scholarly journals Patient attitudes towards faecal sampling for gut microbiome studies and clinical care reveal positive engagement and room for improvement

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249405
Author(s):  
Laura A. Bolte ◽  
Marjolein A. Y. Klaassen ◽  
Valerie Collij ◽  
Arnau Vich Vila ◽  
Jingyuan Fu ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Faecal Sample ◽  
Clinical Care ◽  
Clinical Applications ◽  
Willingness To Participate ◽  
Sample Collection ◽  
General Population Cohort ◽  
Microbiome Research ◽  
Stool Samples ◽  
Sampling Procedures

Faecal sample collection is crucial for gut microbiome research and its clinical applications. However, while patients and healthy volunteers are routinely asked to provide stool samples, their attitudes towards sampling remain largely unknown. Here, we investigate the attitudes of 780 Dutch patients, including participants in a large Inflammatory Bowel Disease (IBD) gut microbiome cohort and population controls, in order to identify barriers to sample collection and provide recommendations for gut microbiome researchers and clinicians. We sent questionnaires to 660 IBD patients and 112 patients with other disorders who had previously been approached to participate in gut microbiome studies. We also conducted 478 brief interviews with participants in our general population cohort who had collected stool samples. Statistical analysis of the data was performed using R. 97.4% of respondents reported that they had willingly participated in stool sample collection for gut microbiome research, and most respondents (82.9%) and interviewees (95.6%) indicated willingness to participate again, with their motivations for participating being mainly altruistic (57.0%). Responses indicated that storing stool samples in the home freezer for a prolonged time was the main barrier to participation (52.6%), but clear explanations of the sampling procedures and their purpose increased participant willingness to collect and freeze samples (P = 0.046, P = 0.003). To account for participant concerns, gut microbiome researchers establishing cohorts and clinicians trying new faecal tests should provide clear instructions, explain the rationale behind their protocol, consider providing a small freezer and inform patients about study outcomes. By assessing the attitudes, motives and barriers surrounding participation in faecal sample collection, we provide important information that will contribute to the success of gut microbiome research and its near-future clinical applications.

scholarly journals Patient attitudes towards faecal sampling for gut microbiome studies and clinical care reveal positive engagement and room for improvement

2019 ◽  
Author(s):  
Laura A. Bolte ◽  
Marjolein A.Y. Klaassen ◽  
Valerie Collij ◽  
Arnau Vich Vila ◽  
Jingyuan Fu ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Faecal Sample ◽  
Clinical Care ◽  
Clinical Applications ◽  
Willingness To Participate ◽  
Sample Collection ◽  
General Population Cohort ◽  
Microbiome Research ◽  
Stool Samples ◽  
Sampling Procedures

Abstract Background: Faecal sample collection is crucial for gut microbiome research and its clinical applications. However, while patients and healthy volunteers are routinely asked to provide stool samples, their attitudes towards sampling remain largely unknown. Here we investigate the attitudes of 780 Dutch patients, including participants in a large Inflammatory Bowel Disease (IBD) gut microbiome cohort, and population controls, to identify barriers to sample collection and provide recommendations for gut microbiome researchers and clinicians. Methods: We sent questionnaires to 660 IBD patients and 112 patients with other disorders who had previously been approached to participate in gut microbiome studies. We also conducted 478 brief interviews with participants in our general population cohort who had collected stool samples. Statistical analysis of the data was performed using R. Results: 97.4% of respondents reported that they had willingly participated in stool sample collection for gut microbiome research, and most respondents (82.9%) and interviewees (95.6%) indicated willingness to participate again, with motivations for participating being mainly altruistic (57.0%). Responses indicated that storing stool samples in the home freezer for a prolonged time was the main barrier to participation (52.6%), but clear explanations of the sampling procedures and their purpose increased willingness to collect and freeze samples (P=0.046, P=0.003). Conclusions: To account for participant concerns, gut microbiome researchers establishing cohorts and clinicians trying new faecal tests should provide clear instructions, explain the rationale behind their protocol, consider providing a small freezer, and inform patients about study outcomes. By assessing the attitudes to, motives for and barriers to participation in faecal sample collection, we can provide important information that will contribute to the success of gut microbiome research and its near-future clinical applications.

scholarly journals The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling

2021 ◽  
Vol 22 (4) ◽  
pp. 1965
Author(s):  
Sheeana Gangadoo ◽  
Piumie Rajapaksha Pathirannahalage ◽  
Samuel Cheeseman ◽  
Yen Thi Hoang Dang ◽  
Aaron Elbourne ◽  
...  
Keyword(s):  
Coeliac Disease ◽  
Gut Microbiome ◽  
Rapid Diagnosis ◽  
Fecal Material ◽  
Sample Collection ◽  
Crucial Component ◽  
The Matrix ◽  
Microbiome Research ◽  
Complex Substance ◽  
Insight Into

Gastrointestinal (GIT) diseases have risen globally in recent years, and early detection of the host’s gut microbiota, typically through fecal material, has become a crucial component for rapid diagnosis of such diseases. Human fecal material is a complex substance composed of undigested macromolecules and particles, and the processing of such matter is a challenge due to the unstable nature of its products and the complexity of the matrix. The identification of these products can be used as an indication for present and future diseases; however, many researchers focus on one variable or marker looking for specific biomarkers of disease. Therefore, the combination of genomics, transcriptomics, proteomics and metabonomics can give a detailed and complete insight into the gut environment. The proper sample collection, sample preparation and accurate analytical methods play a crucial role in generating precise microbial data and hypotheses in gut microbiome research, as well as multivariate data analysis in determining the gut microbiome functionality in regard to diseases. This review summarizes fecal sample protocols involved in profiling coeliac disease.

scholarly journals The Microbiome and p-Inulin in Hemodialysis: A Feasibility Study

Kidney360 ◽  
2021 ◽  
pp. 10.34067/KID.0006132020
Author(s):  
Dominic S. Raj ◽  
Michael B. Sohn ◽  
David M. Charytan ◽  
Jonathan Himmelfarb ◽  
T. Alp Ikizler ◽  
...  
Keyword(s):  
Feasibility Study ◽  
Gut Microbiome ◽  
Post Treatment ◽  
Intestinal Microbiome ◽  
Maintenance Hemodialysis ◽  
Sample Collection ◽  
Microbiome Composition ◽  
Stool Samples ◽  
Pre Treatment ◽  
End Stage

Background: The intestinal microbiome is an appealing target for interventions in end-stage kidney disease (ESKD) because of its likely contribution to uremic toxicity. Before conducting clinical trials of microbiome-altering treatments, it is necessary to understand the within-person and between-person variability in the composition and function of the gut microbiome in patients with ESKD. Methods: Multi-center, non-randomized, crossover feasibility study of maintenance hemodialysis patients consisting of 3 phases: pre-treatment (8 weeks), treatment during which the prebiotic, p-inulin (Prebiotin®), was administered at a dose of 8 gm twice daily (12 weeks), and post-treatment (8 weeks). Stool samples were collected 1-2 times/week and blood was collected weekly for 28 weeks. The gut microbiome was characterized using 16S ribosomal RNA sequencing and metabolomic profiling. Results: Eleven of the 13 participants completed the 28-week study. Inter-participant variability was greater than intra-participant variability for microbiome composition (p<0.001 by UniFrac distances), and metabolomic composition (p<0.001 by Euclidean distances). p-Inulin was well-tolerated by 12 of 13 participants. Adherence to the frequent sample collection and self-aliquoting of stool samples were both 96%. A change in the microbiome composition from pre-treatment to post-treatment was evident by the overall shifts in weighted UniFrac distances (p=0.004) and a progressive decrease in prevalence of high intra-class correlations indicating an increase in intra-participant microbiome diversity during and after p-inulin treatment. An effect of p-inulin on the metabolomic profile was not evident. Conclusions: The intra-participant stability of the gut microbiome under no-treatment conditions, the tolerability of p-inulin, the signals of increased diversity of the microbiome with p-inulin treatment, and the willingness of participants to provide stool samples all support the feasibility of a larger trial to investigate interventions targeting the gut microbiome in patients with ESKD. Whether p-inulin has sufficient efficacy as an intervention requires evaluation in larger studies.

scholarly journals Associations Between Dysmenorrhea Symptom-Based Phenotypes and Vaginal Microbiome: A Pilot Study

2020 ◽  
pp. 109980042097960
Author(s):  
Chen X. Chen ◽  
Janet S. Carpenter ◽  
Tabitha Murphy ◽  
Patricia Brooks ◽  
J. Dennis Fortenberry
Keyword(s):  
Young Adults ◽  
Gut Microbiome ◽  
Treatment Options ◽  
Human Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Adolescents And Young Adults ◽  
Rrna Gene ◽  
Sample Collection ◽  
Microbiome Research ◽  
Prospective Longitudinal

Human microbiome research provides rich opportunities to elucidate factors influencing health, uncover novel biomarkers, and expand disease treatment options. A well-conducted microbiome study depends not only on a rigorous design but also on successfully engaging participants in collecting quality samples. In this paper, we aim to describe (1) strategies our team used to engage adolescents and young adults in vaginal and gut microbiome sample self-collection and (2) their effectiveness. In our prospective, longitudinal, feasibility study of 20 female adolescents and young adults, research participants self-collected vaginal and gut microbiome samples at home. Using a participatory and iterative process, we developed strategies to engage participants in sample self-collection, including (1) providing clear instructions to ensure comprehension and buy-in, (2) providing a user-friendly take-home package, (3) minimizing disgust/embarrassment associated with sample collection, and (4) follow-up communications to facilitate sample collections and return. With these strategies, we achieved 100% participant retention and 100% sample return rates. All samples ( n = 80, 100%) were usable for downstream 16s rRNA gene sequencing and analysis. All participants rated the study procedures as acceptable, and qualitative data showed that strategies were well received by participants. This study suggests that carefully planning and implementing strategies to engage participants in sample self-collection can result in high degrees of participant compliance, sample quality, and participant satisfaction in microbiome research.

scholarly journals Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa

2020 ◽  
Author(s):  
Fiona B. Tamburini ◽  
Dylan Maghini ◽  
Ovokeraye H. Oduaran ◽  
Ryan Brewster ◽  
Michaella R. Hulley ◽  
...  
Keyword(s):  
South African ◽  
Gut Microbiome ◽  
Human Gut ◽  
Microbiome Composition ◽  
African Populations ◽  
Microbiome Research ◽  
Long Read ◽  
Novel Taxa ◽  
Reference Databases ◽  
Stool Samples

AbstractWhile human gut microbiome research often focuses on western populations or nonwestern agriculturalist and hunter-gatherer societies, most of the world’s population resides between these extremes. We present the first study evaluating gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyzed stool samples from adult females (age 40 - 72) living in rural Bushbuckridge municipality (n=117) or urban Soweto (n=51) and find that these microbiomes are intermediate between those of western industrialized and previously studied non-industrialized African populations. We demonstrate that reference collections are incomplete for nonwestern microbiomes, resulting in within-cohort beta diversity patterns that are in some cases reversed compared to reference-agnostic sequence comparison patterns. To improve reference databases, we generated complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas species. Our results suggest that South Africa’s transitional lifestyle and epidemiological conditions are reflected in gut microbiota compositions, and that these populations contain microbial diversity that remains to be described.

scholarly journals Postoperative Complications Are Associated with Long-Term Changes in the Gut Microbiota Following Colorectal Cancer Surgery

Life ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 246
Author(s):  
Felix C.F. Schmitt ◽  
Martin Schneider ◽  
William Mathejczyk ◽  
Markus A. Weigand ◽  
Jane C. Figueiredo ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Postoperative Complications ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Tumor Resection ◽  
Microbial Composition ◽  
Colorectal Cancer Surgery ◽  
Long Term Changes ◽  
Stool Samples

Changes in the gut microbiome have already been associated with postoperative complications in major abdominal surgery. However, it is still unclear whether these changes are transient or a long-lasting effect. Therefore, the aim of this prospective clinical pilot study was to examine long-term changes in the gut microbiota and to correlate these changes with the clinical course of the patient. Methods: In total, stool samples of 62 newly diagnosed colorectal cancer patients undergoing primary tumor resection were analyzed by 16S-rDNA next-generation sequencing. Stool samples were collected preoperatively in order to determine the gut microbiome at baseline as well as at 6, 12, and 24 months thereafter to observe longitudinal changes. Postoperatively, the study patients were separated into two groups—patients who suffered from postoperative complications (n = 30) and those without complication (n = 32). Patients with postoperative complications showed a significantly stronger reduction in the alpha diversity starting 6 months after operation, which does not resolve, even after 24 months. The structure of the microbiome was also significantly altered from baseline at six-month follow-up in patients with complications (p = 0.006). This was associated with a long-lasting decrease of a large number of species in the gut microbiota indicating an impact in the commensal microbiota and a long-lasting increase of Fusobacterium ulcerans. The microbial composition of the gut microbiome shows significant changes in patients with postoperative complications up to 24 months after surgery.

scholarly journals Endocannabinoid system mediates the association between gut-microbial diversity and anhedonia/amotivation in a general population cohort

2021 ◽  
Author(s):  
Amedeo Minichino ◽  
Matthew A. Jackson ◽  
Marta Francesconi ◽  
Claire J. Steves ◽  
Cristina Menni ◽  
...  
Keyword(s):  
General Population ◽  
Microbial Diversity ◽  
Gut Microbiome ◽  
Endocannabinoid System ◽  
Alpha Diversity ◽  
Serum Levels ◽  
Population Cohort ◽  
Random Intercept ◽  
General Population Cohort ◽  
Antidepressant Use

AbstractAnhedonia and amotivation are debilitating symptoms and represent unmet therapeutic needs in a range of clinical conditions. The gut-microbiome-endocannabinoid axis might represent a potential modifiable target for interventions. Based on results obtained from animal models, we tested the hypothesis that the endocannabinoid system mediates the association between gut-microbiome diversity and anhedonia/amotivation in a general population cohort. We used longitudinal data collected from 786 volunteer twins recruited as part the TwinsUK register. Our hypothesis was tested with a multilevel mediation model using family structure as random intercept. The model was set using alpha diversity (within-individual gut-microbial diversity) as predictor, serum and faecal levels of the endocannabinoid palmitoylethanolamide (PEA) as mediator, and anhedonia/amotivation as outcome. PEA is considered the endogenous equivalent of cannabidiol, with increased serum levels believed to have anti-depressive effects, while increased stool PEA levels, reflecting increased excretion, are believed to have opposite, detrimental, effects on mental health. We therefore expected that either reduced serum PEA or increased stool PEA would mediate the association between microbial diversity and anhedonia amotivation. Analyses were adjusted for obesity, diet, antidepressant use, sociodemographic and technical covariates. Data were imputed using multiple imputation by chained equations. Mean age was 65.2 ± 7.6; 93% of the sample were females. We found a direct, significant, association between alpha diversity and anhedonia/amotivation (β = −0.37; 95%CI: −0.71 to −0.03; P = 0.03). Faecal, but not serum, levels of the endocannabinoid palmitoylethanolamide (PEA) mediated this association: the indirect effect was significant (β = −0.13; 95%CI: −0.24 to −0.01; P = 0.03), as was the total effect (β = −0.38; 95%CI: −0.72 to −0.04; P = 0.03), whereas the direct effect of alpha diversity on anhedonia/amotivation was attenuated fully (β = −0.25; 95%CI: −0.60 to 0.09; P = 0.16). Our results suggest that gut-microbial diversity might contribute to anhedonia/amotivation via the endocannabinoid system. These findings shed light on the biological underpinnings of anhedonia/amotivation and suggest the gut microbiota-endocannabinoid axis as a promising therapeutic target in an area of unmet clinical need.

scholarly journals A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Christophe Lay ◽  
Collins Wenhan Chu ◽  
Rikky Wenang Purbojati ◽  
Enzo Acerbi ◽  
Daniela I. Drautz-Moses ◽  
...  
Keyword(s):  
Risk Factor ◽  
Gut Microbiome ◽  
Reference Group ◽  
Mode Of Delivery ◽  
Controlled Study ◽  
Double Blind ◽  
Lipopolysaccharide Biosynthesis ◽  
Infant Gut Microbiome ◽  
Stool Samples ◽  
The Impact

Abstract Background The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD. Results As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome. Conclusions This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development. Trial registration The study was registered in the Dutch Trial Register (Number: 2838) on 4th April 2011.

scholarly journals 781. C.difficile PCR+/ Toxin EIA- treat or not treat? A clinician survey

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S435-S436
Author(s):  
Sarath G Nath ◽  
Francesca Lee ◽  
Anjali Bararia ◽  
Ank E Nijhawan
Keyword(s):  
Clinical Judgment ◽  
Clinical Care ◽  
Cost Effective ◽  
False Positive Diagnosis ◽  
Missed Diagnosis ◽  
Stool Samples ◽  
Polymerase Chain ◽  
Low Sensitivity ◽  
Survey Responses ◽  
And Training

Abstract Background C.difficile Toxin Polymerase Chain Reaction (C.diff PCR) and C.difficile Toxin Enzyme Immunoassays (toxin EIA) are commonly used tests to diagnose Clostridoides difficile infection (CDI). C.diff PCR cannot differentiate between colonization and infection, leading to a higher false-positive diagnosis of CDI. Toxin EIA has low sensitivity leading to a missed diagnosis of CDI. In patients with C.diff PCR positive(+) and Toxin EIA negative(-), clinical judgment is often needed regarding the decision to treat or not to treat. C.diff cytotoxic assay (CCA), is a more sensitive method to detect the toxin but is time-consuming and not readily available. Methods Between 6/2019 and 12/2019, 83 patients who were admitted to the hospital, met our inclusion criteria (C.diff PCR+/EIA-). Clinicians who cared for these patients were contacted and surveyed with a predesigned questionnaire evaluating the rationale of treatment. Also, a simultaneous medical records review was done to ensure consistency. Along with this C.diff PCR+/EIA- stool samples were sent to ARUP laboratories for CCA. The CCA results were not available for clinicians and did not impact clinical care. Average cost for a CCA assay was $29 Results Demographics of the clinicians were variable (Table 1). Several parameters were considered when making decisions regarding treatment and GI/ID were frequently involved (figure 1). Among the 83 patients, 41(49%) were CCA (+) and 42(51%) were CCA (-). 48 of 83 (58%) patients received treatment for CDI. 25 of 48 (52%) patients who were treated were CCA positive while 23 of 48 (48%) patients were CCA negative. Among the untreated patients, 16/35 (46%) were CCA+ while 19/35(54%) were CCA-. There was no statistically significant correlation between clinical judgment and CCA assay results (p: 0.56 on the Chi test). Demographics of the clinicians Clinician survey responses CDI Treatment and by CCA positivity Conclusion Clinicians regardless of their background and training face challenges with the treatment of C.diff PCR+/EIA- patients. Patient outcomes based on the incorporation of CCA assay into an algorithm for C.diff PCR+/EIA- patients, need to be evaluated. But it has a potential role in stopping unnecessary CDI treatment as well as avoidance of missed treatment opportunities while possibly also being cost-effective. Disclosures Ank E. Nijhawan, MD, MPH, Gilead (Grant/Research Support, Scientific Research Study Investigator, Research Grant or Support)

Gut Feeling

2016 ◽  
Vol 33 (S1) ◽  
pp. S504-S505
Author(s):  
C. Cotta ◽  
G. Jesus ◽  
V. Vila Nova ◽  
C. Moreira
Keyword(s):  
Mental Disorders ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Infections ◽  
Human Microbiome ◽  
Dietary Interventions ◽  
Scientific Databases ◽  
Antibiotic Drugs ◽  
Microbiome Research ◽  
Competing Interest

IntroductionThere is growing evidence of the importance of nutrition in mental disorders. Gut microbiota, influenced by environmental factors such as diet and stress, has been proposed as one of the players on a dynamic called gut-brain axis, which is thought to have an influence on behaviour and mental health.Objectives and aimsTo summarize recent evidence on the topic, and its potential role in psychiatric interventions.MethodsThe authors review updated literature collected from online scientific databases.ResultsThe development of the brain itself has been shown to be influenced by the gut microbiome. Research demonstrates that the composition of the microbiota has influence on behaviour through neuroendocrine and other neuroactive messengers production by the bacteria within the gut lumen. Studies in germ-free animals, animals exposed to bacterial infections, probiotic suplements or antibiotic drugs suggest a role for the gut microbiota in the regulation of anxiety, mood, cognition and pain. The gut microbiome has been implicated in brain disorders including anxiety and depression, multiple sclerosis, Alzheimer's disease, Parkinson's disease, and autism.ConclusionsThe treatment of mental disorders is usually based on pharmacological and psychotherapeutic interventions, and little attention is given to dietary interventions. The emerging field of research focused on the human microbiome suggests an important role for the gut microbiota in influencing brain development, behaviour and mood in humans, and points new strategies for developing novel therapeutics for mental disorders.Disclosure of interestThe authors have not supplied their declaration of competing interest.

Sign in / Sign up

Export Citation Format

Share Document