scholarly journals The Microbiome Profile In Ulcerative Colitis And Pouchitis

2021 ◽  
Author(s):  
Xin Gao ◽  
Di Huang ◽  
Lisheng Yang ◽  
Anqi He ◽  
Kaiyu Li ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Metabolic Pathways ◽  
Multiple Infection ◽  
Bacterial Composition ◽  
Microbial Structures ◽  
Microbiome Profile ◽  
Chinese Cohort ◽  
Infection Pathways ◽  
Stool Samples ◽  
Dominant Bacteria

Abstract Both ulcerative colitis and pouchitis are associated with an imbalance in the intestinal microbiota, which may be related to the immune response. The objective was to determine the bacterial composition in pouchitis and ulcerative colitis in order to explore the underlying pathogenesis. Microbiome was profiled and evaluated by 16S ribosomal DNA gene sequencing in stool samples of 37 patients with ulcerative colitis, 15 patients with normal ulcerative colitis-pouch, 15 patients with ulcerative colitis-pouchitis and 18 healthy volunteers, PICRUSt and PICRUSt2 were performed to analyze the function of dominant bacteria. In our Chinese cohort, with aggravation of ulcerative colitis, intestinal microorganisms were characterized by a gradual decreased in diversity and numbers of butyrate-producing bacteria and Bacteroides. Besides, in addition to the decrease of probiotics, the bloom of Escherichia-Shigella and Ruminococcus_gnavus was observed in pouchitis which related to multiple infection pathways according to KEEG pathway analysis. Our results showed that pouchitis and ulcerative colitis differ in their intestinal microbial structures and metabolic pathways, but the reasons need to be further explored.

scholarly journals Predicting disease course in ulcerative colitis using stool proteins identified through an aptamer-based screen

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sanam Soomro ◽  
Suresh Venkateswaran ◽  
Kamala Vanarsa ◽  
Marwa Kharboutli ◽  
Malavika Nidhi ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Fecal Calprotectin ◽  
Disease Monitoring ◽  
Disease Course ◽  
Lipocalin 2 ◽  
Time Points ◽  
Inflammatory Bowel ◽  
Stool Samples

AbstractIn the search for improved stool biomarkers for inflammatory bowel disease (IBD), an aptamer-based screen of 1129 stool proteins was conducted using stool samples from an IBD cohort. Here we report that of the 20 proteins subsequently validated by ELISA, stool Ferritin, Fibrinogen, Haptoglobin, Hemoglobin, Lipocalin-2, MMP-12, MMP-9, Myeloperoxidase, PGRP-S, Properdin, Resistin, Serpin A4, and TIMP-1 are significantly elevated in both ulcerative colitis (UC) and Crohn’s disease (CD) compared to controls. When tested in a longitudinal cohort of 50 UC patients at 4 time-points, fecal Fibrinogen, MMP-8, PGRP-S, and TIMP-2 show the strongest positive correlation with concurrent PUCAI and PGA scores and are superior to fecal calprotectin. Unlike fecal calprotectin, baseline stool Fibrinogen, MMP-12, PGRP-S, TIMP-1, and TIMP-2 can predict clinical remission at Week-4. Here we show that stool proteins identified using the comprehensive aptamer-based screen are superior to fecal calprotectin alone in disease monitoring and prediction in IBD.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis

2020 ◽  
Author(s):  
Qiulong Yan ◽  
Yu Wang ◽  
Xiuli Chen ◽  
Hao Jin ◽  
Guangyang Wang ◽  
...  
Keyword(s):  
Ethnic Origin ◽  
Chinese Adults ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Dna And Rna ◽  
Bacterial Microbiome ◽  
Chinese Cohort ◽  
Host Genetic

AbstractBackgroundTrillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated.Methods and ResultsHere, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals’ gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between virus and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p<0.001), and they both influenced the holistic bacterial composition and vice versa.ConclusionsThis study provides an overview of gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.

scholarly journals Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion

Diagnostics ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 163 ◽  
Author(s):  
Camila Hernandes ◽  
Paola Silveira ◽  
Aline Fernanda Rodrigues Sereia ◽  
Ana Paula Christoff ◽  
Helen Mendes ◽  
...  
Keyword(s):  
Marker Gene ◽  
Amplicon Sequencing ◽  
Vaginal Fluid ◽  
Deep Endometriosis ◽  
Eutopic Endometrium ◽  
Bacterial Composition ◽  
Microbiome Profile ◽  
Genus Lactobacillus ◽  
High Throughput Dna Sequencing ◽  
Bacterial Patterns

This work aimed to identify and compare the bacterial patterns present in endometriotic lesions, eutopic endometrium and vaginal fluid from endometriosis patients with those found in the vaginal fluid and eutopic endometrium of control patients. Vaginal fluid, eutopic endometrium and endometriotic lesions were collected. DNA was extracted and the samples were analyzed to identify microbiome by high-throughput DNA sequencing of the 16S rRNA marker gene. Amplicon sequencing from vaginal fluid, eutopic endometrium and endometriotic lesion resulted in similar profiles of microorganisms, composed most abundantly by the genus Lactobacillus, Gardnerella, Streptococcus and Prevotella. No significant differences were found in the diversity analysis of microbiome profiles between control and endometriotic patients; however deep endometriotic lesions seems to present different bacterial composition, less predominant of Lactobacillus and with more abundant Alishewanella, Enterococcus and Pseudomonas.

scholarly journals P003 Metabolomics for improved patient stratification in inflammatory bowel disease: Characterisation of the ulcerative colitis metabolome

2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S130-S131
Author(s):  
J Diab ◽  
T Hansen ◽  
R Goll ◽  
H Stenlund ◽  
E Jensen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ulcerative Colitis ◽  
Amino Acid ◽  
Metabolic Pathways ◽  
Personalised Medicine ◽  
Healthy Controls ◽  
Patient Stratification ◽  
Metabolomic Profile ◽  
Metabolic Signature ◽  
Treatment Naïve

Abstract Background The onset of ulcerative colitis (UC) is characterised by a dysregulated mucosal immune response triggered by several genetic and environmental factors in the context of host-microbe interaction. This complexity makes UC ideal for metabolomic studies to unravel the disease pathobiology and to improve the patient stratification strategies toward personalised medicine. This study aims to explore the mucosal metabolomic profile in treatment-naïve and deep remission UC patients, and to define the metabolic signature of UC. Methods Treatment-naive UC patients (n = 18), UC patients in deep remission (n = 10), and healthy volunteers (n = 14) were recruited. Mucosa biopsies were collected during colonoscopy. The UC activity and the state of deep remission were assessed by endoscopy, histology, and by measuring TNF gene expression. Metabolomic analysis was performed by combined gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-MS). In total, 177 metabolites from 50 metabolic pathways were identified. Results Multivariate data analysis revealed a distinct metabolomic profile in inflamed mucosa taken from treatment- naïve UC patients compared with non-inflamed mucosa taken from UC remission patients and healthy controls. The mucosal metabolome in UC remission patients differed to a lesser extent from the healthy controls. The most prominent metabolome changes among the study groups were in lysophosphatidylcholine, acylcarnitine, and amino acid profiles. Several metabolic pathways were perturbed, ranging from amino acid metabolism (such as tryptophan metabolism, and alanine, aspartate and glutamate metabolism) to antioxidant defence pathway (glutathione pathway). Furthermore, the pathway analysis revealed a disruption in the long-and short-chain fatty acid (LCFA and SCFA) metabolism, namely linoleic metabolism and butyrate metabolism. Conclusion The mucosal metabolomic profiling revealed a metabolic signature during the onset of UC, and reflected the homeostatic disturbance in the gut. The altered metabolic pathways highlight the importance of system biology approaches to identify key drivers of IBD pathogenesis which prerequisite personalised treatment.

scholarly journals Bacterial Community Associated with Black Band Disease in Corals

2004 ◽  
Vol 70 (10) ◽  
pp. 5955-5962 ◽  
Author(s):  
Jorge Frias-Lopez ◽  
James S. Klaus ◽  
George T. Bonheyo ◽  
Bruce W. Fouke
Keyword(s):  
Bacterial Community ◽  
Coral Species ◽  
Rflp Analysis ◽  
Quantitative Composition ◽  
Black Band Disease ◽  
Bacterial Composition ◽  
Disease Etiology ◽  
Black Band ◽  
Polymicrobial Disease ◽  
Dominant Bacteria

ABSTRACT Black band disease (BBD) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. While it has been well established that the BBD bacterial mat is dominated by a cyanobacterium, the quantitative composition of the BBD bacterial mat community has not described previously. Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to characterize the infectious bacterial community of the bacterial mat causing BBD. These analyses revealed that the bacterial composition of the BBD mat does not vary between different coral species but does vary when different species of cyanobacteria are dominant within the mat. On the basis of the results of a new method developed to identify organisms detected by T-RFLP analysis, our data show that besides the cyanobacterium, five species of the division Firmicutes, two species of the Cytophaga-Flexibacter-Bacteroides (CFB) group, and one species of δ-proteobacteria are also consistently abundant within the infectious mat. Of these dominant taxa, six were consistently detected in healthy corals. However, four of the six were found in much higher numbers in BBD mats than in healthy corals. One species of the CFB group and one species of Firmicutes were not always associated with the bacterial communities present in healthy corals. Of the eight dominant bacteria identified, two species were previously found in clone libraries obtained from BBD samples; however, these were not previously recognized as important. Furthermore, despite having been described as an important component of the pathogenetic mat, a Beggiatoa species was not detected in any of the samples analyzed. These results will permit the dominant BBD bacteria to be targeted for isolation and culturing experiments aimed at deciphering the disease etiology.

scholarly journals Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease

2020 ◽  
Vol 7 ◽  
Author(s):  
Jagadesan Sankarasubramanian ◽  
Rizwan Ahmad ◽  
Nagavardhini Avuthu ◽  
Amar B. Singh ◽  
Chittibabu Guda
Keyword(s):  
Ulcerative Colitis ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Meta Analysis ◽  
Metabolic Effects ◽  
Taxonomic Rank ◽  
Disease Specific

Background: Inflammatory bowel disease (IBD) represents multifactorial chronic inflammatory conditions in the gastrointestinal tract and includes Crohn's disease (CD) and ulcerative colitis (UC). Despite similarities in pathobiology and disease symptoms, UC and CD represent distinct diseases and exhibit diverse therapeutic responses. While studies have now confirmed that IBD is associated with dramatic changes in the gut microbiota, specific changes in the gut microbiome and associated metabolic effects on the host due to CD and UC are less well-understood.Methods: To address this knowledge gap, we performed an extensive unbiased meta-analysis of the gut microbiome data from five different IBD patient cohorts from five different countries using QIIME2, DIAMOND, and STAMP bioinformatics platforms. In-silico profiling of the metabolic pathways and community metabolic modeling were carried out to identify disease-specific association of the metabolic fluxes and signaling pathways.Results: Our results demonstrated a highly conserved gut microbiota community between healthy individuals and IBD patients at higher phylogenetic levels. However, at or below the order level in the taxonomic rank, we found significant disease-specific alterations. Similarly, we identified differential enrichment of the metabolic pathways in CD and UC, which included enriched pathways related to amino acid and glycan biosynthesis and metabolism, in addition to other metabolic pathways.Conclusions: In conclusion, this study highlights the prospects of harnessing the gut microbiota to improve understanding of the etiology of CD and UC and to develop novel prognostic, and therapeutic approaches.

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