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 Impact of Environmental Chemicals on the Gut Microbiome

2020 ◽  
Vol 176 (2) ◽  
pp. 253-284 ◽  
Author(s):  
Karen Chiu ◽  
Genoa Warner ◽  
Romana A Nowak ◽  
Jodi A Flaws ◽  
Wenyan Mei
Keyword(s):  
Gut Microbiome ◽  
Current Knowledge ◽  
Environmental Chemicals ◽  
Microbial Composition ◽  
Multiple Factors ◽  
Microbiome Research ◽  
Health Related ◽  
Exogenous Factors ◽  
The Impact ◽  
Insight Into

Abstract Since the surge of microbiome research in the last decade, many studies have provided insight into the causes and consequences of changes in the gut microbiota. Among the multiple factors involved in regulating the microbiome, exogenous factors such as diet and environmental chemicals have been shown to alter the gut microbiome significantly. Although diet substantially contributes to changes in the gut microbiome, environmental chemicals are major contaminants in our food and are often overlooked. Herein, we summarize the current knowledge on major classes of environmental chemicals (bisphenols, phthalates, persistent organic pollutants, heavy metals, and pesticides) and their impact on the gut microbiome, which includes alterations in microbial composition, gene expression, function, and health effects in the host. We then discuss health-related implications of gut microbial changes, which include changes in metabolism, immunity, and neurological function.

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 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 A predictive index for health status using species-level gut microbiome profiling

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Vinod K. Gupta ◽  
Minsuk Kim ◽  
Utpal Bakshi ◽  
Kevin Y. Cunningham ◽  
John M. Davis ◽  
...  
Keyword(s):  
Health Status ◽  
Gut Microbiome ◽  
Human Microbiome ◽  
Diversity Indices ◽  
Predictive Index ◽  
Α Diversity ◽  
Microbiome Research ◽  
Microbiome Profiling ◽  
Insight Into ◽  
Human Stool

Abstract Providing insight into one’s health status from a gut microbiome sample is an important clinical goal in current human microbiome research. Herein, we introduce the Gut Microbiome Health Index (GMHI), a biologically-interpretable mathematical formula for predicting the likelihood of disease independent of the clinical diagnosis. GMHI is formulated upon 50 microbial species associated with healthy gut ecosystems. These species are identified through a multi-study, integrative analysis on 4347 human stool metagenomes from 34 published studies across healthy and 12 different nonhealthy conditions, i.e., disease or abnormal bodyweight. When demonstrated on our population-scale meta-dataset, GMHI is the most robust and consistent predictor of disease presence (or absence) compared to α-diversity indices. Validation on 679 samples from 9 additional studies results in a balanced accuracy of 73.7% in distinguishing healthy from non-healthy groups. Our findings suggest that gut taxonomic signatures can predict health status, and highlight how data sharing efforts can provide broadly applicable discoveries.

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 Atypical cutaneous and musculoskeletal manifestation of SARS-CoV-2: ‘COVID-19 toes’ and spasticity in a 48-year-old woman

2021 ◽  
Vol 14 (3) ◽  
pp. e241410
Author(s):  
Avery Kopacz ◽  
Cameron Ludwig ◽  
Michelle Tarbox
Keyword(s):  
Nervous System ◽  
Adult Patient ◽  
Early Identification ◽  
Lower Limbs ◽  
Rare Occurrence ◽  
Cutaneous Manifestations ◽  
Crucial Component ◽  
History Of ◽  
Screening Questions ◽  
Insight Into

Establishing accurate symptomatology associated with novel diseases such as COVID-19 is a crucial component of early identification and screening. This case report identifies an adult patient with a history of clotting dysfunction presenting with rare cutaneous manifestations of COVID-19, known as ‘COVID-19 toes’', previously described predominantly in children. Additionally, this patient presented with possible COVID-associated muscle spasticity of the lower limbs, as well as a prolonged and atypical timeline of COVID-19 infection. The rare occurrence of ‘COVID-19 toes’' in this adult patient suggests that her medical history could have predisposed her to this symptom. This supports the coagulopathic hypothesis of this manifestation of COVID-19 and provides possible screening questions for patients with a similar history who might be exposed to the virus. Additionally, nervous system complaints associated with this disease are rare and understudied, so this novel symptom may also provide insight into this aspect of SARS-CoV-2.

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.

scholarly journals Role of Biological Sex in the Cardiovascular-Gut Microbiome Axis

2022 ◽  
Vol 8 ◽  
Author(s):  
Shuangyue Li ◽  
Georgios Kararigas
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Microbial Composition ◽  
Biological Sex ◽  
Technological Advances ◽  
Host Health ◽  
Health And Disease ◽  
And Function ◽  
Insight Into

There has been a recent, unprecedented interest in the role of gut microbiota in host health and disease. Technological advances have dramatically expanded our knowledge of the gut microbiome. Increasing evidence has indicated a strong link between gut microbiota and the development of cardiovascular diseases (CVD). In the present article, we discuss the contribution of gut microbiota in the development and progression of CVD. We further discuss how the gut microbiome may differ between the sexes and how it may be influenced by sex hormones. We put forward that regulation of microbial composition and function by sex might lead to sex-biased disease susceptibility, thereby offering a mechanistic insight into sex differences in CVD. A better understanding of this could identify novel targets, ultimately contributing to the development of innovative preventive, diagnostic and therapeutic strategies for men and women.

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