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

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.

Download Full-text

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

Download Full-text

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

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjz203.978 ◽

2020 ◽

Vol 14 (Supplement_1) ◽

pp. S654-S655

Author(s):

H S Lee ◽

T O Kim ◽

S H Jung ◽

D H Baek

Keyword(s):

Ulcerative Colitis ◽

Sampling Methods ◽

Alpha Diversity ◽

Mantel Test ◽

Endoscopic Biopsy ◽

Intestinal Dysbiosis ◽

Faecal Samples ◽

Healthy Control ◽

Stool Samples ◽

Generation Sequencing

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.

Download Full-text

Distinct effects of over-general autobiographical memory on suicidal ideation among depressed and healthy people

BMC Psychiatry ◽

10.1186/s12888-020-02877-6 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Wen Jiang ◽

Guangtao Hu ◽

Jingxuan Zhang ◽

Ken Chen ◽

Dongni Fan ◽

...

Keyword(s):

Risk Factors ◽

Suicidal Ideation ◽

Autobiographical Memory ◽

Childhood Trauma ◽

Study Data ◽

Path Model ◽

Control Group ◽

Healthy Controls ◽

Healthy Individuals ◽

Healthy Control

Abstract Background Childhood trauma and over-general autobiographical memory (OGM) are crucial risk factors of suicide. This study aimed to investigate whether suicidal ideation was predicted by one’s childhood trauma and OGM and the mechanism of OGM underlying suicidal ideation in depression patients and healthy controls. Methods A total of 180 depression patients and 176 matched healthy individuals were recruited in this study. Data were analyzed using descriptive statistics, and Pearson’s correlation coefficient was obtained. Path analysis was conducted to test a meditational model. The multigroup comparison was applied to find differences between groups. Results Significant differences were detected between depression patients and healthy controls with respect to childhood trauma, OGM, suicidal ideation, and suicidal behavior. OGM was positively correlated with both current and worst-point suicidal ideation in the depression group and significantly correlated with worst-point suicidal ideation in the healthy control group. The path model showed that childhood trauma had a direct impact on the current suicidal ideation directly, and an indirect influence through OGM and worst-point suicidal ideation. Multigroup analysis further demonstrated that OGM affected and mediated the current suicidal ideation due to childhood trauma in depression patients, whereas only worst-point suicidal ideation was affected in healthy controls. Conclusions The OGM mediates suicidal ideation in depression patients, but only affects the worst-point suicidal ideation in the healthy controls. As it is one of the major risk factors of suicidal ideation in depression, amelioration of OGM might be an useful method to reduce or prevent suicidal ideation in depression patients.

Download Full-text

Reduced serum levels of pro-inflammatory chemokines in Fragile X Syndrome

10.21203/rs.2.13398/v3 ◽

2020 ◽

Author(s):

Anke Van Dijck ◽

Susana Barbosa ◽

Patricia Bermudez-Martin ◽

Olfa Khalfallah ◽

Cyprien Gilet ◽

...

Keyword(s):

Fragile X Syndrome ◽

Robust Regression ◽

Fragile X ◽

Serum Levels ◽

Unsupervised Clustering ◽

Healthy Controls ◽

Healthy Individuals ◽

Clustering Method ◽

Inflammatory Chemokines ◽

Healthy Control

Abstract Background: Fragile X syndrome (FXS) is the most frequent cause of inherited intellectual disability and the most commonly identified monogenic cause of autism. Recent studies have shown that long-term pathological consequences of FXS are not solely confined to the central nervous system (CNS) but rather extend to other physiological dysfunctions in peripheral organs. To gain insights into possible immune dysfunctions in FXS, we profiled a large panel of immune-related biomarkers in the serum of FXS patients and healthy controls. Methods: We have used a sensitive and robust Electro Chemi Luminescence (ECL)-based immunoassay to measure the levels of 52 cytokines in the serum of n=25 FXS patients and n=29 healthy controls. We then used univariate statistics and multivariate analysis, as well as an advanced unsupervised clustering method, to identify combinations of immune-related biomarkers that could discriminate FXS patients from healthy individuals. Results: While the majority of the tested cytokines were present at similar levels in FXS patients and healthy individuals, nine chemokines, CCL2, CCL3, CCL4, CCL11, CCL13, CCL17, CCL22, CCL26 and CXCL10, were present at much lower levels in FXS patients. Using robust regression, we show that six of these biomarkers (CCL2, CCL3, CCL11, CCL22, CCL26 and CXCL10) were negatively associated with FXS diagnosis. Finally, applying the K-sparse unsupervised clustering method to the biomarker dataset allowed for the identification of two subsets of individuals, which essentially matched the FXS and healthy control categories. Conclusions: Our data show that FXS patients exhibit reduced serum levels of several chemokines. This paves the way for further study of immune phenotypes in FXS patients.

Download Full-text

Ulcerative Colitis and Its Association withSalmonellaSpecies

Interdisciplinary Perspectives on Infectious Diseases ◽

10.1155/2016/5854285 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 5

Author(s):

Manish Kumar Tripathi ◽

Chandra Bhan Pratap ◽

Vinod K. Dixit ◽

Tej Bali Singh ◽

Sunit K. Shukla ◽

...

Keyword(s):

Ulcerative Colitis ◽

Colon Cancer ◽

Irritable Bowel Syndrome ◽

Healthy Subjects ◽

Healthy Controls ◽

Serological Study ◽

Indirect Haemagglutination ◽

Healthy Control ◽

Irritable Bowel ◽

Specific Sequences

Ulcerative colitis (UC) is characterized by presence of ulcer in colon and bloody diarrhea. The present study explores the possibility of association betweenSalmonellaand ulcerative colitis. The present study comprised 59 cases of UC, 28 of colon cancer (CC), 127 of irritable bowel syndrome (IBS), and 190 of healthy control. The serological study was done by Widal and Indirect Haemagglutination Assay (IHA) for ViAb. Nested PCR was performed targetingfliC,staA,andstkGgene for Typhi and Paratyphi A, respectively. A total of 15.3% patients were positive forSalmonella“O” antigen among them 18.6% UC, 35.5% CC, 12.6% IBS, and 15.3% healthy control. A total of 36.9% patients were positive for “H” antigen including 39.0%, 57.1%, and 67.7% UC, CC, and IBS, respectively. About 1.73% show positive agglutination for AH antigen including 3.4%, 3.6%, and 1.6%, UC, CC, and IBS. A total of 10.89% were positive for ViAb. While 6.8% of UC, 10.7% of CC, 11.0% of IBS, and 12.1% of healthy subjects were positive for the antibody, the PCR positivity rates forSalmonellaspecific sequences were 79.7% in UC, 53.6% in CC, 66.1% in IBS, and 16.3% in healthy controls. The present study suggested that higher prevalence ofSalmonellamight play important role in etiopathogenesis of UC, IBS, and CC.

Download Full-text

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.

Download Full-text

Vitamin D deficiency associated with Crohn’s disease and ulcerative colitis: a meta-analysis of 55 observational studies

Journal of Translational Medicine ◽

10.1186/s12967-019-2070-5 ◽

2019 ◽

Vol 17 (1) ◽

Cited By ~ 3

Author(s):

Xi-Xi Li ◽

Yang Liu ◽

Jie Luo ◽

Zhen-Dong Huang ◽

Chao Zhang ◽

...

Keyword(s):

Ulcerative Colitis ◽

Vitamin D ◽

Crohn’S Disease ◽

Observational Studies ◽

Meta Analysis ◽

Serum Levels ◽

Healthy People ◽

Healthy Controls ◽

Control Groups ◽

Healthy Control

Abstract Purpose To investigate the association of serum levels of 25(OH)D and 1,25(OH)2D3 in healthy and non-healthy controls with Crohn’s disease (CD) and ulcerative colitis (UC). Methods Three electronic databases: PubMed, EMbase and EBSCOhost CINAHL, were searched for observational studies to measure the relationship between serum levels of vitamin D (VitD) and CD (or UC). Results Fifty-five studies were included in the meta-analysis. We found that mean serum 25(OH)D levels in patients with CD were significantly lower than those in healthy controls (MD: − 3.17 ng/mL; 95% CI − 4.42 to − 1.93). Results from the meta-analysis examining 1,25(OH)2D3 levels in Crohn’s patients revealed higher levels in the CD group than in healthy (MD: 3.47 pg/mL; 95% CI − 7.72 to 14.66) and UC group (MD: 5.05 pg/mL; 95% CI − 2.42 to 12.52). Serum 25(OH)D levels were lower in the UC group than in the healthy control group (MD: − 2.52 ng/mL; 95% CI − 4.02 to − 1.02). In studies investigating the level of 1,25(OH)2D3 in UC and healthy control groups, the level of 1,25(OH)2D3 in the UC groups were found to be higher than that in the control groups (MD: 3.76 pg/mL; 95% CI − 8.36 to 15.57). However, the 1,25(OH)2D3 level in patients with UC was lower than that in CD groups (MD: − 6.71 pg/mL; 95% CI − 15.30 to 1.88). No significant difference was noted between CD patients and UC patients in terms of average serum 25(OH)D levels. Conclusions This study found that VitD levels were inversely related to CD and UC. Serum levels of 25(OH)D were lower in patients with CD and UC than in healthy people, and more than half of the patients had insufficient vitamin D levels. The serum level of 1,25(OH)2D3 in both the CD and UC groups was higher than that in healthy people.

Download Full-text

Analyzing Confabulations in Schizophrenia and Healthy Participants

Journal of the International Neuropsychological Society ◽

10.1017/s1355617716000801 ◽

2016 ◽

Vol 22 (9) ◽

pp. 911-919 ◽

Cited By ~ 1

Author(s):

Mohammed K. Shakeel ◽

Nancy M. Docherty ◽

Patrick R. Rich ◽

Maria S. Zaragoza ◽

Quin M. Chrobak ◽

...

Keyword(s):

Thought Disorder ◽

Temporal Context ◽

Positive Symptoms ◽

Healthy Controls ◽

Healthy Individuals ◽

Formal Thought Disorder ◽

Healthy Control ◽

Forced Confabulation ◽

Healthy Participants ◽

Neuropsychiatric Conditions

AbstractObjectives: Confabulations occur in schizophrenia and certain severe neuropsychiatric conditions, and to a lesser degree in healthy individuals. The present study used a forced confabulation paradigm to assess differences in confabulation between schizophrenia patients and healthy controls. Methods: Schizophrenia patients (n=60) and healthy control participants (n=19) were shown a video with missing segments, asked to fill in the gaps with speculations, and tested on their memory for the story. Cognitive functions and severity of symptoms were also evaluated. Results: Schizophrenia patients generated significantly more confabulations than healthy control participants and had a greater tendency to generate confabulations that were related to each other. Schizophrenic confabulations were positively associated with temporal context confusions and formal thought disorder, and negatively with delusions. Conclusions: Our findings show that the schizophrenia patients generate more confabulations than healthy controls and schizophrenic confabulations are associated with positive symptoms. (JINS, 2016, 22, 911–919)

Download Full-text

LncRNA PMS2L2 downregulates miR-24 through methylation to suppress cell apoptosis in ulcerative colitis

Digestive Diseases ◽

10.1159/000513330 ◽

2020 ◽

Author(s):

Ting Yu ◽

Fanyu Meng ◽

Minning Xie ◽

Huajiang Liu ◽

Lei Zhang ◽

...

Keyword(s):

Ulcerative Colitis ◽

Cell Apoptosis ◽

Healthy Controls ◽

Western Blots ◽

Age And Gender ◽

Specific Pcr ◽

Rna Immunoprecipitation ◽

Healthy Control ◽

And Gender

Background: Ulcerative colitis (UC) is an inflammatory bowel disease characterized by chronic inflammation of the colon. It has been reported that PMS2L2 plays protective roles in inflammatory injury. This study aimed to investigate the role of lncRNA PMS2L2 in UC. Methods: 62 patients with UC as well as 62 age- and gender- matched healthy controls were enrolled. Expressions of PMS2L2 and miR-24 in plasma from UC patients and healthy controls were determined by RT-qPCR. The interaction between PMS2L2 and miR-24 was predicted by bioinformatics and confirmed by RNA immunoprecipitation (RIP) and RNA pull-down. The role of PMS2L2 in the regulation of miR-24 gene methylation was analyzed by methylation-specific PCR (MSP). The effects of PMS2L2 and miR-24 on the expressions of apoptosis-related proteins were detected by western blots. Results: PMS2L2 was downregulated in the plasma of UC patients compared to that in age- and gender- matched healthy control. In HCnEpCs, PMS2L2 overexpression inhibited miR-24 expression via promoting the methylation of miR-24 gene. In contrast, miR-24 overexpression failed to affect PMS2L2. In the detection of cell apoptosis, PMS2L2 overexpression could promote the expression of Bcl-2 and inhibit Bax, cleaved-caspase-3 and cleaved-caspase-9 expressions stimulated by LPS. Flow cytometer revealed that PMS2L2 elevation suppressed the apoptosis of HCnEpCs induced by LPS, but miR-24 aggravated the apoptosis. PMS2L2 overexpression rescued the detrimental effect of miR-24 on cell apoptosis. Conclusion: PMS2L2 may downregulate miR-24 via methylation to suppress cell apoptosis in UC.

Download Full-text

A case–control study on the association of intestinal flora with ulcerative colitis

AMB Express ◽

10.1186/s13568-021-01267-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yin-hua Tang ◽

Hong-cheng Liu ◽

Guang Song ◽

Tian-tian Wu ◽

Ying Zhao ◽

...

Keyword(s):

Ulcerative Colitis ◽

Pathogenic Bacteria ◽

Intestinal Flora ◽

16S Rrna Gene Sequencing ◽

Control Group ◽

Rrna Gene ◽

Healthy Controls ◽

Fecal Samples ◽

Healthy Control ◽

Rrna Gene Sequencing

AbstractThe association between intestinal flora and ulcerative colitis (UC) was studied in order to provide a basis and method for clinical treatment. Fresh fecal samples were collected from 30 active UC patients and 10 healthy controls. The intestinal flora DNA from each sample was extracted and 16S rRNA gene sequencing was carried out using HiSeq platform to identify the intestinal flora in fecal samples. The richness and diversity of intestinal flora in UC patients were significantly lower than those in healthy control group (P < 0.05). Significant differences were observed between the intestinal flora-species of UC patients and healthy controls. Synergistetes (P < 0.01) and Firmicutes (P < 0.05), along with probiotics Veillonella (P < 0.01), Ruminococcus and Coprococcus (P < 0.05) in the UC patients were lower than that in the healthy controls significantly. Furthermore, compared with the control group, Tenericutes (P < 0.01) and intestinal pathogenic bacteria, including Bacteroides (P < 0.01), Escherichia and Sutterella (P < 0.05) were significantly increased. The incidence of UC is significantly associated with the changes in intestinal flora. Changes in intestinal flora may lead to a decrease in the diversity of intestinal flora or to the enrichment of a particular intestinal flora.

Download Full-text