scholarly journals P685 Gut microbiota in patients with Inflammatory Bowel Disease during remission

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.

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

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.

scholarly journals Improvement of Gut Diversity and Composition After Direct-Acting Antivirals in Hepatitis C Virus–Infected Patients With or Without Human Immunodeficiency Virus Coinfection

2021 ◽  
Author(s):  
Natthaya Chuaypen ◽  
Thananya Jinato ◽  
Anchalee Avihingsanon ◽  
Sakkarin Chirapongsathorn ◽  
Supapon Cheevadhanarak ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Gut Microbiota ◽  
Alpha Diversity ◽  
Healthy Controls ◽  
Direct Acting Antivirals ◽  
Microbial Dysbiosis ◽  
Immunodeficiency Virus ◽  
Direct Acting

Abstract Background The influence of direct-acting antivirals (DAAs) on the composition of gut microbiota in hepatitis C virus (HCV)–infected patients with or without human immunodeficiency virus (HIV) is unclear. Methods We enrolled 62 patients with HCV monoinfection and 24 patients with HCV/HIV coinfection receiving elbasvir-grazoprevir from a clinical trial. Fecal specimens collected before treatment and 12 weeks after treatment were analyzed using amplicon-based 16S ribosomal RNA sequencing. Results Sustained virological response rates in the monoinfection and coinfection groups were similar (98.4% vs 95.8%). Pretreatment bacterial communities in the patient groups were less diverse and distinct from those of healthy controls. Compared with HCV-monoinfected patients, HCV/HIV-coinfected individuals showed comparable microbial alpha diversity but decreased Firmicutes-Bacteroidetes ratios. The improvement of microbial dysbiosis was observed in responders achieving sustained virological response across fibrosis stages but was not found in nonresponders. Responders with a low degree of fibrosis exhibited a recovery in alpha diversity to levels comparable to those in healthy controls. Reciprocal alterations of increased beneficial bacteria and reduced pathogenic bacteria were also observed in responders. Conclusions This study indicates a short-term effect of direct-acting antivirals in restoration of microbial dysbiosis. The favorable changes in gut microbiota profiles after viral eradication might contribute toward the reduction of HCV-related complications among infected individuals.

scholarly journals Dysbiosis characteristics of gut microbiota in cerebral infarction patients

2020 ◽  
Vol 11 (1) ◽  
pp. 124-133
Author(s):  
Hao Li ◽  
Xiaohui Zhang ◽  
Dengdeng Pan ◽  
Yongqiang Liu ◽  
Xuebing Yan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Cerebral Infarction ◽  
Operating Characteristic ◽  
National Institutes Of Health ◽  
Diagnostic Model ◽  
Healthy Controls ◽  
Characteristic Analysis ◽  
Rrna Sequencing ◽  
Stool Samples ◽  
Microbiota Diversity

AbstractObjectiveThe aim of this study is to investigate the dysbiosis characteristics of gut microbiota in patients with cerebral infarction (CI) and its clinical implications.MethodsStool samples were collected from 79 CI patients and 98 healthy controls and subjected to 16S rRNA sequencing to identify stool microbes. Altered compositions and functions of gut microbiota in CI and its correlation with clinical features were investigated. Random forest and receiver operating characteristic analysis were used to develop a diagnostic model.ResultsMicrobiota diversity and structure between CI patients and healthy controls were overall similar. However, butyrate-producing bacteria (BPB) were significantly reduced in CI patients, while lactic acid bacteria (LAB) were increased. Genetically, BPB-related functional genes were reduced in CI patients, whereas LAB-related genes were enhanced. The interbacterial correlations among BPB in CI patients were less prominent than those in healthy controls. Clinically, BPB was negatively associated with the National Institutes of Health Stroke Scale (NIHSS), while LAB was positively correlated with NIHSS. Both BPB and LAB played leading roles in the diagnostic model based on 47 bacteria.ConclusionsThe abundance and functions of BPB in CI patients were significantly decreased, while LAB were increased. Both BPB and LAB displayed promising potential in the assessment and diagnosis of CI.

scholarly journals Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

Gut ◽  
2016 ◽  
Vol 67 (1) ◽  
pp. 108-119 ◽  
Author(s):  
Floris Imhann ◽  
Arnau Vich Vila ◽  
Marc Jan Bonder ◽  
Jingyuan Fu ◽  
Dirk Gevers ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Genetic Risk ◽  
Genetic Risk Score ◽  
Alpha Diversity ◽  
Host Genome ◽  
Risk Scores ◽  
Rrna Gene ◽  
Control Analysis ◽  
Healthy Controls ◽  
Healthy Individuals

ObjectivePatients with IBD display substantial heterogeneity in clinical characteristics. We hypothesise that individual differences in the complex interaction of the host genome and the gut microbiota can explain the onset and the heterogeneous presentation of IBD. Therefore, we performed a case–control analysis of the gut microbiota, the host genome and the clinical phenotypes of IBD.DesignStool samples, peripheral blood and extensive phenotype data were collected from 313 patients with IBD and 582 truly healthy controls, selected from a population cohort. The gut microbiota composition was assessed by tag-sequencing the 16S rRNA gene. All participants were genotyped. We composed genetic risk scores from 11 functional genetic variants proven to be associated with IBD in genes that are directly involved in the bacterial handling in the gut: NOD2, CARD9, ATG16L1, IRGM and FUT2.ResultsStrikingly, we observed significant alterations of the gut microbiota of healthy individuals with a high genetic risk for IBD: the IBD genetic risk score was significantly associated with a decrease in the genus Roseburia in healthy controls (false discovery rate 0.017). Moreover, disease location was a major determinant of the gut microbiota: the gut microbiota of patients with colonic Crohn's disease (CD) is different from that of patients with ileal CD, with a decrease in alpha diversity associated to ileal disease (p=3.28×10−13).ConclusionsWe show for the first time that genetic risk variants associated with IBD influence the gut microbiota in healthy individuals. Roseburia spp are acetate-to-butyrate converters, and a decrease has already been observed in patients with IBD.

scholarly journals Population Stratification in the Gut Microbiota of Bali is Associated with Transitional Lifestyle

2020 ◽  
Author(s):  
Clarissa Asha Febinia ◽  
Safarina G. Malik ◽  
Ratna Djuwita ◽  
I Wayan Weta ◽  
Desak Made Wihandani ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Additive Model ◽  
Alpha Diversity ◽  
Population Level ◽  
Wilcoxon Test ◽  
Abundance Pattern ◽  
Unifrac Distance ◽  
Transitional State ◽  
Community Types ◽  
The Impact

Abstract Background: Human living conditions, such as food availability and the built environment, contribute to environmental forces that influence gut microbiota composition. Understanding the impact of the environment on microbiota assembly and its association with human health has multiple potential applications. Indonesia is a densely populated country that has been undergoing a dramatic societal change for the past two decades. It is distinctive in that it occupies an archipelago that imposes diverse geographic and cultural boundaries. The relationship between diet, microbiota, and health is poorly known in Indonesians and represents a natural study for the interaction between ethnogeographic factors and nutrition in microbiota assembly. Results: Here we show the first comprehensive report of the gut microbiota in adults from Bali, Indonesia (n=41). Their microbiotas clustered into two distinct community types: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community. The Type-P individuals had lower alpha diversity (p <0.001, Shannon) and more incidence of obesity. The two community types are significantly different in their inter-genus co-abundance pattern (p <0.001, ANOSIM, Wilcoxon test). Further analyses with diet and obesity data showed that the presence of two distinct community types in Bali is a significant confounder for identifying health markers. In a multi-country dataset (n=257), the Bali microbiota indicates a transitional state from a subsistent (Prevotella-dominant) to industrial (Bacteroides-dominant) society. The two largest axes in a Principal Coordinate Analysis of weighted UniFrac distance explained the majority of variance between samples across countries (49.1%). Microbial dissimilarity across populations is significantly associated with Prevotella and Bacteriodes abundance (p <0.001, Generalized Additive Model). Conclusion: Our data showed that lifestyle transitions have a strong influence on the frequency of microbiota community types in a population. The Bali microbiota is undergoing a shift towards a Bacteroides-dominant community which reflects the ongoing transition of nutrition, socio-economy, and lifestyle the society. Although enterotypes obscured the detection of health markers, our findings collectively suggest that enterotypes may be useful in future studies for informing population-level stratification in large heterogenetic datasets.

scholarly journals Trends in Faecal Calprotectin Levels During Pregnancy in Non-IBD Patients

2021 ◽  
Author(s):  
Jayne Doherty ◽  
Rebecca Moore ◽  
Clodagh Kivlehan ◽  
David F Byrne ◽  
Cara A Yelverton ◽  
...  
Keyword(s):  
Post Partum ◽  
Healthy Population ◽  
Healthy Individuals ◽  
Faecal Calprotectin ◽  
Patient Demographics ◽  
Calprotectin Level ◽  
Minimal Data ◽  
Inflammatory Bowel ◽  
Stool Samples ◽  
Physiological Changes In Pregnancy

Abstract Background and Aims: No optimal marker exists to assess activity of inflammatory bowel disease (IBD) during pregnancy, though faecal calprotectin (FCP) is the most commonly used test. However minimal data exists on what a normal calprotectin level is during pregnancy and post-partum in healthy individuals. Objective: Our aim is to determine normal FCP levels during pregnancy and post-partum in a healthy population. Methods: We performed a prospective analysis of FCP levels from pregnant women at 16- and 34-weeks’ gestation and 4- and 12-weeks post-partum. Patient demographics were collected. FCP concentrations were measured with a quantitative ELISA assay. Results: 98 patients were included in our study. 172 maternal stool samples were collected in total; 62 samples at 16-weeks’ gestation, 48 samples at 34-weeks’ gestation, 38 samples from 4-weeks post-partum and 24 samples from 12-weeks post-partum. Median age was 33.0 years. 41 patients had a BMI > 25 (41.8%). 16 patients were ex-smokers (16.3 %). The median FCP levels at 16-weeks’ gestation was 29.5 µg/g (range 10–476 µg/g), median level from 34-weeks’ gestation was 25.6 µg/g (range 10–259 µg/g), from 4-weeks post-partum was 23.4 µg/g (range 10–318 µg/g) and 12-weeks post-partum was 29.4 µg/g (range 10–216 µg/g). There was no significant change in median FCP levels over the course of pregnancy and post-partum (p = 0.294). Conclusion: Faecal calprotectin levels are not affected by physiological changes in pregnancy or post-partum in normal healthy individuals without IBD. This suggests FCP is a useful tool for identifying flares of colitis during pregnancy.

scholarly journals P053 Overabundance of Lactobacillus species in gut microbiota of IBD patients

2021 ◽  
Vol 15 (Supplement_1) ◽  
pp. S160-S161
Author(s):  
D Khusnutdinova ◽  
M Markelova ◽  
M Siniagina ◽  
E Boulygina ◽  
S Abdulkhakov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Active Phase ◽  
Bioinformatic Analysis ◽  
Lactobacillus Species ◽  
Control Group ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing ◽  
Inflammatory Bowel ◽  
Stool Samples

Abstract Background Changes in the composition of gut microbiota, and their metabolic pathways, are important factors in the pathogenesis of inflammatory bowel disease (IBD). Many clinical trials have shown that taking probiotics based on Lactobacillus has a positive effect on patients with IBD. However, Lactobacillus should be used more carefully during the active phase of IBD, since some strains can negatively affect the pathogenesis of the disease1,2. The aim of this study was to assess the diversity of Lactobacillus species in the gut microbiome of IBD patients and healthy volunteers. Methods In the study, 62 stool samples from healthy people, 31 from patients with Crohn’s disease (CD), and 34 - ulcerative colitis (UC) in active phase were analyzed. DNA was isolated using the QIAamp Fast DNA Stool Mini Kit (Qiagen, USA) following with shotgun metagenomic sequencing the NextSeq 500 (project #0671-2020-0058). Bioinformatic analysis was performed with the MetaPhlAn2 package. Results An increased relative abundance of Lactobacillus was found in patients with IBD (3.2% ± 6.6% in CD and 1.6% ± 2.8 in UC) compared to healthy individuals (0.3% ± 1.2%, p&lt;0.05). In the control group, Lactobacillus were absent in 41% of samples and 1–5 species were found in 58% of samples. Most CD and UC patients are characterized by the presence of 3 to 5 species of Lactobacillus (38% and 31%, respectively). For 23% of CD patients and 26% of UC patients, 6 to 9 types of Lactobacillus were found. Some patients with IBD have more than 10 different types of Lactobacillus in the gut microbiota (Fig.1). The intestinal microbiota in IBD patients is characterized by an increased abundance of several species: L. salivarius, L. gasseri, L. mucosae, as well as L. casei paracasei in patients with CD and L. vaginalis in patients with UC (Fig.2). Conclusion The composition of the intestinal microbiota of IBD patients differs significantly in terms of Lactobacillus proportion and species diversity. Overabundance of five Lactobacillus species could be associated with the active phase of IBD. References

scholarly journals Who sleeps better? Sleep patterns and sleep disturbances in adolescents with recurrent abdominal pain or inflammatory bowel disease and healthy controls

2021 ◽  
Vol 3 (1) ◽  
pp. 83-93
Author(s):  
Ann-Kristin Manhart ◽  
◽  
Angelika A. Schlarb ◽  
Keyword(s):  
Abdominal Pain ◽  
Sleep Quality ◽  
Sleep Disturbances ◽  
Sleep Problems ◽  
Recurrent Abdominal Pain ◽  
Control Group ◽  
Healthy Controls ◽  
Healthy Control ◽  
Inflammatory Bowel ◽  
Sleep Difficulties

Background: Sleep difficulties play an important role in the maintenance and course of chronic abdominal pain disorders (RAP and IBD). Particularly among adolescents with inflammatory bowel diseases (IBD) or recurrent abdominal pain (RAP), adequate sleep seems to be important, as the diseases self and the associated symptoms can cause distress and impair daytime functioning. Hence it seems adequate to take a closer look concerning the sleep difficulties within the different conditions of abdominal pain especially in comparison to a healthy control. To our knowledge no former study compared sleep problems in youths with RAP and IBD as well as healthy controls. Thus the aim of the present study was to 1) evaluate sleep problems in the RAP and IBD and 2) compare the sleep problems of these abdominal pain diseases with a healthy control group. Methods: 129 adolescents (14-25 years) took part in the online survey, with 58 suffering from IBD, 23 had RAP and 48 healthy controls. Adolescents completed sleep questionnaires as PSQI, SDSC or NEQ. Data was analysed by conducting MANOVAs to test differences between the three groups followed by a post-hoc analyses. Results: Significant differences between both patient groups and healthy controls regarding sleep quality as well as sleep disturbances were found. Results indicate that especially young IBD patients suffered more often from poor sleep quality, sleep disturbances as well as daily effects of nightmares than the control group. The comparison of adolescents with RAP and healthy controls showed elevated scores concerning sleep disturbances for RAP patients. However, IBD and RAP adolescents did not differ significantly concerning most sleep measurements. Discussion: The study at hand was the first to compare adolescents with IBD and RAP regarding sleep difficulties. Adolescents with IBD and RAP have an impaired sleep quality as well as a higher rate of sleep disturbances and suffer from daily effects of nightmares than the control group. Therefore sleep disturbances should be also addressed when treating IBD and RAP patients to prevent further impairments.

scholarly journals A Pilot Study to Determine the Gut Microbiota of Hong Kong Infants Fed with Breast-milk And/or Infant Formula (P11-101-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Oi Yee Yeung ◽  
Yuk Fan Ng ◽  
Jiachi Chiou ◽  
Man-sau Wong
Keyword(s):  
Hong Kong ◽  
Breast Milk ◽  
Gut Microbiota ◽  
Infant Formula ◽  
Newborn Infants ◽  
Alpha Diversity ◽  
Gut Health ◽  
Unifrac Distance ◽  
Fecal Samples ◽  
The Government

Abstract Objectives Gut microbiome in newborn infants affect their gut health and future development. The major nutrient sources for infants aged 2–4 months are breast-milk or infant formula, hence it is worth investigating whether exclusively breastfed or infant formula-fed does affect the early development of the gut microbiota communities. Metagenomics has been applied to analyse the infant fecal samples in the United State and some European countries, however, similar studies were limited in Asia and especially Hong Kong. Methods Three groups of infants aged 2–4 months which were exclusively breastfed (BF), exclusively infant formula-fed (IF) or mix-fed with breast-milk and infant formula (MF) were recruited. Genomic DNA from the fecal sample and breast-milk was extracted and subjected to 16S rRNA next-generation sequencing to understand the gut microbiota profile, the difference of microbiota diversity and community abundance in these three feeding groups. The sequencing results were processed using pipelines Mothur and Qiime2. Results Overall the breast-milk showed higher alpha-diversity than the fecal samples. The 3 predominant Phyla were Proteobacteria, Firmicutes and Bacteroidetes within the fecal samples from all feeding patterns while the 3 dominant Phyla were Firmicutes, Proteobacteria and Actinobacteria in the breastmilk. Higher abundance of the well-known immune-modulating Genera Bifidobacterium and Lactobacillus were found in the fecal samples of BF and MF groups than the IF group whereas IF group harboured highest abundance of Genus Clostridium among 3 fecal groups. A PCoA based on unweighted UniFrac distance showed that the microbiota from the breastmilk clustered and distinctly separated from those of fecal samples. Moreover, the microbiota of MF subjects were close to BF subjects from the PCoA analysis. Conclusions Our preliminary results suggested that partial feeding with breast-milk could still maintain the major gut community composition as in the BF group. Feeding pattern affect the gut microbiota in Hong Kong infants aged 2–4 month and probiotic genera Bifidobacterium and Lactobacillus were found in the breast-milk, and fecal samples of BF and MF groups. Funding Sources Health and Medical Research Fund, Food and Health Bureau, The Government of the Hong Kong Special Administrative Region.

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