Comparison of sampling methods in assessing the microbiome from patients with ulcerative colitis

Background Dysbiosis of ulcerative colitis (UC) has been frequently investigated using readily accessible stool samples. However, stool samples might insufficiently represent the mucosa-associated microbiome status. We hypothesized that luminal contents including loosely adherent luminal bacteria after bowel preparation may be suitable for diagnosing the dysbiosis of UC. Methods This study included 16 patients with UC (9 men and 7 women, mean age: 52.13 ± 14.09 years) and 15 sex- and age-matched healthy individuals (8 men and 7 women, mean age: 50.93 ± 14.11 years). They donated stool samples before colonoscopy and underwent luminal content aspiration and endoscopic biopsy during the colonoscopy. Then, the composition of each microbiome sample was analyzed by 16S rRNA-based next-generation sequencing. Results The microbiome between stool, luminal contents, and biopsy was significantly different in alpha and beta diversities. However, a correlation existed between stool and luminal contents in the Procrustes test (p = 0.001) and Mantel test (p = 0.0001). The stool microbiome was different between patients with UC and the healthy controls. Conversely, no difference was found in the microbiome of luminal content and biopsy samples between the two subject groups. The microbiome of stool and lavage predicted UC, with AUC values of 0.85 and 0.81, respectively. Conclusion The microbiome of stool, luminal contents, and biopsy was significantly different. However, the microbiome of luminal contents during colonoscopy can predict UC, with AUC values of 0.81. Colonoscopic luminal content aspiration analysis could determine microbiome differences between patients with UC and the healthy control, thereby beneficial in screening dysbiosis via endoscopy. Trial registration: This trial was registered at http://cris.nih.go.kr. Registration No.: KCT0003352), Date: 2018–11-13.

Multimodal Imaging Mass Spectrometry of Murine Gastrointestinal Tract with Retained Luminal Content Shows Molecular Localization Patterns

ABSTRACTDigestive diseases impact 62 million people a year in the United States. Despite the central role of the gut to human health, past imaging mass spectrometry (IMS) investigations into the gastrointestinal tract are incomplete. The gastrointestinal tract, including luminal content, harbors a complex mixture of microorganisms, host dietary content, and immune factors. Existing imaging approaches remove luminal content, and images focus on small regions of tissue. Here, we demonstrate the use of a workflow to collect multimodal imaging data for both intestinal tissue and luminal content. This workflow for matrix-assisted laser desorption/ionization imaging mass spectrometry retains luminal content and expands the amount of tissue imaged on one slide. Results comparing tissue and luminal content show unique molecular distributions using multimodal imaging modalities including protein, lipid, and elemental imaging. Leveraging this method to investigate intestinal tissue infected with Clostridioides difficile compared to control tissue shows clear differences in lipid abundance of various lipid classes in luminal content during infection. These data highlight the potential for this approach to detect unique biological and markers of infection in the gut.

Comparison of Sampling Methods in Assessing the Microbiomefrom Patients with Ulcerative Colitis

Background: Dysbiosis of ulcerative colitis (UC) has been frequently investigated using readily accessible stool samples. However, stool samples might insufficiently represent the mucosa-associated microbiome status. We hypothesized that luminal contents including loosely adherent luminal bacteria after bowel preparation may be suitable for diagnosing the dysbiosis of UC.Methods: This study included 16 patients with UC (9 men and 7 women, mean age: 52.13 ± 14.09 years) and 15 sex- and age-matched healthy individuals (8 men and 7 women, mean age: 50.93 ± 14.11 years). They donated stool samples before colonoscopy and underwent luminal content aspiration and endoscopic biopsy during the colonoscopy. Then, the composition of each microbiome sample was analyzed by 16S rRNA-based next-generation sequencing.Results: The microbiome between stool, luminal contents, and biopsy was significantly different in alpha and beta diversities. However, a correlation existed between stool and luminal contents in the Procrustes test (p = 0.001) and Mantel test (p = 0.0001). The stool microbiome was different between patients with UC and the healthy controls. Conversely, no difference was found in the microbiome of luminal content and biopsy samples between the two subject groups. The microbiome of stool and lavage predicted UC, with AUC values of 0.85 and 0.81, respectively.Conclusion: The microbiome of stool, luminal contents, and biopsy was significantly different. However, the microbiome of luminal contents during colonoscopy can predict UC, with AUC values of 0.81. Colonoscopic luminal content aspiration analysis could determine microbiome differences between patients with UC and the healthy control, thereby beneficial in screening dysbiosis via endoscopy. Trial registration: This trial was registered at http://cris.nih.go.kr.Registration No.: KCT0003352), Date : 2018-11-13

DOP16 The ratio of submucosa thickness to the total bowel wall thickness can be a sonographic parameter to estimate endoscopic remission in Ulcerative Colitis

Background A less invasive examination that can estimate endoscopic remission is needed. Intestinal ultrasound (IUS) is a promising option. The bowel wall thickness (BWT) is a widely-accepted objective parameter in IUS to assess colonic inflammation, but BWT is influenced by intestinal peristalsis and the volume of luminal content. A feasible, objective index that is not affected by these factors could improve the diagnostic potential of IUS. The submucosa, which is observed as the third layer of the intestinal wall on IUS, becomes swollen and standing out in the active UC. Given BWT and submucosa thickness (SMT) can be influenced by the peristalsis and luminal content simultaneously, we hypothesized that the ratio of SMT to BWT can be an index for submucosal swelling regardless of those factors and this index can be a new parameter to estimate endoscopic remission. Methods Inclusion criteria were (1) both IUS and endoscopy (sigmoidoscopy or colonoscopy) for UC were performed in Kyorin University Hospital between April 2019 and December 2020 and (2) time-interval between IUS and endoscopy was within 2 weeks. BWT and SMT were measured based on IUS images for ascending (A/C), transverse (T/C), descending (D/C), and sigmoid colon (S/C), respectively. We defined the submucosa index (SMI) as a percentage of SMT to BWT (Figure 1). When SMT was too thin to be measured, we scored 0 for SMI. The loss of stratification (LOS) was defined as the condition where the submucosa cannot be identified even with BWT > 3 mm (Figure 2). The parts with LOS were considered as inflamed mucosa. Mayo endoscopic subscore (MES) was scored for each part of the colon based on the endoscopic images. MES of 0/1 was defined as the endoscopic remission. Informed consent was obtained in the opt-out method. This study was approved by the Institutional Review Board of Kyorin University School of Medicine (IRB No. 1668). Results In total 68 parts of the colon (A/C: 11, T/C: 12, D/C: 14, and S/C: 31) were analyzed. With ROC analysis with the Youden index, the cutoff value of BWT for endoscopic remission was 3.7 mm (AUC: 0.84). Among the parts without LOS, the cutoff value of SMI for endoscopic remission was 47.9 (AUC: 0.75). The positive predictive value for endoscopic remission of the diagnostic criteria (1) BWT ≤ 3.7 mm, (2) BWT ≤ 3.7 mm and no LOS, (3) SMI ≤ 48 (no LOS), and (4) BWT ≤ 3.7 mm, SMI ≤ 48 (no LOS) was 83.3%, 88.2%, 60.7%, and 93.3%, respectively. The negative predictive value was 88.0%, 88.2%, 90.0%, and 86.8%, respectively. Conclusion Given the feasibility and objectiveness of assessing bowel wall structure, our findings provide “proof of concept” that SMI can be an additional sonographic parameter for endoscopic remission.

The virtual physiological human gets nerves! How to account for the action of the nervous system in multiphysics simulations of human organs

This article shows how to couple multiphysics and artificial neural networks to design computer models of human organs that autonomously adapt their behaviour to environmental stimuli. The model simulates motility in the intestine and adjusts its contraction patterns to the physical properties of the luminal content. Multiphysics reproduces the solid mechanics of the intestinal membrane and the fluid mechanics of the luminal content; the artificial neural network replicates the activity of the enteric nervous system. Previous studies recommended training the network with reinforcement learning. Here, we show that reinforcement learning alone is not enough; the input–output structure of the network should also mimic the basic circuit of the enteric nervous system. Simulations are validated against in vivo measurements of high-amplitude propagating contractions in the human intestine. When the network has the same input–output structure of the nervous system, the model performs well even when faced with conditions outside its training range. The model is trained to optimize transport, but it also keeps stress in the membrane low, which is exactly what occurs in the real intestine. Moreover, the model responds to atypical variations of its functioning with ‘symptoms’ that reflect those arising in diseases. If the healthy intestine model is made artificially ill by adding digital inflammation, motility patterns are disrupted in a way consistent with inflammatory pathologies such as inflammatory bowel disease.

Assessment of Hematological Parameters and Uterine Hemodynamic Indices in Bitches with Pyometra

Background: Pyometra is defined as chronic purulent inflammation of the uterus that causes changes in hematological and biochemical parameters. The disease is characterized with bacterial infection and pus accumulation in the uterus. Transabdominal B-mode ultrasonography provides easy and certain diagnosis of this disease. The hemodynamic changes in pyometra are evaluated by Doppler ultrasonography. The aim of the study is to determine the changes in hematological parameters and Doppler indices in bitches with pyometra, diestrus healthy bitches and evaluate the relationship between hematological parameters and hemodynamic indices within the both groups.Materials, Methods & Results: A total number of 27 bitches were enrolled in the study. The healthy diestrus bitches (group H; n = 7) aged 6.2 ± 1.14 years, weighted 14.57 ± 3.75 kg. The bitches with pyometra (group PYO; n = 20) aged 9.1 ± 0.62 years and weighted 17.65 ± 2.60 kg. Before all bitches had ovariohisterectomy, hematological analyses were performed. Transabdominal ultrasonography (USG) was performed with a 6.6 MHz convex transducer. The widest cross-sectional uterine diameter (UD), wall thickness of uterine horns (UWT) and presence of luminal content were evaluated. Diameter of the uterine artery (DUA) was measured on a mapped color image using the USG software program. The examination was carried out with pulsed-wave Doppler USG to characterize the waveform of the uterine artery (UA). Anechogenic areas in uterine lumen, increase in UD and UWT were observed in group PYO. All cases in group PYO had luminal content in both uterine horns ranging from 1.2 to 5.6 cm. The DUAs were measured in group H and in group PYO as 1.75 ± 0.03 mm, 1.94 ± 0.08 mm; respectively (P < 0.05). The PI and RI values of group PYO were lower than group H (P < 0.001). Hematological analysis results showed that RBC, HGB, HCT levels in group PYO were lower than group H (P < 0.001). However, WBC, NEU, LYM, MONO levels in group PYO were higher than group H. Hemodynamic indices were positively correlated with RBC, HGB, HCT, whereas they were inversely correlated with NEU, WBC, UD and UWT. Also, PI value was negatively correlated with MONO.Discussion: Cystic endometrial hyperplasia (CEH) is a predisposing factor for development of the pyometra in bitches. Besides, naturally occurring CEH and pyometra can arise independently from each other. The enlarged uterine body exhibits the development of intense exudative processes due to the higher proliferative stimulation in uterine infections. Uterine infections were associated with increase in uterine blood flow. Elevated uterine blood flow, vasodilatation and angiogenesis arise during inflammatory response. The inflammatory process leads to a diminution in hemodynamic indices of uterine arteries. Total blood count parameters are affected from the presence of pyometra. Elevated levels of leukocytes in bitches with pyometra are associated with worsening prognosis. Erythrocyte diapedesis into the lumen of the uterus, toxic depression of erythropoiesis in the bone marrow can cause anemia. In conclusion, hematological parameters were strongly correlated with hemodynamic indices in this study. Reduced RBC, HGB and HCT levels, decreased PI and RI values and elevated levels of UD, UWT, DUA were observed in group PYO. To our knowledge, this was the first study that observed the increase in DUA during pyometra in bitches.

The duality between particle methods and artificial neural networks

The algorithm behind particle methods is extremely versatile and used in a variety of applications that range from molecular dynamics to astrophysics. For continuum mechanics applications, the concept of ‘particle’ can be generalized to include discrete portions of solid and liquid matter. This study shows that it is possible to further extend the concept of ‘particle’ to include artificial neurons used in Artificial Intelligence. This produces a new class of computational methods based on ‘particle-neuron duals’ that combines the ability of computational particles to model physical systems and the ability of artificial neurons to learn from data. The method is validated with a multiphysics model of the intestine that autonomously learns how to coordinate its contractions to propel the luminal content forward (peristalsis). Training is achieved with Deep Reinforcement Learning. The particle-neuron duality has the advantage of extending particle methods to systems where the underlying physics is only partially known, but we have observations that allow us to empirically describe the missing features in terms of reward function. During the simulation, the model evolves autonomously adapting its response to the available observations, while remaining consistent with the known physics of the system.

Luminal and Mucosal Microbiota of the Cecum and Large Colon of Healthy and Diarrheic Horses

The aim of this study was to compare the mucosal and luminal content microbiota of the cecum and colon of healthy and diarrheic horses. Marked differences in the richness and in the community composition between the mucosal and luminal microbiota of the cecum and large colon of horses with colitis were observed. Microbial dysbiosis occurs in horses with colitis at different levels of the intestinal tract, and microbiota composition is different between the mucosa and luminal content of diarrheic horses. The changes in some key taxa associated with dysbiosis in the equine intestinal microbiota, such as Escherichia, Fusobacterium and Lactobacillus, deserve further inquiry in order to determine their utility for disease diagnosis and treatment.

Diagnosis and management of iatrogenic endoscopic perforations: European Society of Gastrointestinal Endoscopy (ESGE) Position Statement – Update 2020

Summary of Recommendations 1 ESGE recommends that each center implements a written policy regarding the management of iatrogenic perforations, including the definition of procedures that carry a higher risk of this complication. This policy should be shared with the radiologists and surgeons at each center. 2 ESGE recommends that in the case of an endoscopically identified perforation, the endoscopist reports its size and location, with an image, and statement of the endoscopic treatment that has been applied. 3 ESGE recommends that symptoms or signs suggestive of iatrogenic perforation after an endoscopic procedure should be rapidly and carefully evaluated and documented with a computed tomography (CT) scan. 4 ESGE recommends that endoscopic closure should be considered depending on the type of the iatrogenic perforation, its size, and the endoscopist expertise available at the center. Switch to carbon dioxide (CO2) endoscopic insufflation, diversion of digestive luminal content, and decompression of tension pneumoperitoneum or pneumothorax should also be performed. 5 ESGE recommends that after endoscopic closure of an iatrogenic perforation, further management should be based on the estimated success of the endoscopic closure and on the general clinical condition of the patient. In the case of no or failed endoscopic closure of an iatrogenic perforation, and in patients whose clinical condition is deteriorating, hospitalization and surgical consultation are recommended.

Diagnosis of parasitic infections in vermiform appendix in patients with appendicitis in Kirkuk city, Iraq

The present study is conducted in Kirkuk city, Iraq; between July to December 2018. Within this period 197 resected appendix are examined to investigate the parasitic infections that may associated with appendicitis. Direct with concentrated methods are used in luminal content examinations. Also, histological examination of haematoxylin and eosin stained tissue sections is performed to diagnose the parasitic infections in the lumen and within the appendix tissue. The parasitic infection reported in 12.69% cases included four species, as well as a mixed infection. Entamoeba histolytica (trophozoite and cyst), Giardia lamblia (trophozoite and cyst), Cryptospordium sp.(oocyst) and Enterobious vermicularis (adult worm and ova) are recorded. The most common determined parasite is E. histolytica (8.63%). The parasitic infection within the resected appendix reported in females (8.12%) more than males (4.57%). The parasitic infections in the study are prevalent in patients within the age groups 13 to 18 years and 19 to 24 years (3.55% for each one). http://dx.doi.org/10.25130/tjps.24.2019.123