suggest promising effects of this method in treating patients with IBD, but more studies are urgently needed to confirm its efficacy and safety, since the etiology of this chronic inflammatory disease is not fully understood and caution should be taken when transplanting fecal matters between individuals which might transfer other infectious organisms and diseases.

Gut microbiota fermentation of marine polysaccharides and its effects on intestinal ecology: An overview

The gut microbiota that resides in the mammalian intestine plays a critical role in host health, nutrition, metabolic and immune homeostasis. As symbiotic bacteria, these microorganisms depend mostly on non-digestible fibers and polysaccharides as energy sources. Dietary polysaccharides that reach the distal gut are fermented by gut microbiota and thus exert a fundamental impact on intestinal ecology. Marine polysaccharides contain a class of dietary fibers that are widely used in food and pharmaceutical industries (e.g., agar and carrageenan). In this regard, insights into fermentation of marine polysaccharides and its effects on intestinal ecology are of vital importance for understanding the beneficial effects of these glycans. Here, in this review, to provide an overlook of current advances and facilitate future studies in this field, we describe and summarize up-to-date findings on how marine polysaccharides are metabolized by gut microbiota and what effects these polysaccharides have on intestinal ecology.

Gleaning Insights from Fecal Microbiota Transplantation and Probiotic Studies for the Rational Design of Combination Microbial Therapies

Beneficial microorganisms hold promise for the treatment of numerous gastrointestinal diseases. The transfer of whole microbiota via fecal transplantation has already been shown to ameliorate the severity of diseases such as Clostridium difficile infection, inflammatory bowel disease, and others. However, the exact mechanisms of fecal microbiota transplant efficacy and the particular strains conferring this benefit are still unclear. Rationally designed combinations of microbial preparations may enable more efficient and effective treatment approaches tailored to particular diseases. Here we use an infectious disease, C. difficile infection, and an inflammatory disorder, the inflammatory bowel disease ulcerative colitis, as examples to facilitate the discussion of how microbial therapy might be rationally designed for specific gastrointestinal diseases. Fecal microbiota transplantation has already shown some efficacy in the treatment of both these disorders; detailed comparisons of studies evaluating commensal and probiotic organisms in the context of these disparate gastrointestinal diseases may shed light on potential protective mechanisms and elucidate how future microbial therapies can be tailored to particular diseases.

Association of altered gut microbiota composition with chronic urticaria

BACKGROUND

An altered gut microbiota composition has recently been linked to some types of allergies.

OBJECTIVE

To compare the relative amounts of Akkermansia muciniphila, Clostridium leptum, Faecalibacterium prausnitzii, and Enterobacteriaceae as members of gut microbiota among patients with chronic urticaria (CU) and healthy controls.

METHODS

A total of 20 patients with CU and 20 healthy individuals matched by age and sex participated in the study. Fresh fecal samples were collected, and DNA extracted from stool samples was analyzed by real-time polymerase chain reaction for the qualitative and quantitative assays of the so-called bacteria.

RESULTS

The frequencies of A muciniphila, C leptum, and F prausnitzii in healthy controls' stool samples were significantly more than those of patients with CU (P < .001, P < .01, and P < .05, respectively), whereas the Enterobacteriaceae family was detected in all patients and healthy controls' stool samples. The relative amounts of A muciniphila in healthy control positive samples were significantly higher than those of samples from patients with CU (P < .001). Furthermore, there was a corresponding increase of relative amounts of C leptum and F prausnitzii in healthy control positive samples compared with those of patients with CU (P = .09 and P = .08, respectively). The mean of the relative amounts of Enterobacteriaceae family in the stool samples from patients with CU was more than that of healthy controls; however, the difference was nearly significant (P = .12).

CONCLUSION

The results reveal a change of frequency and relative amounts of A muciniphila, C leptum, and F prausnitzii in patients with CU compared with healthy controls. This is the first study, to our knowledge, to show the change of microbiota composition in patients with CU.

Lactadherin orthologs inhibit migration of human, porcine and murine intestinal epithelial cells

Lactadherin was originally described due to its appearance in milk, but is abundantly expressed especially by professional and nonprofessional phagocytes. The proteins has been shown to have a multitude of bioactive effects, including inhibition of inflammatory phospholipases, induction of effero‐ and phagocytosis, prevent rotavirus induced gastroenteritis, and modulate intestinal homeostasis by regulating epithelial cell migration. The level of expression seems to be important in a row of serious pathologies linked to the intestinal epithelial barrier function, vascular‐ and autoimmune disease. This study examines the ability of lactadherin to modulate migration of intestinal epithelium. A cell exclusion assay is used to quantify the ability of human, bovine and murine lactadherin orthologs to affect migration of primary small intestine epithelium cells. Previous reports show that recombinant murine lactadherin stimulate rat small intestine cell migration. The present study could not confirm this. Conversely, 10 μg/ml lactadherin inhibits migration. Therefore, as lactadherins enteroprotective properties is well established using in vivo models we conclude that the protective effects are linked to lactadherins ability operate as an opsonin, or other modulating effects, and not a direct lactadherin‐cell induction of migration. Thus, the molecular mechanism behind the enteroprotective role of lactadherin remains to be established.

Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium

OBJECTIVE

To compare colonic microbial composition in systemic sclerosis (SSc) patients and healthy controls and to determine whether certain microbial genera are associated with gastrointestinal (GI) tract symptoms in patients with SSc.

METHODS

Healthy controls were age- and sex-matched (1:1) with adult SSc patients. Cecum and sigmoid mucosal lavage samples were obtained during colonoscopy. The microbiota in these samples were determined by Illumina HiSeq 2000 16S sequencing, and operational taxonomic units were selected. Linear discriminant analysis effect size was used to identify the genera that showed differential expression in SSc patients versus controls. Differential expression analysis for sequence count data was used to identify specific genera associated with GI tract symptoms.

RESULTS

Among 17 patients with SSc (88% female; median age 52.1 years), the mean ± SD total GI Tract 2.0 score was 0.7 ± 0.6. Principal coordinate analysis illustrated significant differences in microbial communities in the cecum and sigmoid regions in SSc patients versus healthy controls (both P = 0.001). Similar to the findings in inflammatory disease states, SSc patients had decreased levels of commensal bacteria, such as Faecalibacterium and Clostridium, and increased levels of pathobiont bacteria, such as Fusobacterium and γ-Proteobacteria, compared with healthy controls. Bifidobacterium and Lactobacillus, which are typically reduced under conditions of inflammation, were also increased in abundance in patients with SSc. In SSc patients with moderate/severe GI tract symptoms, the abundance of Bacteroides fragilis was decreased, and that of Fusobacterium was increased, compared with patients who had no or mild symptoms.

CONCLUSION

This study demonstrates a distinct colonic microbial signature in SSc patients compared with healthy controls. This unique ecologic change may perpetuate immunologic aberrations and contribute to clinical manifestations of SSc.

The human digestive tract has proteases capable of gluten hydrolysis

OBJECTIVE

To identify, purify, and characterize the proteins responsible for glutenase activity in the feces of healthy subjects and patients with celiac disease (CD).

METHODS

Sixteen subjects were included in this study; 8 were healthy with no known food intolerances, and 8 were treated CD patients on a gluten-free diet. Fecal samples were homogenized, and precipitated proteins were purified by chromatography. Glutenase activity was evaluated by bioassays, zymography, and high-performance liquid chromatography with immunogenic 33-mer, 19-mer, and 13-mer gliadin peptides.

RESULTS

The gastrointestinal elastase 3B (CEL3B), elastase 2A (CEL2A), and carboxypeptidase A1 (CBPA1) enzymes degraded human gluten. These proteins fully hydrolyzed 13-mer and 19-mer gliadin peptides that trigger immune-mediated enteropathy in individuals genetically predisposed to CD and partially digested a 33-mer. Feces from patients with CD showed more glutenase activity than feces from individuals without CD (171-466% higher). Peptidase activity against the gliadin peptides also increased in patients with CD.

CONCLUSION

The digestive tracts of patients with CD and healthy subjects have enzymatic machinery needed for gluten degradation. Patients with CD showed more gluten hydrolysis than did healthy individuals, although, in both cases, a fraction of 33-mer peptide remained intact. Gliadin peptides derived from gastrointestinal digestion, especially the 33-mer, can potentially be used by commensal microbiota from both CD-positive and CD-negative individuals, and differences in bacterial hydrolysis can modify its immunogenic capacity.

TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome

Dysbiosis of the gut microbiome via antibiotics, changes in diet and infection can select for bacterial groups that more frequently harbor antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, the impact of environmental toxicants on the reservoir of ARGs in the gut microbiome has received less attention. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist with multiple toxic health effects including immune dysfunction. The selective pressure of TCDD on the abundance of ARG and MGE-harboring gut populations was examined using C57BL/6 mice exposed to 0-30 μg/kg TCDD for 28 and 92 days with the latter having a 30-day recovery period. DNA extracted from temporally collected fecal pellets was characterized using a qPCR array with 384 assays targeting ARGs and MGEs. Fourteen genes, typically observed in Enterobacteriaceae, increased significantly within 8 days of initial dosing, persisted throughout the treatment period, and remained induced 30 days post dosing. A qPCR primer set targeting Enterobacteriaceae also showed 10- to 100-fold higher abundance in TCDD-treated groups, which was further verified using metagenomics. Results show a bloom of ARG-harboring bacterial groups in the gut due to a xenobiotic compound that is not a metal, biocide or antimicrobial.

Gut microbiota of mice putatively modifies amino acid metabolism in the host brain

Recently, it has been found that the gut microbiota influences functions of the host brain by affecting monoamine metabolism. The present study focused on the relationship between the gut microbiota and the brain amino acids. Specific pathogen-free (SPF) and germ-free (GF) mice were used as experimental models. Plasma and brain regions were sampled from mice at 7 and 16 weeks of age, and analysed for free d- and l-amino acids, which are believed to affect many physiological functions. At 7 weeks of age, plasma concentrations of d-aspartic acid (d-Asp), l-alanine (l-Ala), l-glutamine (l-Gln) and taurine were higher in SPF mice than in GF mice, but no differences were found at 16 weeks of age. Similar patterns were observed for the concentrations of l-Asp in striatum, cerebral cortex and hippocampus, and l-arginine (l-Arg), l-Ala and l-valine (l-Val) in striatum. In addition, the concentrations of l-Asp, d-Ala, l-histidine, l-isoleucine (l-Ile), l-leucine (l-Leu), l-phenylalanine and l-Val were significantly higher in plasma of SPF mice when compared with those of GF mice. The concentrations of l-Arg, l-Gln, l-Ile and l-Leu were significantly higher in SPF than in GF mice, but those of d-Asp, d-serine and l-serine were higher in some brain regions of GF mice than in those of SPF mice. In conclusion, the concentration of amino acids in the host brain seems to be dependent on presence of the gut microbiota. Amino acid metabolism in the host brain may be modified by manipulating microbiota communities.

Systemic sclerosis is associated with specific alterations in gastrointestinal microbiota in two independent cohorts

OBJECTIVE

To compare faecal microbial composition in patients with systemic sclerosis (SSc) from 2 independent cohorts with controls and to determine whether certain genera are associated with SSc-gastrointestinal tract (GIT) symptoms.

DESIGN

Adult patients with SSc from the University of California, Los Angeles (UCLA) and Oslo University Hospital (OUH) and healthy controls participated in this study (1:1:1). All participants provided stool specimens for 16S rRNA sequencing. Linear discriminant analysis effect size demonstrated genera with differential expression in SSc. Differential expression analysis for sequence count data identified specific genera associated with GIT symptoms as assessed by the GIT 2.0 questionnaire.

RESULTS

The UCLA-SSc and OUH-SSc cohorts were similar in age (52.1 and 60.5 years, respectively), disease duration (median (IQR): 6.6 (2.5-16.4) and 7.0 (1.0-19.2) years, respectively), gender distribution (88% and 71%, respectively), and GIT symptoms (mean (SD) total GIT 2.0 scores of 0.7 (0.6) and 0.6 (0.5), respectively). Principal coordinate analysis illustrated significant microbial community differences between SSc and controls (UCLA: p=0.001; OUH: p=0.002). Patients with SSc had significantly lower levels of commensal genera deemed to protect against inflammation, such as Bacteroides (UCLA and OUH), Faecalibacterium (UCLA), Clostridium (OUH); and significantly higher levels of pathobiont genera, such as Fusobacterium (UCLA), compared with controls. Increased abundance of Clostridium was associated with less severe GIT symptoms in both cohorts.

CONCLUSIONS

The present analysis detected specific aberrations in the lower GIT microbiota of patients with SSc from 2 geographically and ethnically distinct cohorts. These findings suggest that GIT dysbiosis may be a pathological feature of the SSc disease state.

Mend Your Fences: The Epithelial Barrier and its Relationship With Mucosal Immunity in Inflammatory Bowel Disease

The intestinal epithelium can be easily disrupted during gut inflammation as seen in inflammatory bowel disease (IBD), such as ulcerative colitis or Crohn's disease. For a long time, research into the pathophysiology of IBD has been focused on immune cell-mediated mechanisms. Recent evidence, however, suggests that the intestinal epithelium might play a major role in the development and perpetuation of IBD. It is now clear that IBD can be triggered by disturbances in epithelial barrier integrity via dysfunctions in intestinal epithelial cell-intrinsic molecular circuits that control the homeostasis, renewal, and repair of intestinal epithelial cells. The intestinal epithelium in the healthy individual represents a semi-permeable physical barrier shielding the interior of the body from invasions of pathogens on the one hand and allowing selective passage of nutrients on the other hand. However, the intestinal epithelium must be considered much more than a simple physical barrier. Instead, the epithelium is a highly dynamic tissue that responds to a plenitude of signals including the intestinal microbiota and signals from the immune system. This epithelial response to these signals regulates barrier function, the composition of the microbiota, and mucosal immune homeostasis within the lamina propria. The epithelium can thus be regarded as a translator between the microbiota and the immune system and aberrant signal transduction between the epithelium and adjacent immune cells might promote immune dysregulation in IBD. This review summarizes the important cellular and molecular barrier components of the intestinal epithelium and emphasizes the mechanisms leading to barrier dysfunction during intestinal inflammation.

Alterations in Intestinal Permeability: The Role of the "Leaky Gut" in Health and Disease

All species, including horses, suffer from alterations that increase intestinal permeability. These alterations, also known as "leaky gut," may lead to severe disease as the normal intestinal barrier becomes compromised and can no longer protect against harmful luminal contents including microbial toxins and pathogens. Leaky gut results from a variety of conditions including physical stressors, decreased blood flow to the intestine, inflammatory disease, and pathogenic infections, among others. Several testing methods exist to diagnose these alterations in both a clinical and research setting. To date, most research has focused on regulation of the host immune response due to the wide variety of factors that can potentially influence the intestinal barrier. This article serves to review the normal intestinal barrier, measurement of barrier permeability, pathogenesis and main causes of altered permeability, and highlight potential alternative therapies of leaky gut in horses while relating what has been studied in other species. Conditions resulting in barrier dysfunction and leaky gut can be a major cause of decreased performance and also death in horses. A better understanding of the intestinal barrier in disease and ways to optimize the function of this barrier is vital to the long-term health and maintenance of these animals.

Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period

Pregnancy is a special physical period in reproductive age women, which has a beneficial influence on the course of certain autoimmune diseases. It has been recently suggested that the microbiome undergoes profound changes during pregnancy that are associated with host physiological and immunological adaptations. The maternal microbiome remodeling during pregnancy is an active response of the mother, possibly to alter immune system status and to facilitate metabolic and immunological adaptations, which are needed for a successful pregnancy. In this review, we attempt to discuss (i) the role of maternal microbiome in pregnancy outcomes known to adversely influence neonatal and infant health, including preterm birth, cardiometabolic complications of pregnancy, and gestational weight gain; (ii) the association of microbiome with autoimmunity, allergy diseases, and asthma during pregnancy; and (iii) the impact of helminth infection during pregnancy.

The prevalence of bacterial overgrowth syndrome and its associated factors in patients with inflammatory bowel diseases (according to the data of the Novosibirsk registry)

Aim. To assess the prevalence of bacterial overgrowth syndrome (BOS) and its risk factors in patients with inflammatory bowel diseases (IBD). Subjects and methods. The patients from the Novosibirsk IBD registry, who had undergone a hydrogen breath test (HBT) using a Gastro+ device, were examined. Results. In 93 IBD patients who had undergone a HBD, the prevalence of BOS was 48% (46.2% for ulcerative colitis and 51.2% for Crohn’s disease). There was a strong correlation between abdominal bloating, abdominal rumbling, and positive HBT results in both patient groups. During the HBT, the patients with BOS frequently complained of diarrhea, borborygmi, belching, and anxiety. Conclusion. The findings suggest that BOS is highly prevalent among patients with IBD. BOS is associated with clinical symptoms, such as abdominal bloating, abdominal rumbling, tearfulness, and irritability.

Eukaryotic protein glycosylation: a primer for histochemists and cell biologists

Proteins undergo co- and posttranslational modifications, and their glycosylation is the most frequent and structurally variegated type. Histochemically, the detection of glycan presence has first been performed by stains. The availability of carbohydrate-specific tools (lectins, monoclonal antibodies) has revolutionized glycophenotyping, allowing monitoring of distinct structures. The different types of protein glycosylation in Eukaryotes are described. Following this educational survey, examples where known biological function is related to the glycan structures carried by proteins are given. In particular, mucins and their glycosylation patterns are considered as instructive proof-of-principle case. The tissue and cellular location of glycoprotein biosynthesis and metabolism is reviewed, with attention to new findings in goblet cells. Finally, protein glycosylation in disease is documented, with selected examples, where aberrant glycan expression impacts on normal function to let disease pathology become manifest. The histological applications adopted in these studies are emphasized throughout the text.

Microbiome and chronic inflammatory bowel diseases

It is nowadays generally accepted that the microbiome is a central driver of chronic inflammatory bowel diseases based on observations from human patients as well as inflammatory rodent models. Many studies focussed on different aspects of microbiota and some scientists believe that a primary dis-balance results in a direct microbial induced inflammatory situation. It is also clear that the microbiome is influenced by environmental and genetic factors and is also tightly regulated by host defense molecules such as antimicrobial peptides (defensins et al.). Different lines of investigations showed different complex antimicrobial barrier defects in inflammatory bowel diseases which also influence the composition of the microbiome and generally impact on the microbial-mucosal interface. In this review, we aim to discuss the bigger picture of these different aspects and current views and conclude about therapeutic consequences for future concepts beyond anti-inflammatory treatment.

Microbiome-Linked Crosstalk in the Gastrointestinal Exposome towards Host Health and Disease

The gastrointestinal exposome represents the integration of all xenobiotic components and host-derived endogenous components affecting the host health, disease progression and ultimately clinical outcomes during the lifespan. The human gut microbiome as a dynamic exposome of commensalism continuously interacts with other exogenous exposome as well as host sentineling components including the immune and neuroendocrine circuit. The composition and diversity of the microbiome are established on the basis of the luminal environment (physical, chemical and biological exposome) and host surveillance at each part of the gastrointestinal lining. Whereas the chemical exposome derived from nutrients and other xenobiotics can influence the dynamics of microbiome community (the stability, diversity, or resilience), the microbiomes reciprocally alter the bioavailability and activities of the chemical exposome in the mucosa. In particular, xenobiotic metabolites by the gut microbial enzymes can be either beneficial or detrimental to the host health although xenobiotics can alter the composition and diversity of the gut microbiome. The integration of the mucosal crosstalk in the exposome determines the fate of microbiome community and host response to the etiologic factors of disease. Therefore, the network between microbiome and other mucosal exposome would provide new insights into the clinical intervention against the mucosal or systemic disorders via regulation of the gut-associated immunological, metabolic, or neuroendocrine system.

Dissecting the Interplay Between Intestinal Microbiota and Host Immunity in Health and Disease: Lessons Learned from Germfree and Gnotobiotic Animal Models

This review elaborates the development of germfree and gnotobiotic animal models and their application in the scientific field to unravel mechanisms underlying host-microbe interactions and distinct diseases. Strictly germfree animals are raised in isolators and not colonized by any organism at all. The germfree state is continuously maintained by birth, raising, housing and breeding under strict sterile conditions. However, isolator raised germfree mice are exposed to a stressful environment and exert an underdeveloped immune system. To circumvent these physiological disadvantages depletion of the bacterial microbiota in conventionally raised and housed mice by antibiotic treatment has become an alternative approach. While fungi and parasites are not affected by antibiosis, the bacterial microbiota in these "secondary abiotic mice" have been shown to be virtually eradicated. Recolonization of isolator raised germfree animals or secondary abiotic mice results in a gnotobiotic state. Both, germfree and gnotobiotic mice have been successfully used to investigate biological functions of the conventional microbiota in health and disease. Particularly for the development of novel clinical applications germfree mice are widely used tools, as summarized in this review further focusing on the modulation of bacterial microbiota in laboratory mice to better mimic conditions in the human host.

Brief Report: Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis

OBJECTIVE

Dysbiosis of the intestinal microbiota has been widely established in inflammatory bowel disease (IBD). There is significant clinical and genetic overlap between spondyloarthritis (SpA) and IBD, and up to 50% of all patients with SpA exhibit microscopic signs of bowel inflammation, often bearing particular resemblance to early Crohn's disease, a subtype of IBD. This study was undertaken to assess the relationship between intestinal microbial composition, gut histology, and disease activity markers in SpA.

METHODS

Gene analysis by 16S ribosomal RNA amplicon sequencing was used to compare the microbial composition in ileal and colonic biopsy specimens from 27 patients with SpA (14 with microscopic bowel inflammation, 13 without) and 15 healthy control subjects (ileal samples from all 15 subjects and colonic samples from 6). Spearman's rank correlation tests were used to assess correlations of the microbial composition with disease activity measures.

RESULTS

The intestinal inflammation status (histologically normal versus acute or chronic inflammation) was strongly associated with the mucosal microbiota profile of patients with SpA. In inflamed biopsy tissue, the detected bacterial community composition clustered separately from that in noninflamed biopsy tissue (P < 0.05 by permutational multivariate analysis of variance, using hierarchical clustering on Bray-Curtis distances). Interestingly, abundance of the genus Dialister was found to be positively correlated with the Ankylosing Spondylitis Disease Activity Score (Spearman's rho = 0.62, false discovery rate-corrected q < 0.01). This finding was further supported by the low frequency of Dialister observed in noninflamed ileal and colonic biopsy tissue from patients with SpA and healthy controls.

CONCLUSION

These findings demonstrate a significant difference in the intestinal microbial composition in patients with SpA who have microscopic gut inflammation compared to those without microscopic gut inflammation. Moreover, Dialister may represent a potential microbial marker of disease activity in SpA.