scholarly journals A wipe-based stool collection and preservation kit for microbiome community profiling

2021 ◽  
Author(s):  
Hui Hua ◽  
Cem Meydan ◽  
Evan E. Afshin ◽  
Loukia Lili ◽  
Christopher R. D’Adamo ◽  
...  
Keyword(s):  
Room Temperature ◽  
Ethylenediaminetetraacetic Acid ◽  
Sample Collection ◽  
Community Profiling ◽  
Comparable Performance ◽  
Capture Method ◽  
Inflammatory Bowel ◽  
Stool Samples ◽  
Irritable Bowel ◽  
Human Stool

AbstractWhile a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. Future studies will be needed to further explore sample processing options and their applications in non-healthy subjects, particularly patients with irritable bowel syndrome, inflammatory bowel disease, and colorectal cancer, but these data suggest the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.

scholarly journals BLASTOCYSTIS HOMINIS: A MYSTERIOUS AND COMMONLY DISREGARDED PARASITE

2017 ◽  
pp. 39 ◽  
Author(s):  
Nataša Tasić ◽  
Tatjana Milenković ◽  
Vera Bujić ◽  
Dragan Zdravković ◽  
Aleksandar Tasić
Keyword(s):  
Developed Countries ◽  
Oral Route ◽  
Chronic Inflammatory Bowel Disease ◽  
Blastocystis Hominis ◽  
Inflammatory Bowel ◽  
Stool Samples ◽  
Conventional Microscopy ◽  
Irritable Bowel ◽  
Chronic Inflammatory Bowel

Blastocystis hominis (B. hominis) is an anaerobic, single-cell protozoan, commonly present in human and animal stool samples. It can be found in healthy people as well and it still has not been elucidated whether it is a commensal organism or a pathogen. Blastocystosis is a disease caused by the protozoan in humans. The prevalence of the parasitosis varies both between the countries, and between certain population groups within individual countries. Due to poor hygienic conditions, common exposure to animals and intake of contaminated water and food, people in the developing countries have got a higher prevalence of blastocystosis, but economically developed countries have not been spared either. The taxonomy of B. hominis is still a matter of debates. For the reasons of genetic diversity, it has been suggested that the name B. hominis should be replaced with „Blastocystis species‟. Seventeen subtypes of the species have been so far identified, and a definitive characterization of Blastocystis spp. is possible at the molecular level only. The parasite is transferred by the fecal-oral route. A variety of hosts have been identified, and animal-to-human and vice versa transfers have been documented. The most common manifestations of the infection with the organism are diarrhea, abdominal pain, nausea, and bloating. This infection has also been associated with the irritable bowel syndrome (IBS), non-specific colitis, chronic inflammatory bowel disease (CIBD), and urticaria. The diagnosis can be made using the methods of conventional microscopy (CVM), phase-contrast and electron microscopy, cultivation, serodiagnosis, and by using molecular methods. The infection caused by the parasite does not always require treatment. In symptomatic patients, the first line medical treatment is metronidazole. Further studies are required to resolve all dilemmas regarding the parasite.

Are Viruses and Parasites Linked to Celiac Disease? A Question that Still has no Definite Answer

2019 ◽  
Vol 20 (14) ◽  
pp. 1181-1193 ◽  
Author(s):  
Aref Shariati ◽  
Hamid R. Aslani ◽  
Mohammad R.H. Shayesteh ◽  
Ali Taghipour ◽  
Ahmad Nasser ◽  
...  
Keyword(s):  
Celiac Disease ◽  
Multiple Roles ◽  
Barr Virus ◽  
The People ◽  
Intestinal Infections ◽  
Inflammatory Bowel ◽  
Epstein Barr ◽  
Irritable Bowel ◽  
Related Proteins

Celiac Disease (CD) is a complex autoimmune enteropathy of the small intestine that commonly occurs in genetically predisposed individuals due to intake of gluten and related proteins. Gluten consumption, duration of breast-feeding, various infections, especially frequent intestinal infections, vaccinations and use of antibiotics can be linked to CD. It is predicted that it affects 1% of the global population and its incidence rate is increasing. Most of the people with the HLA-DQ2 or HLADQ8 are at a higher risk of developing this disease. The link between infections and autoimmune diseases has been very much considered in recent years. In several studies, we explained that pathogenic and non-pathogenic microorganisms might have multiple roles in initiation, exacerbation, and development of Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD). In various studies, the relationship between infections caused by viruses, such as Epstein-Barr Virus (EBV), Rotavirus, Hepatitis C (HCV), Hepatitis B virus (HBV), Cytomegalovirus (CMV), and Influenza virus, and parasites including Giardia spp. and Toxoplasma gondii with CD has been raised. However, increasing evidence proposes that some of these microorganisms, especially helminths, can also have protective and even therapeutic roles in the CD process. Therefore, in order to determine the role of microorganisms in the process of this disease, we attempted to summarize the evidence suggesting the role of viral and parasitic agents in pathogenesis of CD.

scholarly journals Differing Effects of Standard and Harsh Nucleic Acid Extraction Procedures on Diagnostic Helminth Real-Time PCRs Applied to Human Stool Samples

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 188
Author(s):  
Tanja Hoffmann ◽  
Andreas Hahn ◽  
Jaco J. Verweij ◽  
Gérard Leboulle ◽  
Olfert Landt ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Real Time Pcr ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Pcr Assay ◽  
Bead Beating ◽  
Stool Samples ◽  
Pcr Assays ◽  
Human Stool

This study aimed to assess standard and harsher nucleic acid extraction schemes for diagnostic helminth real-time PCR approaches from stool samples. A standard procedure for nucleic acid extraction from stool and a procedure including bead-beating as well as proteinase K digestion were compared with group-, genus-, and species-specific real-time PCR assays targeting helminths and nonhelminth pathogens in human stool samples. From 25 different in-house and commercial helminth real-time PCR assays applied to 77 stool samples comprising 67 historic samples and 10 external quality assessment scheme samples positively tested for helminths, higher numbers of positive test results were observed after bead-beating-based nucleic acid extraction for 5/25 (20%) real-time PCR assays irrespective of specificity issues. Lower cycle threshold values were observed for one real-time PCR assay after the standard extraction scheme, and for four assays after the bead-beating-based scheme. Agreement between real-time PCR results after both nucleic acid extraction strategies according to Cohen’s kappa ranged from poor to almost perfect for the different assays. Varying agreement was observed in eight nonhelminth real-time PCR assays applied to 67 historic stool samples. The study indicates highly variable effects of harsh nucleic acid extraction approaches depending on the real-time PCR assay used.

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

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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