scholarly journals Characterization of biliary microbiota dysbiosis in extrahepatic cholangiocarcinoma

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247798
Author(s):  
Massa Saab ◽  
Denis Mestivier ◽  
Masoudreza Sohrabi ◽  
Christophe Rodriguez ◽  
Mahmood Reza Khonsari ◽  
...  
Keyword(s):  
Endoscopic Retrograde ◽  
Extrahepatic Cholangiocarcinoma ◽  
Bacterial Dna ◽  
Associated Diseases ◽  
Digestive Cancers ◽  
Rrna Sequencing ◽  
Inflammatory Bowel ◽  
Bacterial Dna Extraction

Extrahepatic cholangiocarcinoma (CCA) accounts for 3% of digestive cancers. The role of biliary microbiota as an environment-related modulator has been scarcely investigated in CCA, and the putative impact of associated diseases has not been yet assessed. We characterized the biliary microbiota in CCA patients in order to identify a specific CCA-related dysbiosis. The biliary effluents were collected through an endoscopic retrograde pancreatic cholangiography (ERCP) examination involving 28 CCA and 47 patients with gallstones, herein considered as controls. The biliary effluents were submitted to bacterial DNA extraction and 16S rRNA sequencing, using Illumina technology. Overall, 32% of CCA and 22% of controls displayed another associated disease, such as diabetes, pancreatitis, inflammatory bowel disease, or primary sclerosing cholangitis. Such associated diseases were considered in the comparisons that were made. Principal coordinate analysis (PCoA) detected a significant disparity of biliary microbiota composition between CCA patients and controls without an associated disease. Amongst the most abundant phyla, Proteobacteria did not significantly differ between CCA patients and controls, whereas Firmicutes levels were lower and Bacteroidetes higher in CCAs’ biliary microbiota than in the controls’ microbiota. The most abundant genera were Enterococcus, Streptococcus, Bacteroides, Klebsiella, and Pyramidobacter in CCA’s biliary microbiota. Additionally, levels of Bacteroides, Geobacillus, Meiothermus, and Anoxybacillus genera were significantly higher in CCA patients’ biliary microbiota, without an associated disease, in comparison with controls. A specific CCA-related dysbiosis was identified as compared to controls independently from associated diseases. This suggests that a microorganism community may be involved in CCA pathogenesis.

scholarly journals Microbiota Profile with Stunting Children in West Sumatera Province, Indonesia

2020 ◽  
Vol 8 (E) ◽  
pp. 334-340
Author(s):  
Masrul Masrul ◽  
Doddy Izwardy ◽  
Ikhwan Resmala Sudji ◽  
Idral Purnakarya ◽  
Syahrial Syahrial ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Bioinformatic Analysis ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
West Sumatra ◽  
Dominant Bacteria ◽  
Microbial Dna ◽  
Bacterial Dna Extraction

BACKGROUND: Microbiota profile plays an important role in the growth of children. Recently, a number of microbiota profile studies have illustrated association with child stunting. AIM: Here, this study applied microbiota profile for stunting children in Indonesia to know a framework for future activities toward further characterization of microbiota profile contribution to stunting. METHODS: In this case–control study, we collected 96 samples with 48 stunting children and 48 non-stunting children in Pasaman and West Pasaman district as stunting locus areas in West Sumatra Province, Indonesia. All study subjects met the inclusion criteria: Children ≤3 years of age and they did not suffer from gastrointestinal disorders. Samples collected were then carried out by intestinal bacterial DNA extraction. All sequences were obtained from the bacterial 16S rRNA gene, which was amplified from microbial DNA extracted from a child fecal sample. Bioinformatic analysis of microbiota DNA sequencing results compared with the intestinal microbiota profile of infants. RESULTS: This study found in intestinal of stunting children identified 61 species of bacteria which were only found in the intestines of stunting children and not found in non-stunting children. The dominant bacteria in intestinal microbiota profile of Pasaman and West Pasaman district, West Sumatera Province, Indonesia, among stunting children were Firmicutes (47.52%), Proteobacteria (21.12%), and Bacteroidetes (16.15%). The high number of these microbiota associated with high amount of carbohydrate intake among stunting children than dietary protein. CONCLUSION: This study confirmed the role of microbiota profile in the incidence of stunting children.

scholarly journals Application of artificial intelligence in pancreaticobiliary diseases

2021 ◽  
Vol 14 ◽  
pp. 263177452199305
Author(s):  
Hemant Goyal ◽  
Rupinder Mann ◽  
Zainab Gandhi ◽  
Abhilash Perisetti ◽  
Zhongheng Zhang ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Response To Treatment ◽  
Endoscopic Retrograde ◽  
Artificial Intelligence Techniques ◽  
Computer Aided ◽  
Rapid Pace ◽  
Cystic Pancreatic Lesions ◽  
Aided Diagnosis

The role of artificial intelligence and its applications has been increasing at a rapid pace in the field of gastroenterology. The application of artificial intelligence in gastroenterology ranges from colon cancer screening and characterization of dysplastic and neoplastic polyps to the endoscopic ultrasonographic evaluation of pancreatic diseases. Artificial intelligence has been found to be useful in the evaluation and enhancement of the quality measure for endoscopic retrograde cholangiopancreatography. Similarly, artificial intelligence techniques like artificial neural networks and faster region-based convolution network are showing promising results in early and accurate diagnosis of pancreatic cancer and its differentiation from chronic pancreatitis. Other artificial intelligence techniques like radiomics-based computer-aided diagnosis systems could help to differentiate between various types of cystic pancreatic lesions. Artificial intelligence and computer-aided systems also showing promising results in the diagnosis of cholangiocarcinoma and the prediction of choledocholithiasis. In this review, we discuss the role of artificial intelligence in establishing diagnosis, prognosis, predicting response to treatment, and guiding therapeutics in the pancreaticobiliary system.

scholarly journals Characterization of fungal and bacterial dysbiosis in young adult Chinese patients with Crohn’s disease

2020 ◽  
Vol 13 ◽  
pp. 175628482097120
Author(s):  
Xinyun Qiu ◽  
Xiaojing Zhao ◽  
Xiufang Cui ◽  
Xiaqiong Mao ◽  
Nana Tang ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Chinese Patients ◽  
Bacterial Composition ◽  
Structural Differences ◽  
Inflammatory Bowel ◽  
Fungal Microbiome ◽  
Chinese Subjects

Intestinal microbiota dysbiosis has been described in inflammatory bowel disease (IBD), but data from China are limited. In this study, we performed molecular analysis of the fecal microbial community from 20 healthy Chinese subjects and 25 patients with Crohn’s disease (CD), and evaluated associations with bacterial and fungal compositions. Decreased richness and diversity of bacterial composition was observed in the CD group compared with healthy (H) subjects. Significant structural differences in bacterial (but not fungal) composition among healthy controls and CD patients were found. A reduction in Firmicutes and Actinobacteria abundance, and overrepresentation of Proteobacteria were observed in the CD patients compared with the H group. The Escherichia-Shigella genus was overrepresented in the CD group, whereas Faecalibacterium, Gemmiger, Bifidobacterium, Romboutsia, Ruminococcus, Roseburia, and Fusicatenibacter abundance were decreased in the CD group compared with H subjects. Differences in fungal microbiota between the H and CD groups were observed at the genus rather than at the phylum level. The Candida genus was overrepresented in the CD (active disease) group compared with the H group, whereas no difference between CD (remission) and H groups was observed. Aspergillus, unclassified_Sordariomycetes, and Penicillium genera had greater representation in the H subjects compared with the CD group. Bacterial and fungal intra- and inter-kingdom correlations were observed between the H and CD groups. Therefore, fecal bacterial and fungal microbiome communities differed considerably between H and CD patients, and between Chinese and Western populations. The role of gut microbiota in homeostasis and in gastrointestinal disorders should be investigated further.

scholarly journals 4483 Activity and Abundance of Mucus-degrading Microbes in Inflammatory Bowel Disease

2020 ◽  
Vol 4 (s1) ◽  
pp. 92-92
Author(s):  
Matthew Ostrowski ◽  
Eric C. Martens
Keyword(s):  
Inflammatory Bowel Disease ◽  
New Species ◽  
Bowel Disease ◽  
Human Colon ◽  
Healthy Controls ◽  
Solid Culture ◽  
Rrna Sequencing ◽  
Study Population ◽  
Inflammatory Bowel

OBJECTIVES/GOALS: This study seeks to culture and characterize mucus-degrading microbes from the microbiome of inflammatory bowel disease (IBD) patients. METHODS/STUDY POPULATION: Stool will be collected from IBD patients and healthy first-degree relatives, then enriched for mucin-degrading microbes through growth on porcine rectal mucin. Dilution plating in both liquid and solid culture formats will be employed to isolate strains capable of growth on mucin. Cultures that are positive for mucin degradation will be identified with 16S rRNA sequencing; unique isolates will be genome sequenced and transcriptionally profiled on simple monosaccharides and mucin in order to identify putative mucin-degrading genes. The abundance of novel enzymes, pathways, and microbes will be compared in healthy and IBD patient populations using existing datasets in the literature. RESULTS/ANTICIPATED RESULTS: We expect to isolate previously uncultured mucin-degrading microbes, which will likely include new strains and possibly new species of bacteria. Through the transcriptomic characterization of mucin-degrading pathways, we will expand the lexicon of known mucin-degrading enzymes and pathways used by bacteria in the human colon. We expect mucin-degrading microbes to be more abundant and active in IBD patients compared to healthy controls. DISCUSSION/SIGNIFICANCE OF IMPACT: There is no cure for IBD and treatment relies heavily on suppressing a patient’s immune system. This research seeks to understand the contribution of the gut microbiota in the pathogenesis of IBD, which may lead to future therapeutic targets.

scholarly journals Analyzing the Role of Gut Microbiota on the Onset of Autoimmune Diseases Using TNFΔARE Murine Model

2021 ◽  
Vol 10 (1) ◽  
pp. 73
Author(s):  
Vivienne Edwards ◽  
Dylan L. Smith ◽  
Francoise Meylan ◽  
Linda Tiffany ◽  
Sarah Poncet ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Disease Transmission ◽  
Bioinformatics Analysis ◽  
Inflammatory Diseases ◽  
Anaerobic Conditions ◽  
Fecal Matter ◽  
Rrna Sequencing ◽  
Inflammatory Bowel ◽  
Transmission Status

Very little is known about disease transmission via the gut microbiome. We hypothesized that certain inflammatory features could be transmitted via the gut microbiome and tested this hypothesis using an animal model of inflammatory diseases. Twelve-week-old healthy C57 Bl/6 and Germ-Free (GF) female and male mice were fecal matter transplanted (FMT) under anaerobic conditions with TNFΔARE−/+ donors exhibiting spontaneous Rheumatoid Arthritis (RA) and Inflammatory Bowel Disease (IBD) or with conventional healthy mice control donors. The gut microbiome analysis was performed using 16S rRNA sequencing amplification and bioinformatics analysis with the HIVE bioinformatics platform. Histology, immunohistochemistry, ELISA Multiplex analysis, and flow cytometry were conducted to confirm the inflammatory transmission status. We observed RA and IBD features transmitted in the GF mice cohort, with gut tissue disruption, cartilage alteration, elevated inflammatory mediators in the tissues, activation of CD4/CD8+ T cells, and colonization and transmission of the gut microbiome similar to the donors’ profile. We did not observe a change or transmission when conventional healthy mice were FMT with TNFΔARE−/+ donors, suggesting that a healthy microbiome might withstand an unhealthy transplant. These findings show the potential involvement of the gut microbiome in inflammatory diseases. We identified a cluster of bacteria playing a role in this mechanism.

Whole Food–Based Approaches to Modulating Gut Microbiota and Associated Diseases

2020 ◽  
Vol 11 (1) ◽  
pp. 119-143 ◽  
Author(s):  
Yanhui Han ◽  
Hang Xiao
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Bowel Disease ◽  
Fruits And Vegetables ◽  
Beneficial Effects ◽  
Associated Diseases ◽  
Associated Functions ◽  
Inflammatory Bowel ◽  
Whole Foods

Intake of whole foods, such as fruits and vegetables, may confer health benefits to the host. The beneficial effects of fruits and vegetables were mainly attributed to their richness in polyphenols and microbiota-accessible carbohydrates (MACs). Components in fruits and vegetables modulate composition and associated functions of the gut microbiota, whereas gut microbiota can transform components in fruits and vegetables to produce metabolites that are bioactive and important for health. The progression of multiple diseases, such as obesity and inflammatory bowel disease, is associated with diet and gut microbiota. Although the exact causality between these diseases and specific members of gut microbiota has not been well characterized, accumulating evidence supported the role of fruits and vegetables in modulating gut microbiota and decreasing the risks of microbiota-associated diseases. This review summarizes the latest findings on the effects of whole fruits and vegetables on gut microbiota and associated diseases.

scholarly journals Human RIPK1 deficiency causes combined immunodeficiency and inflammatory bowel diseases

2018 ◽  
Vol 116 (3) ◽  
pp. 970-975 ◽  
Author(s):  
Yue Li ◽  
Marita Führer ◽  
Ehsan Bahrami ◽  
Piotr Socha ◽  
Maja Klaudel-Dreszler ◽  
...  
Keyword(s):  
Cell Death ◽  
Intestinal Inflammation ◽  
Intestinal Epithelial ◽  
Loss Of Function ◽  
Monogenic Disorders ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Human Immune

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is a critical regulator of cell death and inflammation, but its relevance for human disease pathogenesis remains elusive. Studies of monogenic disorders might provide critical insights into disease mechanisms and therapeutic targeting of RIPK1 for common diseases. Here, we report on eight patients from six unrelated pedigrees with biallelic loss-of-function mutations in RIPK1 presenting with primary immunodeficiency and/or intestinal inflammation. Mutations in RIPK1 were associated with reduced NF-κB activity, defective differentiation of T and B cells, increased inflammasome activity, and impaired response to TNFR1-mediated cell death in intestinal epithelial cells. The characterization of RIPK1-deficient patients highlights the essential role of RIPK1 in controlling human immune and intestinal homeostasis, and might have critical implications for therapies targeting RIPK1.

scholarly journals Microbiota-Immune Interactions in Ulcerative Colitis and Colitis Associated Cancer and Emerging Microbiota-Based Therapies

2021 ◽  
Vol 22 (21) ◽  
pp. 11365
Author(s):  
Jelena Popov ◽  
Valentina Caputi ◽  
Nandini Nandeesha ◽  
David Avelar Rodriguez ◽  
Nikhil Pai
Keyword(s):  
Ulcerative Colitis ◽  
Intestinal Inflammation ◽  
Autoimmune Disorder ◽  
Mucosal Barrier ◽  
Host Immune System ◽  
Intestinal Dysbiosis ◽  
Inflammatory Bowel ◽  
Genetic And Environmental Factors

Ulcerative colitis (UC) is a chronic autoimmune disorder affecting the colonic mucosa. UC is a subtype of inflammatory bowel disease along with Crohn’s disease and presents with varying extraintestinal manifestations. No single etiology for UC has been found, but a combination of genetic and environmental factors is suspected. Research has focused on the role of intestinal dysbiosis in the pathogenesis of UC, including the effects of dysbiosis on the integrity of the colonic mucosal barrier, priming and regulation of the host immune system, chronic inflammation, and progression to tumorigenesis. Characterization of key microbial taxa and their implications in the pathogenesis of UC and colitis-associated cancer (CAC) may present opportunities for modulating intestinal inflammation through microbial-targeted therapies. In this review, we discuss the microbiota-immune crosstalk in UC and CAC, as well as the evolution of microbiota-based therapies.

scholarly journals Elucidating Role of Bacteria in Psoriatic Disease: From Skin and Gut Perspectives

2018 ◽  
Author(s):  
Bakytgul Yermekbayeva ◽  
Togzhan Algazina ◽  
Madina Razbekova ◽  
Albert Pinhasov ◽  
Gulnar Batpenova ◽  
...  
Keyword(s):  
Skin Lesions ◽  
Chronic Inflammatory Disease ◽  
Microbial Composition ◽  
Bacterial Dna ◽  
Bacterial Phyla ◽  
Psoriatic Disease ◽  
Inflammatory Bowel ◽  
Genetic And Environmental Factors ◽  
The Given

Psoriasis is a chronic inflammatory disease characterized by skin lesions. Psoriasis development has been associated both with genetic and environmental factors. Though skin and gut microbiota has been implicated in number of pathologies including atopic dermatitis, inflammatory bowel disease, Crohn’s disease, allergy, obesity, its role has been poorly studied in psoriatic disease, which incorporates both psoriasis and psoriatic arthritis. This literature review summarizes the most recent and major findings on microbiota features in psoriatic disease as well as gives immune system role in the given condition. Despite conflicting findings, psoriasis patients were frequently found to have distinct microbial composition in both skin and guts especially in the major bacterial phyla, Firmicutes, Bacteroidetes, and Akkermansia. Furthermore, bacterial DNA has been found in psoriatic patients both locally and systemically, and altogether suggesting role of bacteria in the chronic disease and future studies in this field.

Digital x-ray mapping of nanometer-size supported bimetallic catalysts

1988 ◽  
Vol 46 ◽  
pp. 530-531
Author(s):  
L. T. Germinario
Keyword(s):  
Background Radiation ◽  
Metal Cluster ◽  
Single Element ◽  
Beam Diameter ◽  
X Rays ◽  
X Ray ◽  
Major Interest ◽  
Induced Changes

Understanding the role of metal cluster composition in determining catalytic selectivity and activity is of major interest in heterogeneous catalysis. The electron microscope is well established as a powerful tool for ultrastructural and compositional characterization of support and catalyst. Because the spatial resolution of x-ray microanalysis is defined by the smallest beam diameter into which the required number of electrons can be focused, the dedicated STEM with FEG is the instrument of choice. The main sources of errors in energy dispersive x-ray analysis (EDS) are: (1) beam-induced changes in specimen composition, (2) specimen drift, (3) instrumental factors which produce background radiation, and (4) basic statistical limitations which result in the detection of a finite number of x-ray photons. Digital beam techniques have been described for supported single-element metal clusters with spatial resolutions of about 10 nm. However, the detection of spurious characteristic x-rays away from catalyst particles produced images requiring several image processing steps.

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