Role of commensal gut bacteria in inflammatory bowel diseases

Dietary Curdlan Enhances Bifidobacteria and Reduces Intestinal Inflammation in Mice

β-glucan consumption is known for its beneficial health effects, but the mode of action is unclear. While humans and mice lack the required enzymes to digest β-glucans, certain intestinal microbes can digest β-glucans, triggering gut microbial changes. Curdlan, a particulate β-glucan isolated from Alcaligenes faecalis, is used as a food additive. In this study we determined the effect of curdlan intake in mice on the intestinal microbiota and dextran sodium sulfate (DSS)-induced intestinal inflammation. The effect of curdlan on the human intestinal microbiota was assessed using i-screen, an assay for studying anaerobic microbial interactions. Mice received oral gavage with vehicle or curdlan for 14 days followed by DSS for 7 days. The curdlan-fed group showed reduced weight loss and colonic inflammation compared to the vehicle-fed group. Curdlan intake did not induce general microbiota community changes, although a specific Bifidobacterium, closely related to Bifidobacterium choerinum, was observed to be 10- to 100-fold more prevalent in the curdlan-fed group under control and colitis conditions, respectively. When tested in i-screen, curdlan induced a global change in the microbial composition of the healthy intestinal microbiota from a human. Overall, these results suggest that dietary curdlan induces microbiota changes that could reduce intestinal inflammation.

Potassium bromate (KBrO3) modulates oxidative stress and inflammatory biomarkers in sodium hydroxide (NaOH) - induced Crohn's colitis in Wistar rats

Potassium bromate (KBrO₃) present in consumed ozonised water was recently documented to exacerbate experimental gastric ulcer. Information, however, is vague as regards its effects in the colon where water reabsorption occurs. In this study, we observed the possible effects of KBrO₃ on oxidative stress and inflammatory biomarkers in sodium hydroxide (NaOH) - induced Crohn's colitis (CC). Wistar rats (180-200 g) were divided into six groups (n = 10): (i) control; (ii) untreated CC (induced by 1.4% NaOH; intra-rectal administration); and (iii-vi) CC treated with vitamin E, KBrO₃, vitamin E+KBrO₃, and sulphazalazine, respectively, for 7 days. Body weight and stool score were monitored daily. By day 3 and 7, excised colon was evaluated for ulcer scores and biochemical and histological analysis. Blood samples collected on days 3 and 7 were assayed for haematological indices using standard methods. Data were subjected to analysis of variance (ANOVA) and p ≤ 0.05 considered significant. Platelet/lymphocyte ratio, colonic ulcer score, malondialdehyde, and mast cells were significantly decreased while colonic sulfhydryl, and Ca²⁺- and Na⁺/K⁺-ATPase activities were increased following KBrO₃ treatment compared with untreated CC. These findings suggest that KBrO₃ may mitigate against NaOH-induced CC via inhibiting mast cell population and oxidative and inflammatory content but stimulating colonic sulfhydryl and Ca²⁺- and Na⁺/K⁺-ATPase activities.

Characterization and Functional Test of Canine Probiotics

Probiotics can modulate the composition of gut microbiota and benefit the host animal health in multiple ways. Lactic acid bacteria (LAB), mainly Lactobacillus and Bifidobacterium species, are well-known microbes with probiotic potential. In the present study, 88 microbial strains were isolated from canine feces and annotated. Among these, the four strains CACC517, 537, 558, and 566 were tested for probiotic characteristics, and their beneficial effects on hosts were evaluated both in vitro and in vivo; these strains exhibited antibiosis, antibiotic activity, acid and bile tolerance, and relative cell adhesion to the HT-29 monolayer cell line. Byproducts of these strains increased the viability and decreased oxidative stress in mouse and dog cell lines (RAW264.7 and DH82, respectively). Subsequently, when the probiotics were applied to the clinical trial, changes in microbial composition and relative abundance of bacterial strains were clearly observed in the experimental animals. Experimental groups before and after the application were obviously separated from PCA analysis of clinical results. Conclusively, these results could provide comprehensive understanding of the effects of probiotic strains (CACC517, 537, 558, and 566) and their industrial applications.

Extracellular Vesicles in Inflammatory Bowel Disease: Small Particles, Big Players

Extracellular vesicles are nanovesicles released by many cell types into the extracellular space. They are important mediators of intercellular communication, enabling the functional transfer of molecules from one cell to another. Moreover, their molecular composition reflects the physiological status of the producing cell and tissue. Consequently, these vesicles have been involved in many [patho]physiological processes such as immunomodulation and intestinal epithelial repair, both key processes involved in inflammatory bowel disease. Given that these vesicles are present in many body fluids, they also provide opportunities for diagnostic, prognostic, and therapeutic applications. In this review, we summarise functional roles of extracellular vesicles in health and disease, with a focus on immune regulation and intestinal barrier integrity, and review recent studies on extracellular vesicles and inflammatory bowel disease. We also elaborate on their clinical potential in inflammatory bowel disease.

Fusobacterium nucleatum Secretes Outer Membrane Vesicles and Promotes Intestinal Inflammation

Multiple studies have implicated microbes in the development of inflammation, but the mechanisms remain unknown. Bacteria in the genus Fusobacterium have been identified in the intestinal mucosa of patients with digestive diseases; thus, we hypothesized that Fusobacterium nucleatum promotes intestinal inflammation. The addition of >50 kDa F. nucleatum conditioned media, which contain outer membrane vesicles (OMVs), to colonic epithelial cells stimulated secretion of the proinflammatory cytokines interleukin-8 (IL-8) and tumor necrosis factor (TNF). In addition, purified F. nucleatum OMVs, but not compounds <50 kDa, stimulated IL-8 and TNF production; which was decreased by pharmacological inhibition of Toll-like receptor 4 (TLR4). These effects were linked to downstream effectors p-ERK, p-CREB, and NF-κB. F. nucleatum >50-kDa compounds also stimulated TNF secretion, p-ERK, p-CREB, and NF-κB activation in human colonoid monolayers. In mice harboring a human microbiota, pretreatment with antibiotics and a single oral gavage of F. nucleatum resulted in inflammation. Compared to mice receiving vehicle control, mice treated with F. nucleatum showed disruption of the colonic architecture, with increased immune cell infiltration and depleted mucus layers. Analysis of mucosal gene expression revealed increased levels of proinflammatory cytokines (KC, TNF, IL-6, IFN-γ, and MCP-1) at day 3 and day 5 in F. nucleatum-treated mice compared to controls. These proinflammatory effects were absent in mice who received F. nucleatum without pretreatment with antibiotics, suggesting that an intact microbiome is protective against F. nucleatum-mediated immune responses. These data provide evidence that F. nucleatum promotes proinflammatory signaling cascades in the context of a depleted intestinal microbiome.IMPORTANCE Several studies have identified an increased abundance of Fusobacterium in the intestinal tracts of patients with colon cancer, liver cirrhosis, primary sclerosing cholangitis, gastroesophageal reflux disease, HIV infection, and alcoholism. However, the direct mechanism(s) of action of Fusobacterium on pathophysiological within the gastrointestinal tract is unclear. These studies have identified that F. nucleatum subsp. polymorphum releases outer membrane vesicles which activate TLR4 and NF-κB to stimulate proinflammatory signals in vitro Using mice harboring a human microbiome, we demonstrate that F. nucleatum can promote inflammation, an effect which required antibiotic-mediated alterations in the gut microbiome. Collectively, these results suggest a mechanism by which F. nucleatum may contribute to intestinal inflammation.

New insights into the interactions between Blastocystis, the gut microbiota, and host immunity

The human gut microbiota is a diverse and complex ecosystem that is involved in beneficial physiological functions as well as disease pathogenesis. Blastocystis is a common protistan parasite and is increasingly recognized as an important component of the gut microbiota. The correlations between Blastocystis and other communities of intestinal microbiota have been investigated, and, to a lesser extent, the role of this parasite in maintaining the host immunological homeostasis. Despite recent studies suggesting that Blastocystis decreases the abundance of beneficial bacteria, most reports indicate that Blastocystis is a common component of the healthy gut microbiome. This review covers recent finding on the potential interactions between Blastocystis and the gut microbiota communities and its roles in regulating host immune responses.

Putting Crohn's on the MAP: Five Common Questions on the Contribution of Mycobacterium avium subspecies paratuberculosis to the Pathophysiology of Crohn's Disease

For decades, Mycobacterium avium subspecies paratuberculosis (MAP) has been linked to the pathogenesis of Crohn's disease. Despite many investigations and research efforts, there remains no clear unifying explanation of its pathogenicity to humans. Proponents argue Crohn's disease shares many identical features with a granulomatous infection in ruminants termed Johne's disease and similarities with ileo-cecal tuberculosis. Both are caused by species within the Mycobacterium genus. Sceptics assert that since MAP is found in individuals diagnosed with Crohn's disease as well as in healthy population controls, any association with CD is coincidental. This view is supported by the uncertain response of patients to antimicrobial therapy. This report aims to address the controversial aspects of this proposition with information and knowledge gathered from several disciplines, including microbiology and veterinary medicine. The authors hope that this discussion will stimulate further research aimed at confirming or refuting the contribution of MAP to the pathogenesis of Crohn's disease and ultimately lead to advanced targeted clinical therapies.

Role of diet and nutrition in inflammatory bowel disease

Inflammatory bowel diseases (IBDs) are closely linked to nutrition. The latest research indicates that diet and nutrition are significantly involved in the etiopathogenesis of the disease, although their specific role throughout its clinical course still remains unclear. This study reviewed how diet and nutrition are associated with IBD development and management. Even though specific diets have been shown to bring about positive outcomes, there is currently no scientific consensus regarding an appropriate diet that would benefit all IBD patients. We suggest that individualized dietary recommendations are of the greatest importance and that diets should be planned to provide individual IBD patients with specific nutrient requirements while keeping all the clinical aspects of the patients in mind. Further research is clearly necessary to investigate nutritional factors involved in IBD development and, especially, to evaluate the applications of the diets during the course of the disease.

Enteric bacteria induce IFNγ and Granzyme B from human colonic Group 1 Innate Lymphoid Cells

Group 1 Innate Lymphoid Cells (which include Natural Killer cells and ILC1s) aid in gut anti-bacterial defense through the production of IFNγ, which is critical for mobilizing protective responses against enteric pathogens. When intestinal epithelial barrier integrity is compromised, commensal bacteria are likely to translocate from the gut lumen into the lamina propria. Few studies have addressed the mechanisms by which commensal bacteria impact the function of gut Group 1 ILCs, especially ILC1s. Utilizing an in vitro human colonic lamina propria mononuclear cell (LPMC) model, we evaluated Group 1 ILC cytokine and cytolytic protein production in response to a panel of enteric Gram-positive and Gram-negative commensal and pathogenic bacteria. IFNγ-production by NK cells and ILC1s was significantly increased after LPMC exposure to Gram-negative commensal or pathogenic bacteria, but not after exposure to the Gram-positive bacteria commensals tested. Stimulation of IFNγ production from Group 1 ILCs was not through direct recognition of bacteria by NK cells or ILC1s, but rather required accessory cells within the LPMC population. Myeloid dendritic cells generated IL-12p70, IL-18, and IL-1β upon exposure to enteric bacteria and these cytokines contributed to Group 1 ILC production of IFNγ. Furthermore, Gram-negative commensal or pathogenic bacteria induced significant expression of Granzyme B in NK cells and ILC1s. Overall, these data demonstrate that some enteric commensal bacteria indirectly induce inflammatory cytokine production and cytolytic protein expression from human colonic Group 1 ILCs, a process which could contribute to inflammation in the setting of microbial translocation.

Reduction of gut microbial diversity and short chain fatty acids in BALB/c mice exposure to microcystin-LR

Gut microbiota has been shown to play critical roles in host health. The present study was to determine the toxicological effects of microcystin-LR (MCLR) on gut microbial community and metabolites using 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS). MCLR was administered to BALB/c mice by gavage for eight weeks. Results of the microbial alpha-diversity (Sobs, Chao1, ACE and Shannon indexes) decreased in MCLR-treated group versus controls. Phylum Candidatus Saccharibacteria decreased significantly in MCLR-treated group versus controls. Correspondingly, more than thirties genera in relative abundance decreased, especially short chain fatty acid (SCFA)-producing bacteria (e.g., Alistipes and Ruminococcus). These results indicated that the gut microbial community structure was remarkably changed by MCLR. Furthermore, concentrations of SCFAs were significantly decreased after MCLR exposure (P < 0.01), where butyrate decreased as high as 4.9-fold. Consequently, sub-chronic exposure to MCLR could not only alter the microbial composition but metabolites. This study offered novel insights into the toxic mechanism of MCs from gut microbiota, and facilitated further clarification of risks to human health from MCs exposure.

Microbiota characterization in Blastocystis-colonized and Blastocystis-free school-age children from Colombia

BACKGROUND

Blastocystis is a protist that lives in the intestinal tract of a variety of hosts, including humans. It is still unclear how Blastocystis causes disease, which presents an ongoing challenge for researchers. Despite the controversial findings on the association between Blastocystis and clinical digestive manifestations, there is currently no consensus as to whether this protozoan actually behaves as a pathogen in humans. Furthermore, the relationship between Blastocystis and the intestinal microbiota composition is not yet clear. For that reason, the aim of this study was to identify if colonization by Blastocystis is related to changes in the diversity and relative abundance of bacterial communities, compared with those of Blastocystis-free individuals in a group of Colombian children.

METHODS

We took stool samples from 57 school-aged children attending a daycare institution in Popayán (Southwest Colombia). Whole DNA was extracted and examined by 16S-rRNA amplicon-based sequencing. Blastocystis was detected by real time PCR and other intestinal parasites were detected by microscopy. We evaluated if Blastocystis was associated with host variables and the diversity and abundance of microbial communities.

RESULTS

The composition of the intestinal bacterial community was not significantly different between Blastocystis-free and Blastocystis-colonized children. Despite this, we observed a higher microbial richness in the intestines of children colonized by Blastocystis, which could, therefore, be considered a benefit to intestinal health. The phylum Firmicutes was the predominant taxonomic unit in both groups analyzed. In Blastocystis-free individuals, there was a higher proportion of Bacteroidetes; similarly, in children colonized by Blastocystis, there was a higher relative abundance of the phylum Proteobacteria; however, no statistically significant differences were found between the comparison groups.

CONCLUSIONS

The presence of Blastocystis showed a decrease in Bacteroides, and an increase in the relative abundance of the genus Faecalibacterium. It was also evident that the presence of Blastocystis was unrelated to dysbiosis at the intestinal level; on the contrary, its presence did not show statistically differences in the intestinal microbiota composition. Nevertheless, we believe that Blastocystis plays a role in the ecology of the intestinal microbiota through its interaction with other microbial components.

Resveratrol Modulates the Gut Microbiota and Inflammation to Protect Against Diabetic Nephropathy in Mice

Oral administration of resveratrol is able to ameliorate the progression of diabetic nephropathy (DN); however, its mechanisms of action remain unclear. Recent evidence suggested that the gut microbiota is involved in the metabolism therapeutics. In the current study, we sought to determine whether the anti-DN effects of resveratrol are mediated through modulation of the gut microbiota using the genetic db/db mouse model of DN. We demonstrate that resveratrol treatment of db/db mice relieves a series of clinical indicators of DN. We then show that resveratrol improves intestinal barrier function and ameliorates intestinal permeability and inflammation. The composition of the gut microbiome was significantly altered in db/db mice compared to control db/m mice. Dysbiosis in db/db mice characterized by low abundance levels of Bacteroides, Alistipes, Rikenella, Odoribacter, Parabacteroides, and Alloprevotella genera were reversed by resveratrol treatment, suggesting a potential role for the microbiome in DN progression. Furthermore, fecal microbiota transplantation, derived from healthy resveratrol-treated db/m mice, was sufficient to antagonize the renal dysfunction, rebalance the gut microbiome and improve intestinal permeability and inflammation in recipient db/db mice. These results indicate that resveratrol-mediated changes in the gut microbiome may play an important role in the mechanism of action of resveratrol, which provides supporting evidence for the gut–kidney axis in DN.

The role of the microbiota in periodontal disease

The last decade has witnessed unparalleled advances in our understanding of the complexity of the oral microbiome and the compositional changes that occur in subgingival biofilms in the transition from health to gingivitis and to destructive periodontal disease. The traditional view, which has held sway for the last 2 decades, that disease is characterized by the outgrowth of a consortium, or consortia, of a limited number of potentially pathogenic organisms, has given way to an alternative paradigm. In this new view, the microbiological changes associated with disease represent whole-scale alterations to the overall microbial population structure and to the functional properties of the entire community. Thus, and in common with other microbially mediated diseases of the gastrointestinal tract, the normally balanced, symbiotic, and generally benign commensal microbiome of the tooth-associated biofilm undergoes dysbiosis to a potentially deleterious microbiota. Coincident with progress in defining the microbiology of these diseases, there have been equally important advances in our understanding of the inflammatory systems of the periodontal tissues, their control, and how inflammation may contribute both to the development of dysbiosis and, in a deregulated state, the destructive disease process. One can therefore speculate that the inflammatory response and the periodontal microbiome are in a bidirectional balance in oral health and a bidirectional imbalance in periodontitis. However, despite these clear insights into both sides of the host/microbe balance in periodontal disease, there remain several unresolved issues concerning the role of the microbiota in disease. These include, but are not limited to, the factors which determine progression from gingivitis to periodontitis in a proportion of the population, whether dysbiosis causes disease or results from disease, and the molecular details of the microbial stimulus responsible for driving the destructive inflammatory response. Further progress in resolving these issues may provide significant benefit to diagnosis, treatment, and prevention.

Effect of Alfalfa Hay and Starter Feeding Intervention on Gastrointestinal Microbial Community, Growth and Immune Performance of Yak Calves

The present study aims to evaluate the effects of different early weaning paradigms, which supplied with extra alfalfa hay, or starter feeding, or both alfalfa hay and starter feeding, along with the milk replacer, on the gastrointestinal microbial community, growth, and immune performance of yak calves. Twenty 30-day-old male yak calves were randomly assigned to four groups, including the control (CON), alfalfa hay (A), starter feeding (S), and starter plus alfalfa hay (SA) groups. The gastrointestinal microbial colonization, the gastrointestinal development and function, and the growth and immune performance of all the yak calves were separately measured. Supplementation with alfalfa and starter feeding during the pre-weaning period significantly increased body weight, body height, body length, and chest girth. The significantly improved rumen fermentation and promoted intestinal digestion-absorption function in alfalfa and starter feeding groups, including the identified significantly increased concentrations of ruminal total volatile fatty acid (VFA); the significantly increased concentrations and proportions of acetate, butyrate, and isovalerate; the increased α-amylase activities in the duodenum, jejunum, and ileum; the increased papillae length and width of rumen epithelium and rumen wall thickness; and the increased villus height and crypt depth of the duodenum, jejunum, and ileum, could all contribute to promote the growth of calves. These significant improvements on rumen fermentation and intestinal digestion-absorption function could be further attributed to the increased proliferation of starch-decomposing, and cellulose- or hemicellulose-decomposing bacteria identified in the rumen, jejunum, and ileum. Furthermore, based on the expression of intestinal inflammatory cytokines and the rumen epithelial RNA sequencing results, alfalfa supplementation reduced the occurrence of ruminal and intestinal inflammation, whereas starter feeding supplementation was mainly beneficial to the differentiation of immune cells and the improved immune function. Meanwhile, the significantly altered relative abundances of genera in the SA group, including increased relative abundance of Limnobacter, Escherichia/Shigella, and Aquabacterium in the rumen and increased relative abundance of Coprococcus, Pseudobutyrivibrio, Flavonifractor, Synergistes, and Sutterella in jejunum, were able to reduce gastrointestinal inflammation and enhance the immune function, which enhanced the immune function of the yak calves fed with alfalfa and starter feeding. Overall, milk replacer supplemented with alfalfa and starter feeding during the pre-weaning period could alter gastrointestinal microbiota and then benefit the gastrointestinal development, digestion-absorption function, growth, and immune performance of the yak calves.

MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions

Microbiome–host interactions play significant roles in health and in various diseases including autoimmune disorders. Uncovering these inter-kingdom cross-talks propels our understanding of disease pathogenesis and provides useful leads on potential therapeutic targets. Despite the biological significance of microbe–host interactions, there is a big gap in understanding the downstream effects of these interactions on host processes. Computational methods are expected to fill this gap by generating, integrating, and prioritizing predictions—as experimental detection remains challenging due to feasibility issues. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins together with host molecular networks. Using the concept of network diffusion, MicrobioLink can analyse how microbial proteins in a certain context are influencing cellular processes by modulating gene or protein expression. We demonstrated the applicability of the pipeline using a case study. We used gut metaproteomic data from Crohn’s disease patients and healthy controls to uncover the mechanisms by which the microbial proteins can modulate host genes which belong to biological processes implicated in disease pathogenesis. MicrobioLink, which is agnostic of the microbial protein sources (bacterial, viral, etc.), is freely available on GitHub.

Dietary AhR Ligands Regulate AhRR Expression in Intestinal Immune Cells and Intestinal Microbiota Composition

A diet rich in vegetables and fruit is generally considered healthy because of a high content of phytochemicals, vitamins, and fiber. The phytochemical indole-3-carbinol (I3C), a derivative of glucobrassicin, is sold as a dietary supplement promising diverse health benefits. I3C metabolites act as ligands of the aryl hydrocarbon receptor (AhR), an important sensor for environmental polyaromatic chemicals. Here, we investigated how dietary AhR ligand supplementation influences AhR target gene expression and intestinal microbiota composition. For this, we used AhR repressor (AhRR)-reporter mice as a tool to study AhR activation in the intestine following dietary I3C-supplementation in comparison with AhR ligand-deprived diets, including a high fat diet. AhRR expression in intestinal immune cells was mainly driven by dietary AhR ligands and was independent of microbial metabolites. A lack of dietary AhR ligands caused enhanced susceptibility to dextran sodium sulfate (DSS)-induced colitis and correlated with the expansion of Enterobacteriaceae, whereas Clostridiales, Muribaculaceae, and Rikenellaceae were strongly reduced. I3C supplementation largely reverted this effect. Comparison of I3C-induced changes in microbiota composition using wild-type (WT), AhRR-deficient, and AhR-deficient mice revealed both AhR-dependent and -independent alterations in the microbiome. Overall, our study demonstrates that dietary AhR ligand supplementation has a profound influence on Ahrr expression in intestinal immune cells as well as microbiota composition.

Involvement of the Gut Microbiota and Barrier Function in Glucocorticoid-Induced Osteoporosis

Glucocorticoids (GCs) are potent immune-modulating drugs with significant side effects, including glucocorticoid-induced osteoporosis (GIO). GCs directly induce osteoblast and osteocyte apoptosis but also alter intestinal microbiota composition. Although the gut microbiota is known to contribute to the regulation of bone density, its role in GIO has never been examined. To test this, male C57/Bl6J mice were treated for 8 weeks with GC (prednisolone, GC-Tx) in the presence or absence of broad-spectrum antibiotic treatment (ABX) to deplete the microbiota. Long-term ABX prevented GC-Tx-induced trabecular bone loss, showing the requirement of gut microbiota for GIO. Treatment of GC-Tx mice with a probiotic (Lactobacillus reuteri [LR]) prevented trabecular bone loss. Microbiota analyses indicated that GC-Tx changed the abundance of Verrucomicobiales and Bacteriodales phyla and random forest analyses indicated significant differences in abundance of Porphyromonadaceae and Clostridiales operational taxonomic units (OTUs) between groups. Furthermore, transplantation of GC-Tx mouse fecal material into recipient naïve, untreated WT mice caused bone loss, supporting a functional role for microbiota in GIO. We also report that GC caused intestinal barrier breaks, as evidenced by increased serum endotoxin level (2.4-fold), that were prevented by LR and ABX treatments. Enhancement of barrier function with a mucus supplement prevented both GC-Tx-induced barrier leakage and trabecular GIO. In bone, treatment with ABX, LR or a mucus supplement reduced GC-Tx-induced osteoblast and osteocyte apoptosis. GC-Tx suppression of Wnt10b in bone was restored by the LR and high-molecular-weight polymer (MDY) treatments as well as microbiota depletion. Finally, we identified that bone-specific Wnt10b overexpression prevented GIO. Taken together, our data highlight the previously unappreciated involvement of the gut microbiota and intestinal barrier function in trabecular GIO pathogenesis (including Wnt10b suppression and osteoblast and osteocyte apoptosis) and identify the gut as a novel therapeutic target for preventing GIO. © 2019 American Society for Bone and Mineral Research.

The association among enterobacterial flora, dietary factors, and prognosis in patients with ulcerative colitis

The role of enterobacterial flora in the onset and progression of inflammatory bowel diseases is a topic of considerable interest. Here, we assessed the association among enterobacterial flora, dietary factors, and ulcerative colitis (UC) progression. Forty-six patients with UC who were diagnosed as being in remission were enrolled. We collected each patient's stool sample one or two days before diagnostic colonoscopy. After colonoscopy, we observed the patients for one year and then retrospectively divided them into two groups: remission (n = 39) and relapse (n = 7) groups, depending on whether the relapse occurred during the follow-up period, and analyzed the relationship among patient characteristics, dietary factors, enterobacterial flora, and UC relapse. Overall, there were no significant differences in bacterial community populations between the remission and relapse groups, except that the order Lactobacillales was detected at a significantly higher rate in the relapse than in the remission group (100% vs 71.4%, p<0.05). Vitamin C intake was significantly higher in the remission than in the relapse group (p<0.05). Although there were no obvious differences in enterobacterial flora between the remission and relapse groups, there was a relationship among enterobacterial flora, diet, and UC progression. Given that the enterobacterial flora was only analyzed at the initiation of the study, we conclude that in future analyses, enterobacterial flora should be sampled at numerous time points to examine its role in UC progression. Further long-term longitudinal studies examining enterobacterial flora, dietary factors, and UC progression are also required.

Effect of prebiotic and synbiotic supplementation in diet on growth performance, small intestinal morphology, stress, and bacterial population under high stocking density condition of broiler chickens

The current study investigated the effect of prebiotic mannan-oligosaccharide (MOS) and synbiotic (MOS mixed with Bacillus subtilis and Bacillus licheniformis) on growth performance and bacterial population under high stocking density (HSD) conditions in broilers. A total of 605 one-day-old male Arbor Acres broiler chickens were randomly assigned to 4 treatments: normal stocking density (NSD; 30 kg/m2 fed basal diets), HSD (40 kg/m2 fed basal diets), HSD chickens fed 0.1% prebiotic (HSDp), and HSD fed 0.1% synbiotic (HSDs). At 35 D of age, the body weight of HSD and HSDp were poorer than NSD group (P < 0.01), whereas the feed conversion ratio (FCR) of the HSDs) group was better than the NSD group (P < 0.01). The HSDp and HSDs groups improved FCR (P < 0.01) and has cheaper feed cost per gain compared to the HSD group. Moreover, the body weight of HSDs group was heavier than the HSDp group (P < 0.05). The level of corticosterone and the heterophil to lymphocyte ratio were highest in the HSD group, whereas these indexes were reduced in both HSDp and HSDs groups (P < 0.05). Duodenal, jejunal, and ileal villus heights were shortest in the HSD group (P < 0.01), and the lowest ileal segment goblet cell counts were also observed in this group (P < 0.05). The HSDp and HSDs groups improved the morphology of gastrointestinal (GI) tract (P < 0.05). The Lactobacillus sp. and Clostridium sp. count in the GI tract of HSD group were low (P < 0.01), whereas Escherichia coli was high (P < 0.01), and Salmonella spp. in jejunum and cecum were detectable when compared with NSD group. Conversely, Bacillus sp., Lactobacillus sp., and Clostridium sp. in HSDp and HSDs groups were increased, and E. coli was reduced in the HSDs group (P < 0.01). Therefore, it is clear that stress from HSD negatively affected growth performance, gut morphology, and microbial population, whereas the supplementation of prebiotic or synbiotic can mitigate the effect of stress and microbial dysbiosis in gut of broiler chickens under HSD condition. Comparatively, under this condition, using synbiotic appears to have more beneficial effects than using the prebiotic.

Small intestinal bacterial overgrowth is associated with Diarrhea-predominant irritable bowel syndrome by increasing mainly Prevotella abundance

Objective: Diarrhea-predominant irritable bowel syndrome (IBS-D) is the main subtype of IBS, a chronic functional gastrointestinal disorder. Small intestinal bacterial overgrowth (SIBO), which is characterized by dysbiosis of the bowel, causes gastrointestinal symptoms quite similar to IBS-D. However, whether SIBO correlates with IBS-D and its further mechanism remain unknown.Materials and Methods: The study included 60 IBS-D patients that fulfilled Rome IV criteria and 60 healthy controls. All subjects were undergoing a lactose breath test (LBT) to diagnose SIBO. IBS-D patients were further assigned to negative SIBO (SIBO^-) subgroup and positive SIBO (SIBO⁺) subgroup to analyze the scores of symptoms and differences in the fecal microbiota.Results: The prevalence of SIBO in IBS-D patients was higher than that in healthy controls (51.7% vs. 16.7%, p ≤ .001). In addition, IBS-SSS in SIBO⁺ subgroup was significantly higher than SIBO^- subgroup (p = .015). The 16S rRNA analyses showed that composition and abundance of fecal microbiota were obviously different between the two subgroups. There was a remarkable increase in Prevotella in IBS-D patients, especially in IBS-D SIBO⁺ sufferers. Meanwhile, there were a moderately positive correlation of the abundance of Prevotella (rho = 0.458, p ≤ .001) with IBS-SSS.Conclusion: SIBO is associated with IBS-D, which may be related to alteration in the intestinal microbiota. These findings suggest the potent role of Prevotella in gastrointestinal symptoms between SIBO and IBS-D, thus provide a novel insight into the connection between SIBO and IBS-D.

Microbiota of Inflammatory Bowel Disease Models

Gut microbiome plays an important role in inflammatory bowel disease (IBD), a group of intestinal chronic inflammation conditions that affect a large population. The animal models of IBD have long been established on basis of pathological features, but their ability to recapitulate patient gut microbiota is unknown. We investigated and compared the composition and biodiversity of bacterial population in the fecal samples from rat models of the two IBD subtypes, and compared them with patient samples. Our analyses revealed that inflammation reduces overall microbiome diversity and increased variation between individuals. We identified specific microbial signatures associated with the two IBD subtypes that were consistent between the animal models and human IBD patients, suggesting that the animal models can partially recapitulate the microbiota in human diseases. Furthermore, metagenome prediction analysis suggested microbial functions that were likely altered by host-microbiota interactions in IBD models.

Equibiotic-GI Consumption Improves Intestinal Microbiota in Subjects with Functional Dyspepsia

Background:

At present, the interpretation of any dysfunction by pathogenic microbial colonization of the digestive tract can be considered as the rupture of the microbiotic balance in the injured or infected area. Phytodrugs with useful properties to balance the intestinal microbiota equibiotics represent an alternative recently proposed by the Medicinal Plant Research Company Phytomedicamenta S.A. The Equibiotic-GI® is a phytodrug developed as a combination of two plant extracts, obtained from the leaves of Psidium guajava L, (Myrtaceae) and the roots of Coptis chinensis Franch. (Racunculaceae). Both plants used traditionally for the treatment of several gastrointestinal disorders.

Objective:

The aim of the current study was to assess the effect of Equibiotic-GI® suspension on intestinal microbiota of subjects with functional dyspepsia.

Methods:

An open-label study performed in 8 adult subjects with functional dyspepsia receiving orally 20 mL of the suspension, daily for two weeks. Fecal samples were collected at baseline and the end of treatment for assessing gut microbiota composition by sequencing the V3-V4 region of the 16S rRNA gene.

Results:

Equibiotic-GI modified the Bacteriodetes/Firmicutes proportion increasing the richness of the microbiota composition and Rikenellaceae and Alistipes abundance.

Conclusion:

Together with the improvement in the gastrointestinal symptomatology after the consumption of the product, the present study is the first clinical demonstration of the capacity of the Equibiotic-GI® to restore and balance the intestinal microbiota.

Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics

Background

The gut microbiota plays important roles in modulating host metabolism. Previous studies have demonstrated differences in the gut microbiome of T2D and prediabetic individuals compared to healthy individuals, with distinct disease-related microbial profiles being reported in groups of different age and ethnicity. However, confounding factors such as anti-diabetic medication hamper identification of the gut microbial changes in disease development.

Method

We used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naïve type 2 diabetic (TN-T2D, n = 77), pre-diabetic (Pre-DM, n = 80), and normal glucose tolerant (NGT, n = 97) individuals to investigate compositional and functional changes of the gut microbiota and the faecal content of microbial and host proteins in Pre-DM and treatment-naïve T2D individuals to elucidate possible host-microbial interplays characterizing different disease stages.

Findings

We observed distinct differences characterizing the gut microbiota of these three groups and validated several key features in an independent TN-T2D cohort. We also demonstrated that the content of several human antimicrobial peptides and pancreatic enzymes differed in faecal samples between three groups.

Interpretation

Our findings suggest a complex, disease stage-dependent interplay between the gut microbiota and the host and point to the value of metaproteomics to gain further insight into interplays between the gut microbiota and the host.

Fund

The study was supported by the National Natural Science Foundation of China (No. 31601073), the National Key Research and Development Program of China (No. 2017YFC0909703) and the Shenzhen Municipal Government of China (No. JCYJ20170817145809215). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Probiotics Efficacy on Oxidative Stress Values in Inflammatory Bowel Disease: A Randomized Double-Blinded Placebo-Controlled Pilot Study

BACKGROUND

Inflammatory bowel diseases (IBD), which include Crohn's disease (CD) and ulcerative colitis (UC), are described as a chronic inflammation of the small intestine and colon, caused by a dysregulated immune response to host intestinal microbiota in genetically susceptible subjects.

OBJECTIVE

The aim of this study was to compare probiotic therapy versus placebo in Oxidative Stress Values and clinical features in patients affected by IBD.

METHOD

Forty (40) patients previously diagnosed for IBD were recruited and randomized to receive probiotics (test group, n=20) or placebo (control group, n=20) administered for 90 days. Subjects in both the groups were assessed for overall oxidant ability (d-ROMs test) and for the antioxidant response (BAP test): data were reported at baseline, after 1 and 3 months. Additional data from anamnesis and haematological investigation were also reported during the study.

RESULTS

d-ROM assay clearly showed that the values observed in the test group were significantly improved, leading to oxidative stress values which are not pathological. The test group showed increasing BAP values, thus confirming the overall improvements of patients 'health following administration of probiotics.

CONCLUSION

Oral administration of the specific probiotics demonstrated its efficacy and safety on patients affected by IBD.

Mechanism-Based Treatment Strategies for IBD: Cytokines, Cell Adhesion Molecules, JAK Inhibitors, Gut Flora, and More

Background

Although TNF inhibitors revolutionized the therapy of inflammatory bowel disease (IBD), we have been reaching a point where other therapies with different mechanisms of action are necessary. A rising number of elderly IBD patients with contraindications to established therapies and a growing group of patients losing response to anti-TNF therapy compel us to find safer, better-tolerated, and, ideally, personalized treatment options. However, in order to choose the right drug to fit a patient, it is indispensable to understand the pathomechanism involved in IBD.

Summary

The aim of this review is to explain the inflammatory signaling pathways in IBD and how to inhibit them with current and future therapeutic approaches. Next to biologic agents targeting inflammatory cytokines (anti-TNF agents, anti-IL-12/-23 agents, and specific inhibitors of IL-23), biologics blocking leukocyte trafficking to the gut (anti-integrin antibodies) are available nowadays. More recently, small molecules inhibiting the JAK-STAT pathway (JAK inhibitors) or preventing lymphocyte trafficking (sphingosine-1-phosphate modulators) have been approved or are under investigation. Furthermore, modifying the microbiota has potential therapeutic effects on IBD, and autologous hematopoietic or mesenchymal stem cell transplantation may be considered for a highly selected group of IBD patients.

Key Message

Physicians should understand the different mechanisms of action of the potential therapies for IBD to select the right drug for the right patient.

Oral Vancomycin as an Adjuvant Treatment in IBD

Objective

To study the efficacy of oral vancomycin (POV) treatment in pediatric inflammatory bowel disease (IBD).

Methods

We conducted retrospective and prospective chart reviews, identifying patients using the Division’s Inflammatory Bowel Disease (IBD) registry, ICD-9 and ICD-10 codes for IBD, and recall of patients receiving POV. Patients aged 2–21 years with active IBD at initiation of POV were included unless they had Clostridium difficile infection or primary sclerosing cholangitis (PSC). Pre- and posttreatment analysis included a Physician Global Assessment (PGA), pediatric ulcerative colitis (UC) activity index (PUCAI), and an abbreviated pediatric Crohn’s disease (CD) activity index (PCDAI). The Wilcoxon Signed Ranks test, determined if pre- and post-POV rankings of symptom severity differed. Mann–Whitney U tests assessed improvement in presenting symptoms.

Results

Nineteen patients met inclusion criteria (12 CD and 7 UC). POV improved the PGA score in 16 of 19 patients (P < 0.001). Mean PGA score pretreatment was 3 ± 0.471; posttreatment mean of 1.58 ± 0.769. Abdominal pain (P < 0.001), diarrhea (P < 0.002), anemia (P < 0.002), and blood in stool (P < 0.001) showed significant improvement. PUCAI and PCDAI scores, pretreatment means of 50 ± 17 and 33 ± 9, respectively, also improved with mean score reduction of 23 in CD and 38 in UC patients after POV initiation (P-value < 0.0001). This improvement was noted for both IBD subtypes.

Conclusions

POV may be an effective adjuvant treatment for pediatric IBD. Its effectiveness is likely due to a combination of its anti-tumor necrosis factor alpha-α activity and its influence on the gut microbiome. Further controlled studies of POV in IBD are warranted to determine the most efficacious use of POV in pediatric IBD.

Aim

This study attempts to expand on the current literature to determine efficacy of POV as an adjuvant therapy in treating active IBD in children.

Clostridium butyricum Strains Suppress Experimental Acute Pancreatitis by Maintaining Intestinal Homeostasis

SCOPE

Acute pancreatitis (AP) is a common abdominal inflammatory disease. Disturbed gut homeostasis secondary to pancreatic inflammation aggravates the condition retroactively. The current study investigates potential beneficial effects of Clostridium butyricum (C. butyricum) strains on AP and underlying mechanisms.

METHODS AND RESULTS

C. butyricum strains MIYAIRI 588 (CBM588) and CGMCC0313.1 (CB0313.1) were supplemented to mice for three weeks before experimental AP or SAP induction. Both CBM588 and CB0313.1 protected against AP, as evidenced by reduced serum amylase and lipase levels, pancreatic edema, and myeloperoxidase activity. Amelioration of both experimental AP and SAP by CB0313.1 indicated a non-model-specific effect. Moreover, C. butyricum inhibited pancreatic neutrophil and dendritic cell infiltration, nucleotide-binding domain leucine-rich repeat-containing family, pyrin domain-containing 3 inflammasome activation, and pro-inflammatory pathways. Additionally in the gut, C. butyricum strains attenuated AP-associated intestinal inflammation and barrier dysfunction, accompanied with reduced pathogenic bacteria Escherichia coli and Enterococcus penetration into pancreas. Gut microbiome analyses further revealed that beneficial effects of C. butyricum on pancreatic-gut homeostasis were correlated with improved dysbiosis. In particular, relative abundance of Desulfovibrionaceae decreased, and Verrucomicrobiaceae Clostridiaceae and Lactobacillaceae increased.

CONCLUSIONS

For the first time, a protective effect of C. butyricum in AP by modulating intestinal homeostasis is demonstrated.

Structural characterization of phosphoethanolamine-modified lipid A from probiotic Escherichia coli strain Nissle 1917

Gut microbiota, a complex microbial community inhabiting human or animal intestines recently regarded as an endocrine organ, has a significant impact on human health. Probiotics can modulate gut microbiota and the gut environment by releasing a range of bioactive compounds. Escherichia coli (E. coli) strain Nissle 1917 (EcN), a Gram-negative bacterial strain, has been used to treat gastrointestinal (GI) disorders (i.e., inflammatory bowel disease, diarrhea, ulcerative colitis, and so on). However, endotoxicity of lipopolysaccharide (LPS), a major component of the cell wall of Gram-negative bacteria in the gut, is known to have a strong influence on gut inflammation and maintenance of gut homeostasis. Therefore, characterizing the chemical structure of lipid A which determines the toxicity of LPS is needed to understand nonpathogenic colonization and commensalism properties of EcN in the gut more precisely. In the present study, MALDI multiple-stage mass spectrometry analysis of lipid A extracted from EcN demonstrates that hexaacylated lipid A (m/z 1919.19) contains a glucosamine disaccharide backbone, a myristate, a laurate, four 3-hydroxylmyristates, two phosphates, and phosphoethanolamine (PEA). PEA modification of lipid A is known to contribute to cationic antimicrobial peptide (CAMP) resistance of Gram-negative bacteria. To confirm the role of PEA in CAMP resistance of EcN, minimum inhibitory concentrations (MICs) of polymyxin B and colistin were determined using a wild-type strain and a mutant strain with deletion of eptA gene encoding PEA transferase. Our results confirmed that MICs of polymyxin B and colistin for the wild-type were twice as high as those for the mutant. These results indicate that EcN can more efficiently colonize the intestine through PEA-mediated tolerance despite the presence of CAMPs in human gut such as human defensins. Thus, EcN can be used to help treat and prevent many GI disorders.

Aquaporin 4 deficiency alleviates experimental colitis in mice

Aquaporin (AQP) 4 is expressed in the basolateral membrane of colonic epithelial cells, and the purpose of this study was to explore the mechanistic role of AQP4 in experimental colitis. Experimental colitis was induced in AQP4 knockout (AQP4^-/-) CD-1 mice and AQP4 wild-type (AQP4^wt) mice by oral administration of dextran sulfate sodium (DSS). Experimental colitis was clinically established. Compared with AQP4^wt mice, AQP4^-/- mice showed increased tolerance to DSS-induced experimental colitis, including lesser degree of weight loss, diarrhea and bleeding, lower disease activity index scores, longer colon lengths, and lesser histologic scores. DSS-treated AQP4^-/- mice had lower serum levels of IL-6 and TNF, higher IL-10 level, and lesser inflammatory cell infiltration. DSS-treated AQP4^-/- mice also had lower immunostaining of NF-κB p65 as well as nuclear levels of p65 and phosphorylated p65. Sequencing of 16S rRNA indicated that DSS-treated AQP4^-/- mice maintained intestinal microbial diversity and had higher Firmicutes/Bacteroidetes ratios and greater relative abundance of Erysipelotrichaceae species. These results suggested for the first time that AQP4 deficiency alleviates experimental colitis in mice. Our study helps to understand the pathogenesis of inflammatory bowel diseases, and blocking AQP4 may represent a novel therapeutic approach for ulcerative colitis.-Wang, L., Tang, H., Wang, C., Hu, Y., Wang, S., Shen, L. Aquaporin 4 deficiency alleviates experimental colitis in mice.

Probiotic Lactobacillus reuteri Prevents Postantibiotic Bone Loss by Reducing Intestinal Dysbiosis and Preventing Barrier Disruption

Antibiotic treatment, commonly prescribed for bacterial infections, depletes and subsequently causes long-term alterations in intestinal microbiota composition. Knowing the importance of the microbiome in the regulation of bone density, we investigated the effect of postantibiotic treatment on gut and bone health. Intestinal microbiome repopulation at 4-weeks postantibiotic treatment resulted in an increase in the Firmicutes:Bacteroidetes ratio, increased intestinal permeability, and notably reduced femoral trabecular bone volume (approximately 30%, p < 0.01). Treatment with a mucus supplement (a high-molecular-weight polymer, MDY-1001 [MDY]) prevented the postantibiotic-induced barrier break as well as bone loss, indicating a mechanistic link between increased intestinal permeability and bone loss. A link between the microbiome composition and bone density was demonstrated by supplementing the mice with probiotic bacteria. Specifically, Lactobacillus reuteri, but not Lactobacillus rhamnosus GG or nonpathogenic Escherichia coli, reduced the postantibiotic elevation of the Firmicutes:Bacteroidetes ratio and prevented femoral and vertebral trabecular bone loss. Consistent with causing bone loss, postantibiotic-induced dysbiosis decreased osteoblast and increased osteoclast activities, changes that were prevented by both L. reuteri and MDY. These data underscore the importance of microbial dysbiosis in the regulation of intestinal permeability and bone health, as well as identify L. reuteri and MDY as novel therapies for preventing these adverse effects. © 2018 American Society for Bone and Mineral Research.

The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease

The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient's genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn's disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these. Technologies such as metagenomics, metataxomics, metatranscriptomics, metaproteomics and metabonomics are therefore allowing us a deeper understanding of the role of the microbiota in IBD. Furthermore, the integration of these systems biology technologies through advancing computational and statistical techniques are beginning to understand the microbiome interactions that both contribute to health and diseased states in IBD. This review aims to explore how such systems biology technologies are advancing our understanding of the gut microbiota, and their potential role in delineating the aetiology, development and clinical care of IBD.

Escherichia coli promotes DSS‑induced murine colitis recovery through activation of the TLR4/NF‑κB signaling pathway

Increasing evidence suggests that intestinal microbiota have critical function in the pathogenesis of inflammatory bowel disease. This present study investigated the effects of Escherichia coli (E. coli) in mice with dextran sulfate sodium (DSS)-induced colitis. Furthermore, Toll-like receptor 4 (TLR4) and nuclear factor-κB (NF-κB) gene expression was measured by reverse transcription-quantitative polymerase chain reaction. In total, two experiments were performed. In the first experiment, four groups were established in BALB/c mice: i) Group A, control (no treatments); ii) group B, DSS-induced colitis; iii) group C, DSS-induced colitis bacteria depleted (BD) mice; and iv) group D, E. coli-treated DSS-induced colitis BD mice. In the second experiment, there were three groups: i) Group A1, control C57BL/6 mice; ii) group B1, E. coli-treated DSS-induced colitis BD C57BL/6 mice; and iii) E. coli-treated DSS-induced colitis BD TLR4^−/− mice. Clinical outcomes, colon and immune histopathology and tissue myeloperoxidase activity were assessed. Mice with DSS-induced colitis that were treated with E. coli exhibited enhanced recovery, with significantly improved clinical and histological scores compared with the DSS only group. The mRNA expression of TLR4 and NF-κB in the E. coli-treated group was also significantly higher. These effects were abolished in TLR4^−/− mice, suggesting that E. coli may have promoted recovery through the TLR4 pathway. The present study indicated that E. coli promoted recovery from DSS-induced colitis in mice, potentially through activation of the TLR4/NF-κB signaling pathway.

Association of Fucosyltransferase 2 Gene Variant with Inflammatory Bowel Diseases: A Meta-Analysis

BACKGROUND Ulcerative colitis (UC) and Crohn's disease (CD) are the 2 main type of inflammatory bowel diseases (IBDs). Several studies have been conducted to investigate the association of fucosyltransferase 2 gene (rs601338) variant with UC and CD, but the results were inconsistent. Here, we performed a meta-analysis to clarify this issue based on a relatively larger sample size. MATERIAL AND METHODS A systematic literature search was conducted in PubMed, Embase, CNKI, and Chinese Wangfang databases up to 31 May 2018. Meta results were synthesized by using crude odds ratio with 95% confidence interval. Heterogeneity, sensitivity analysis, subgroup analysis, and publication bias were assessed using STATA 11.0 software. RESULTS A total of 8 relevant studies including 3874 IBDs patients (1872 UC cases, 2002 CD cases) and 5445 controls were included for meta-analysis. We found a significant association between rs601338 A allele and risk of IBDs in the Chinese population (OR=2.35, 95%CI=1.66~3.34, P=0.001), but not in whites. Stratified by disease type, we found a significant association between rs601338 polymorphism with CD and UC in the Chinese population, but not in the white population. In addition, funnel plot and Egger's linear regression test suggests no publication bias in all genetic models. CONCLUSIONS Fucosyltransferase 2 gene (rs601338) polymorphism is associated with susceptibility to IBD, UC, and CD in the Chinese population, but these results might not be generalizable to other ethnic populations. Further well-designed studies are needed to confirm these findings.

Development of multiplex PCR and multi-color fluorescent in situ hybridization (m-FISH) coupled protocol for detection and imaging of multi-pathogens involved in inflammatory bowel disease

Background

Several pathogens have been debated to play a role in inflammatory bowel disease (IBD) including Crohn's disease (CD). None of these pathogens have been investigated together in same clinical samples. We developed a multiplex PCR and multi-color fluorescent in situ hybridization (m-FISH) protocols for simultaneous detection of CD-associated pathogens including Mycobacterium avium subspecies paratuberculosis (MAP), Klebsiella pneumoniae, and adherent-invasive Escherichia coli strain LF82.

Methods

The multiplex PCR is based on 1-h DNAzol^® extraction protocol modified for rapid extraction of bacterial DNA from culture, blood, and intestinal biopsies. Oligonucleotide primers sequences unique to these pathogens were evaluated individually and in combinations using bioinformatics and experimental approaches. m-FISH was based on fluorescent-tagged oligonucleotides and confocal scanning laser microscopy (CSLM).

Results

Following several attempts, the concentration of the oligonucleotide primers and DNA templates and the PCR annealing temperatures were optimized. Multiplex PCR analyses revealed excellent amplification signal in trials where a single primer set and combinations of two and three primers sets were tested against a mixture of DNA from three different bacteria or a mixture of three bacterial cultures mixed in one tube before DNA extraction. Slides with individual and mixtures of bacterial cultures and intestinal tissue sections from IBD patients were tested by m-FISH and the CSLM images verified multiplex PCR results detected on 3% agarose gel.

Conclusion

We developed a 4-h multiplex PCR protocol, which was validated by m-FISH images, capable of detecting up to four genes from major pathogens associated with CD. The new protocol should serve as an excellent tool to support efforts to study multi-pathogens involved in CD and other autoimmune disease.

Effects of the 1975 Japanese diet on the gut microbiota in younger adults

Japan is known for its longevity worldwide; the Japanese diet is thought to contribute to this longevity. However, the Japanese diet has become westernized over the past years, with a parallel increase in the incidence of lifestyle diseases. Thus, whether the modern Japanese diet is still healthy requires investigation. A diet with characteristics of the 1975 Japanese diet (JD) was previously shown to have beneficial effects on mice and humans. In this study, we examined whether intestinal bacteria are involved in the health benefits of this diet by analyzing changes in the composition of the fecal microbiota between humans who ingested the JD and those consuming a modern Japanese diet (MD). We also examined correlations between intestinal bacteria and biological parameters. A randomized controlled trial was performed to determine the effects of the 1975 JD compared to those of the MD. Subjects aged 20-29 years were randomly assigned to the JD (n=11) and MD (n=10) groups. Each subject consumed their respective diet three times per day for 28 days, and changes in intestinal bacteria before to after this period were evaluated. Four genera (unclassified Lachnospiraceae, Parabacteroides, Sutterella and unclassified Rikenellaceae) were significantly changed upon intake of the JD. Based on correlation analysis, relationships were found between changes in these genera and decreases in fat%; fat mass; and levels of blood glutamic oxaloacetic transaminase, blood triacylglycerols and hemoglobin A1c. These results suggest that changes in intestinal bacteria are involved in the health benefits of the JD.

Psychological co-morbidities in COPD: Targeting systemic inflammation, a benefit for both?

COPD is a chronic lung disease characterized by persistent respiratory symptoms and airflow limitation due to airway and/or alveolar abnormalities. Furthermore, COPD is often characterized by extrapulmonary manifestations and comorbidities worsening COPD progression and quality of life. A neglected comorbidity in COPD management is mental health impairment defined by anxiety, depression and cognitive problems. This paper summarizes the evidence for impaired mental health in COPD and focuses on current pharmacological intervention strategies. In addition, possible mechanisms in impaired mental health in COPD are discussed with a central role for inflammation. Many comorbidities are associated with multi-organ-associated systemic inflammation in COPD. Considering the accumulative evidence for a major role of systemic inflammation in the development of neurological disorders, it can be hypothesized that COPD-associated systemic inflammation also affects the function of the brain and is an interesting therapeutic target for nutra- and pharmaceuticals.

Seven days triple therapy for eradication of Helicobacter pylori does not alter the disease activity of patients with inflammatory bowel disease

Background/Aims

The influences of Helicobacter pylori eradication therapy on the disease course of inflammatory bowel disease (IBD) are still unclear. We therefore conducted a multicenter, retrospective cohort study to evaluate the safety of H. pylori eradication therapy for IBD patients.

Methods

IBD patients with H. pylori eradication from 2005 to 2015 (eradication group) and control patients (non-eradication group; 2 paired IBD patients without H. pylori eradication matched with each eradicated patient) were included. IBD exacerbation (increased/additional IBD drug or IBD-associated hospitalization/surgery) and disease improvement based on the physicians’ global assessment were investigated at baseline, and at 2 and 6 months after eradication or observation.

Results

A total of 429 IBD (378 ulcerative colitis, 51 Crohn’s disease) patients, comprising 144 patients in the eradication group and 285 patients in the non-eradication group, were enrolled at 25 institutions. IBD exacerbation was comparable between groups (eradication group: 8.3% at 2 months [odds ratio, 1.76; 95% confidence interval, 0.78–3.92; P=0.170], 11.8% at 6 months [odds ratio, 1.60; 95% confidence interval, 0.81–3.11; P=0.172]). Based on the physicians’ global assessment at 2 months, none of the patients in the eradication group improved, whereas 3.2% of the patients in the non-eradication group improved (P=0.019). Multivariate analysis revealed that active disease at baseline, but not H. pylori eradication, was an independent factor for IBD exacerbation during 2 months’ observation period. The overall eradication rate was 84.0%–comparable to previous reports in non-IBD patients.

Conclusions

H. pylori eradication therapy does not alter the short-term disease activity of IBD.

Actinomyces and Alimentary Tract Diseases: A Review of Its Biological Functions and Pathology

Actinomyces are nonmotile, filamentous, Gram-positive bacteria that cause actinomycosis in immunodeficiency patients. Although the prognosis of actinomycosis is good, the diagnosis of actinomycosis is quite difficult. Recent studies on actinomycosis have shown that Actinomyces play an important role in various biological and clinical processes, such as the formation of dental plaque and the degradation of organics in the gastrointestinal tract. Here, the distribution of Actinomyces in the digestive tract, and different biological effects of actinomycosis, and its clinical association with inflammatory diseases are discussed. Furthermore, an overview of the most commonly used treatment methods and drugs used to treat Actinomyces infected alimentary canal diseases is presented.

The Polysaccharides from Codonopsis pilosula Modulates the Immunity and Intestinal Microbiota of Cyclophosphamide-Treated Immunosuppressed Mice

Based on previous studies about microflora regulation and immunity enhancement activities of polysaccharides from Codonopsis pilosula Nannf. var. modesta (Nannf.) L. T. Shen (CPP), there is little study on intestinal mucosal immunity, which is a possible medium for contacting microflora and immunity. In the present study, the BALB/c mice were divided into five groups (eight mice in each group), including a normal group (Con), a model control group (Model), and model groups that were administered CPP (50, 100, 200 mg/kg/d) orally each day for seven days after intraperitoneal injection of 60 mg/kg BW/d cyclophosphamide (CP) for three days. CPP recovered the spleen index and restored the levels of IFN-γ, IL-2, IL-10, as well as serum IgG. In addition, it elevated ileum secretory immunoglobulin A (sIgA), the number of Lactobacillus and acetic acid content in cecum. These results indicated that CPP plays an important role in the protection against immunosuppression, especially mucosa immune damage, and the inhibition of pathogenic bacteria colonization, which could be considered a potential natural source of immunoregulator.

Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions

Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice. In the GIT of humans, fungi belonging to the phyla Ascomycota, Basidiomycota and Chytridiomycota are predominant. The murine intestines harbor a more diverse assemblage of fungi. Diet is one of the major factors influencing colonization of fungi in the GIT. Presence of the genus Candida is positively associated with dietary carbohydrates, but are negatively correlated with dietary amino acids, proteins, and fatty acids. However, the relationship between diet and the fungal community (and functions), as well as the underlying mechanisms remains unclear. Dysbiosis of intestinal fungi can cause invasive infections and inflammatory bowel diseases (IBD). However, it is not clear whether dysbiosis of the mycobiome is a cause, or a result of IBD. Compared to non-inflamed intestinal mucosa, the abundance and diversity of fungi is significantly increased in the inflamed mucosa. The commonly observed commensal fungal species Candida albicans might contribute to occurrence and development of IBD. Limited studies show that Candida albicans might interact with immune cells of the host intestines through the pathways associated with Dectin-1, Toll-like receptor 2 (TLR2), and TLR4. This review is expected to provide new thoughts for future studies on intestinal fungi and for new therapies to fungal infections in the GIT of human and animals.

The Effect of Feeding Cocoa Powder and Lactobacillus rhamnosus on the Composition and Function of Pig Intestinal Microbiome

BACKGROUND

Dietary habits have been linked with variability of gut microbiota composition and disease risk.

OBJECTIVE

The aim of this study was to evaluate the effect of feeding a cocoa powder with or without a probiotic on the composition and function of the fecal microbiome of pigs.

METHODS

Four groups of 8 pigs each were fed a standard growth diet supplemented with cocoa powder, Lactobacillus rhamnosus (LGG), cocoa powder + LGG, or an equal amount of fiber similar to that found in cocoa powder (control group). Fecal samples were collected prior to and 4 wk after initiation of the dietary intervention. Microbiota composition was determined after amplification of the first 2 variable regions of the 16S ribosomal DNA (rDNA). Predictions of metagenomic function were calculated using 16S rDNA sequence data through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt).

RESULTS

After 4 wk of treatment, bacterial abundance analysis demonstrated a prebiotic effect of cocoa powder on endogenous Bifidobacteriaceae and Lactobacillaceae and increased abundance of saccharolytic butyrate-producing bacteria like Roseburia. An increased bacterial evenness, Shannon diversity index, and diverse metabolic profile were detected in microbiomes of pigs fed the cocoa powder + LGG (P < 0.05) but not in pigs in the other 3 groups.

CONCLUSION

The data generated from this work demonstrated that 4-wk dietary treatment with cocoa powder alone or in combination with LGG probiotic had an impact on the composition and function of the fecal microbiota of healthy pigs.

The Potential of Probiotics as a Therapy for Osteoporosis

Osteoporosis, characterized by low bone mass and micro-architectural deterioration of bone tissue with increased risk of fracture, can be categorized into two forms: primary and secondary, depending on whether it occurs as part of the natural aging process (estrogen deficiency) or as part of disease pathology. In both forms bone loss is due to an imbalance in the bone remodeling process, with resorption/formation skewed more toward bone loss. Recent studies and emerging evidence consistently demonstrate the potential of the intestinal microbiota to modulate bone health. This review discusses the process of bone remodeling and the pathology of osteoporosis and introduces the intestinal microbiota and its potential to influence bone health. In particular, we highlight recent murine studies that examine how probiotic supplementation can both increase bone density in healthy individuals and protect against primary (estrogen deficiency) as well as secondary osteoporosis. Potential mechanisms are described to account for how probiotic treatments could be exerting their beneficial effect on bone health.

Advances in Probiotic Regulation of Bone and Mineral Metabolism

Probiotics have been consumed by humans for thousands of years because they are beneficial for long-term storage of foods and promote the health of their host. Ingested probiotics reside in the gastrointestinal tract where they have many effects including modifying the microbiota composition, intestinal barrier function, and the immune system which result in systemic benefits to the host, including bone health. Probiotics benefit bone growth, density, and structure under conditions of dysbiosis, intestinal permeability, and inflammation (recognized mediators of bone loss and osteoporosis). It is likely that multiple mechanisms are involved in mediating probiotic signals from the gut to the bone. Studies indicate a role for the microbiota (composition and activity), intestinal barrier function, and immune cells in the signaling process. These mechanisms are not mutually exclusive, but rather, may synergize to provide benefits to the skeletal system of the host and serve as a starting point for investigation. Given that probiotics hold great promise for supporting bone health and are generally regarded as safe, future studies identifying mechanisms are warranted.

Effects of Melatonin on Intestinal Microbiota and Oxidative Stress in Colitis Mice

This study investigated the antioxidant capacity and intestinal bacteria community in a mouse model of DSS-induced colitis. Twenty mice were randomly assigned to two treatments: mice with colitis induced by 5% DSS (DSS group) and mice with colitis induced by 5% DSS that also received melatonin treatment (MEL group). The DSS group showed significantly less antioxidant capability than the MEL group, but the two groups did not differ significantly in terms of diversity index (Shannon and Simpson), bacterial culture abundance (Chao1 and ACE), and coverage (Good's coverage estimator). Bacteroidetes were the most abundant phylum in the DSS group (58.93%), followed by Firmicutes with 31.46% and Proteobacteria with 7.97%. In contrast, Firmicutes were the most abundant in the MEL group (49.48%), followed by Bacteroidetes with 41.63% and Proteobacteria with 7.50%. The results support the use of melatonin for prevention of intestinal bowel disease due to its modulatory effect on antioxidant capability and microbiota in mice with colitis. Melatonin was demonstrated to improve the oxidative stress resistance of mice with colitis and regulate the intestinal microbial flora, thus improving intestinal health.

The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota

Inflammation plays pivotal roles in different stages of tumor development. Screening for predisposing genetic abnormalities and understanding the roles these genes play in the crosstalk between immune and cancer cells will provide new targets for cancer therapy and prevention. The interferon inducible transmembrane (IFITM) genes are involved in pathogenesis of the gastro-intestinal tract. We aimed at delineating the role of IFITM3 in colonic epithelial homeostasis, inflammation and colitis-associated tumorigenesis using IFITM3-deficient mice. Chemical induction of colitis in IFITM3-deficient mice results in significantly increased clinical signs of inflammation and induction of invasive tumorigenesis. Bone marrow transplantation showed that cells of the hematopoietic system are responsible for colitis deterioration. In these mice, impaired cytokine expression skewed inflammatory response toward pathogenic Th17 with reduced expression of the anti-inflammatory cytokine IL10 during the recovery phase. Intriguingly, mice lacking the entire IFITM locus developed spontaneous chronic colitis from the age of 14 weeks. Sequencing the 16S rRNA of naïve mice lacking IFITM3 gene, or the entire locus containing five IFITM genes, revealed these mice had significant bacterial differences from their wild-type littermates. Our novel results provide strong evidence for the essential role of IFITM genes in ameliorating colitis and colitis-associated tumorigenesis.

Resveratrol and inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract, comprising ulcerative colitis (UC) and Crohn's disease (CD). Progression of IBD leads to long-term impairment of intestinal structure and function. The pathogenesis of IBD is complex, involving environmental, immunological, genetic, microbial, and psychological factors. The conventional therapies and many existing biopharmaceuticals for IBD have limited efficacy or adverse effects. As a promising safe and effective therapy for IBD, resveratrol has been studied widely, as it has shown anti-inflammatory and antioxidant activity. Resveratrol's mechanism of action involves multiple immune responses and signaling pathways; it is absorbed quickly and metabolized into various derivatives. However, the poor water solubility and low bioavailability of resveratrol limit its clinical applications. Further research should attempt to improve the stability and oral bioavailability of resveratrol by modification and various delivery systems.

Animal models for studying epithelial barriers in neonatal necrotizing enterocolitis, inflammatory bowel disease and colorectal cancer

The intestinal epithelial cells line the luminal surface of the entire gastrointestinal tract which is crucial for the absorption of nutrients and prevention of pathogens entering from the external environment. The epithelial barrier plays an important role in organ development, disease pathogenesis, and aging. The major component of an epithelial barrier is the single columnar epithelium and tight junctions. Tight junctions are located at the most apical region of the junctional complex and contain many integral membrane proteins, such as occludin, the claudin family, and junctional adhesion molecules (JAMs). The disruption of intestinal epithelial barriers may lead to several pathophysiological conditions causing malabsorption of nutrition and chronic inflammation. In this review, we provide an update on the alterations of epithelial barriers associated with gut diseases using experimental animal models; we appraise the role of tight junctions in neonatal necrotizing enterocolitis (NEC), inflammatory bowel disease (IBD), and colorectal cancer; we also compare some common features as well as differences and similarities in the pathophysiology of intestinal inflammation in neonatal (NEC) and adult (IBD) gut.