P850 Comparison of sampling methods in assessing the microbiome from patients with ulcerative colitis

Abstract Background Most of studies have reported a dysbiosis of ulcerative colitis (UC) using readily accessible stool samples. However, the faecal samples might not fully represent mucosa-associated microbiome. We hypothesised that luminal contents including loosely adherent luminal bacteria after bowel preparation may be suitable for diagnosing the dysbiosis of UC. Methods Sixteen 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) participated in the study. The subjects donated faecal samples before colonoscopy and received luminal contents aspiration and endoscopic biopsy during the colonoscopy. The composition of each microbiome samples was analysed by 16S rRNA-based nest-generation sequencing. Results Microbiome of stool, luminal contents and biopsy was significantly different from each other in alpha diversity and beta diversity. However, another analysis showed a correlation between the stool and luminal contents in Procrustes test (p = 0.001) and Mantel test (p = 0.0001). Stool microbiome in patients with UC was different from stool microbiome in healthy control. Microbiome of luminal contents microbiome and biopsy samples in patients with UC were not different from that of healthy control. Stool and lavage predicted UC in accuracy of AUC 0.85 and 0.81, respectively Conclusion Microbiome of stool, luminal contents and biopsy were significantly different from each other. Further studies would be needed to know optimal sampling of intestinal dysbiosis.

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

BMC Gastroenterology ◽

10.1186/s12876-021-01975-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Dan Kim ◽

Jun-Young Jung ◽

Hyun-Seok Oh ◽

Sam-Ryong Jee ◽

Sung Jae Park ◽

...

Keyword(s):

Ulcerative Colitis ◽

Sampling Methods ◽

Mantel Test ◽

Endoscopic Biopsy ◽

Healthy Controls ◽

Healthy Individuals ◽

Luminal Content ◽

Healthy Control ◽

Stool Samples ◽

Generation Sequencing

Abstract 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.

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

10.21203/rs.3.rs-540741/v1 ◽

2021 ◽

Author(s):

Dan Kim ◽

Jun-Young Jung ◽

Hyun-Seok Oh ◽

Sam-Ryong Jee ◽

Sung Jae Park ◽

...

Keyword(s):

Ulcerative Colitis ◽

Sampling Methods ◽

Mantel Test ◽

Endoscopic Biopsy ◽

Healthy Controls ◽

Healthy Individuals ◽

Luminal Content ◽

Healthy Control ◽

Stool Samples ◽

Generation Sequencing

Abstract 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

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P685 Gut microbiota in patients with Inflammatory Bowel Disease during remission

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjab076.805 ◽

2021 ◽

Vol 15 (Supplement_1) ◽

pp. S604-S605

Author(s):

A Pisani ◽

P Rausch ◽

S Ellul ◽

C Bang ◽

T Tabone ◽

...

Keyword(s):

Gut Microbiota ◽

Alpha Diversity ◽

Health Condition ◽

Healthy Controls ◽

Unifrac Distance ◽

Healthy Control ◽

Minimal Data ◽

Inflammatory Bowel ◽

Stool Samples ◽

Curtis Dissimilarity

Abstract Background Dysbiosis in patients with active IBD has been described in many studies and populations. There is, however, minimal data on whether dysbiosis persists during remission and the extent to which it does. The aim of this study was to assess the gut microbiota in Maltese IBD patients who are in remission as compared to a healthy control population. Methods Stool samples of patients with IBD in remission and healthy controls were analyzed by 16S rRNA sequencing. High quality Amplicon sequence variants (ASV) were derived and classified via DADA2. Results Ninety-eight patients with IBD (UC: 67.3%; CD: 32.7%) and 97 controls were recruited. Patients with IBD had a decrease in alpha diversity compared to healthy controls (Figure 1) with significant differences in beta diversity (Bray-Curtis dissimilarity, Jaccard distance and Generalized UniFrac distance: all p=0.0001). At the phylum level, abundances differed significantly with respect to health condition (Figure 2). Twenty-five ASVs that were differentially abundant between the different cohorts were identified (Table 1); 13 being over abundant in healthy individuals, while 6 being least abundant among controls. In both CD and UC, 3 different ASVs were found to be more abundant. Conclusion Despite remission, the faecal gut microbiota in IBD is dysbiotic. Future studies could be directed at assessing whether species identified as being more abundant in controls can be used as probiotics to either reduce or be able to stop the standard medications.

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Comparison of Endoscopic Brush And Net Catheters As Sampling Tools To Analyze Lower Rectum Intestinal Mucus Samples of Patients With Ulcerative Colitis

10.21203/rs.3.rs-618800/v1 ◽

2021 ◽

Author(s):

Masanao Nakamura ◽

Keiko Maeda ◽

Kenta Yamamoto ◽

Takeshi Yamamura ◽

Tsunaki Sawada ◽

...

Keyword(s):

Ulcerative Colitis ◽

Protein Content ◽

Sampling Methods ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Oral Bacteria ◽

Rrna Gene ◽

Intestinal Fluid ◽

Lower Rectum ◽

Intestinal Mucus

Abstract Background and aims: The pathophysiology of ulcerative colitis remains unclear, but early lesions on the colorectal mucosal surface may play an important role in its etiology. Intestinal mucus samples, including inner and outer layers, are collected by net or brush catheters, but the quality of the samples obtained by each method has not been fully investigated. The aim of this study was to compare the microbiome and protein content of Intestinal mucus collected by net and brush catheters during colonoscopy.Methods: Intestinal mucus samples from the lower rectum of four patients with ulcerative colitis were collected using a net catheter, a brush catheter, and intestinal fluid suction. Microbiome and protein content were analyzed using 16S rRNA gene sequencing and mass spectrometry.Results: The patients demonstrated significant differences in microbiome alpha diversity (p <0.05), but this difference was not observed between the sampling methods. Net catheter samples demonstrated higher total protein concentrations than brush catheter samples. Mucus-associated proteins (Mucin-2, Mucin-5B, Mucin-13, and IgGFc-binding protein) were more abundantly collected by nets in three patients with active ulcerative colitis, but more abundant by brushes in patients with inactive ulcerative colitis.　Bifidobacterium and some oral bacteria were similarly associated with ulcerative colitis activity.Conclusions: Brush catheters are more likely to collect the intestinal mucus of inner layer, whereas net catheters are more likely to collect larger samples that include the outer mucus layer, as well as intestinal fluid. Two sampling methods with different types of work on the mucosa may lead different results among patients with mucosal vulnerabilities.

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COT-04 Circulating biomarker for glioblastoma and primary central nervous system lymphoma -Next Generation Sequencing of small noncoding RNA-

Neuro-Oncology Advances ◽

10.1093/noajnl/vdaa143.093 ◽

2020 ◽

Vol 2 (Supplement_3) ◽

pp. ii21-ii21

Author(s):

Shumpei Onishi ◽

Fumiyuki Yamasaki ◽

Motoki Takano ◽

Ushio Yonezawa ◽

Kazuhiko Sugiyama ◽

...

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Noncoding Rna ◽

Central Nervous System Lymphoma ◽

Serum Samples ◽

Small Noncoding Rna ◽

Non Invasive ◽

Diagnostic Models ◽

Healthy Control ◽

Generation Sequencing

Abstract Objective: Glioblastoma (GBM) and Primary Central Nervous System Lymphoma (PCNSL) are common intracranial malignant tumors. They sometimes present similar radiological findings and diagnoses could be difficult without surgical biopsy. For improving the current management, development of non-invasive biomarkers are desired. In this study, we explored the differently expressed circulating small noncoding RNA (sncRNA) in serum for specific diagnostic tool of GBM and PCNSL. Material & Methods: Serum samples were obtained from three groups: 1) GBM patients (N=26), 2) PCNSL patients (N=14) 3) healthy control (N=114). The total small RNAs were extracted from serum. The whole expression profiles of serum sncRNAs were measured using Next-Generation Sequencing System. We analyzed serum levels of sncRNAs (15–55 nt) in each serum samples. The difference of sncRNAs expression profile among three groups were compared. Data analysis was performed by logistic regression analysis followed by leave-one-out cross-validation (LOOCV). The accuracy of diagnostic models of sncRNAs combination were evaluated by receiver operating characteristic (ROC) analysis. Results: We created the combination models using three sncRNA in each models based on the logistic regression analysis. The model 1 (based on sncRNA-X1, X2 and X3) enabled to differentiate GBM patients form healthy control with a sensitivity of 92.3% and a specificity of 99.2% (AUC: 0.993). The model 2 (based on sncRNA-Y1, Y2 and Y3) enabled to differentiate PCNSL patients form healthy control with a sensitivity of 100% and a specificity of 93.9% (AUC: 0.984). The model 3 (based on sncRNA-Z1, Z2 and Z3) enabled to differentiate GBM patients form PCNSL patients with a sensitivity of 92.3% and a specificity of 78.6% (AUC: 0.920). Conclusion: We found three diagnostic models of serum sncRNAs as non-invasive biomarkers potentially useful for detection of GBM and PCNSL from healthy control, and for differentiation GBM from PCNSL.

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Comparative analysis of bacterioplankton assemblages from two subtropical karst reservoirs of southwestern China with contrasting trophic status

Scientific Reports ◽

10.1038/s41598-020-78459-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Qiang Li ◽

Yadan Huang ◽

Shenglin Xin ◽

Zhongyi Li

Keyword(s):

Trophic Status ◽

Alpha Diversity ◽

Decisive Role ◽

Sensu Stricto ◽

Karst Area ◽

Southwestern China ◽

Rrna Gene ◽

Karst Water ◽

Bacterioplankton Community ◽

Generation Sequencing

AbstractAlthough bacterioplankton play an important role in aquatic ecosystems, less is known about bacterioplankton assemblages from subtropical karst reservoirs of southwestern China with contrasting trophic status. Here, 16S rRNA gene next-generation sequencing coupled with water chemistry analysis was applied to compare the bacterioplankton communities from a light eutrophic reservoir, DL Reservoir, and a mesotrophic reservoir, WL Reservoir, in subtropical karst area of southwestern China. Our findings indicated that Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia dominated bacterioplankton community with contrasting relative frequency in the two subtropical karst reservoirs. Proteobacteria and Bacteroidetes were the core communities, which played important roles in karst biogeochemical cycles. Though WT, TN and DOC play the decisive role in assembling karst aquatic bacterioplankton, trophic status exerted significantly negative direct effects on bacterioplankton community composition and alpha diversity. Due to contrasting trophic status in the two reservoirs, the dominant taxa such as Enterobacter, Clostridium sensu stricto, Candidatus Methylacidiphilum and Flavobacteriia, that harbor potential functions as valuable and natural indicators of karst water health status, differed in DL Reservoir and WL Reservoir.

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

Nature Communications ◽

10.1038/s41467-021-24235-0 ◽

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.

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Administration of β-lactam antibiotics and delivery method correlate with intestinal abundances of Bifidobacteria and Bacteroides in early infancy, in Japan

Scientific Reports ◽

10.1038/s41598-021-85670-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Naruaki Imoto ◽

Chie Kano ◽

Yumi Aoyagi ◽

Hiroto Morita ◽

Fumitaka Amanuma ◽

...

Keyword(s):

Early Infancy ◽

Intestinal Microbiome ◽

Intestinal Immunity ◽

Delivery Method ◽

Premature Rupture ◽

Delivery Methods ◽

Faecal Samples ◽

Observational Cohort ◽

Group B ◽

Generation Sequencing

AbstractThe intestinal microbiome changes dynamically in early infancy. Colonisation by Bifidobacterium and Bacteroides and development of intestinal immunity is interconnected. We performed a prospective observational cohort study to determine the influence of antibiotics taken by the mother immediately before delivery on the intestinal microbiome of 130 healthy Japanese infants. Faecal samples (383) were collected at 1, 3, and 6 months and analysed using next-generation sequencing. Cefazolin was administered before caesarean sections, whereas ampicillin was administered in cases with premature rupture of the membranes and in Group B Streptococcus-positive cases. Bifidobacterium and Bacteroides were dominant (60–70% mean combined occupancy) at all ages. A low abundance of Bifidobacterium was observed in infants exposed to antibiotics at delivery and at 1 and 3 months, with no difference between delivery methods. A lower abundance of Bacteroides was observed after caesarean section than vaginal delivery, irrespective of antibiotic exposure. Additionally, occupancy by Bifidobacterium at 1 and 3 months and by Bacteroides at 3 months differed between infants with and without siblings. All these differences disappeared at 6 months. Infants exposed to intrapartum antibiotics displayed altered Bifidobacterium abundance, whereas abundance of Bacteroides was largely associated with the delivery method. Existence of siblings also significantly influenced the microbiota composition of infants.

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Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota

International Journal of Molecular Sciences ◽

10.3390/ijms22042131 ◽

2021 ◽

Vol 22 (4) ◽

pp. 2131

Author(s):

Stefania Pane ◽

Anna Sacco ◽

Andrea Iorio ◽

Lorenza Romani ◽

Lorenza Putignani

Keyword(s):

Gut Microbiota ◽

Bacterial Species ◽

Alpha Diversity ◽

Strongyloides Stercoralis ◽

Pulmonary Involvement ◽

Diversity Indices ◽

Parasite Infection ◽

Intestinal Nematode ◽

Immune Mediated ◽

Stool Samples

Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples’ ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.

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Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome

Viruses ◽

10.3390/v13102093 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2093

Author(s):

Shen-Yuan Hsieh ◽

Mohammad A. Tariq ◽

Andrea Telatin ◽

Rebecca Ansorge ◽

Evelien M. Adriaenssens ◽

...

Keyword(s):

Alpha Diversity ◽

Diversity Indices ◽

P Value ◽

Library Preparation ◽

High Genetic Diversity ◽

Sequencing Platform ◽

Viral Genomes ◽

Healthy Donors ◽

Faecal Samples ◽

Sequencing Platforms

The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as “viral dark matter”. However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating “rare” members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

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