scholarly journals Investigation of the impact of stool collection methods on the metabolomics analysis/profiles of infant fecal samples

2021 ◽  
Author(s):  
Chiara-Maria Homann ◽  
Sara Dizzell ◽  
Sandi Azab ◽  
Eileen K Hutton ◽  
Katherine M Morrison ◽  
...  
Keyword(s):  
Stool Sample ◽  
Short Chain Fatty Acids ◽  
Sample Collection ◽  
Fecal Samples ◽  
Wide Range ◽  
Metabolite Profiles ◽  
Comprehensive Metabolomics ◽  
The Impact ◽  
Collection Methods ◽  
Metabolomics Analysis

Metabolomic studies are important to understand microbial metabolism and interaction between the host and the gut microbiome. Although there have been efforts to standardize sample processing in metabolomic studies, infant samples are mostly disregarded. In birth cohort studies, the use of diaper liners is prevalent and its impact on fecal metabolic profile remains untested. In this study, we compared metabolite profiles of fecal samples collected as solid stool and those collected from stool saturated liner. One infant's stool sample was collected in triplicate for solid stool and stool saturated liner. Comprehensive metabolomics analysis of the fecal samples was performed using NMR, UPLC and DI-MS. The total number, identities and concentrations of the metabolites were determined and compared between stool sample collection methods (stool vs. liner). The number and identity of metabolites did not differ between collection methods for NMR and DI-MS when excluding metabolites with a coefficient of variation (CV) > 40%. NMR analysis demonstrated lowest bias between collection methods, and lowest technical precision between triplicates of the same method followed by DI-MS then UPLC. Concentrations of many metabolites from stool and stool saturated liner differed significantly as revealed by Bland-Altman plots and t-tests. Overall, a mean bias of 10.2% in the Bland-Altman analysis was acceptable for some metabolites confirming mutual agreement but not for others with a wide range of bias (-97-117%). Consequently, stool and stool-saturated liner could be used interchangeably only for some select metabolite classes e.g. amino acids. Differences between the metabolomic profiles of solid stool samples and stool saturated liner samples for some important molecules e.g., ethanol, fumarate, short chain fatty acids and bile acids, indicate the need for standardization in stool collection method for metabolomic studies performed in infants.

scholarly journals Differences in the Fecal Metabolome and Microbiome Between Exclusive and Partial Breastfed Infants are More Pronounced at 2 Months Compared to 5 Months

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1097-1097 ◽  
Author(s):  
Aidong Wang ◽  
Aly Diana ◽  
Sofa Rahmannia ◽  
Rosalind Gibson ◽  
Lisa Houghton ◽  
...  
Keyword(s):  
Exclusive Breastfeeding ◽  
Feeding Practices ◽  
Illumina Miseq ◽  
Short Chain Fatty Acids ◽  
P Value ◽  
Fecal Samples ◽  
Breastfed Infants ◽  
Funding Sources ◽  
Gates Foundation ◽  
The Impact

Abstract Objectives This study aimed to characterize the impact of feeding practices on the infant fecal metabolome and microbiome at 2 months and 5 months of age in exclusive breastfeeding (EBF) and partial breastfeeding (PBF) infants. Methods Fecal samples were collected from infants at 2 months and 5 months of age from Bandung, Indonesia. Exclusive breastfeeding was determined using the stable isotope deuterium dose-to-mother (DTM) technique. Fecal metabolites were extracted using Dulbecco's phosphate-buffered saline, and analyzed using NMR spectroscopy. Fecal microbial DNA was extracted at the same time using the MoBio PowerLyzer PowerSoil DNA isolation kit (MoBio, Carlsbad, CA). The V4 region of 16SrRNA was targeted. The DNA library sample was analyzed via 300-bp paired-end sequencing on the Illumina MiSeq platform. Results Fecal samples from EBF infants at 2 months of age revealed significantly higher human milk oligosaccharides (HMOs), short-chain fatty acids and related metabolites compared to PBF infants. However, fecal samples from infants at 5 months of age revealed no differences in metabolome between EBF and PBF after p-value adjustment for multiple comparisons. Gut microbes, especially Bifidobacterium were higher in EBF infants at age 2 months even though not statistically significant. However, this difference was eliminated at age 5 months. Conclusions In the present study, infant feeding practices had a stronger influence on the infant fecal metabolome and microbiome at the age of 2 months as compared to 5 months. Funding Sources 2014 Bill & Melinda Gates Foundation. CS would also like to acknowledge funding from the Kinsella endowed chair in Food, Nutrition, and health as well as USDA-NIFA Hatch project 1,021,411.

scholarly journals Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Doratha A. Byrd ◽  
Rashmi Sinha ◽  
Kristi L. Hoffman ◽  
Jun Chen ◽  
Xing Hua ◽  
...  
Keyword(s):  
Ambient Temperature ◽  
Fecal Sample ◽  
Gold Standard ◽  
Beta Diversity ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Sample Collection ◽  
Fecal Samples ◽  
Shotgun Metagenomic Sequencing ◽  
Collection Methods

ABSTRACT Few previous studies have assessed stability and “gold-standard” concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies. IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.

scholarly journals Epidemiology of constipation in adults: Why estimates of prevalence differ

2019 ◽  
Vol 5 (1) ◽  
pp. 37
Author(s):  
Barry Werth
Keyword(s):  
Data Collection ◽  
Older Adult ◽  
Epidemiological Studies ◽  
Community Dwelling ◽  
Data Collection Methods ◽  
Wide Range ◽  
Prevalence Estimates ◽  
Age Range ◽  
The Impact ◽  
Collection Methods

This review of over 80 articles published in the last 30 years shows that estimates of the prevalence of chronic constipation in community-dwelling adults varied widely from 2.4% to 39.6% in general adult populations and from 4% to 25.8% in older adult populations. Estimates of the prevalence of any constipation (including both chronic and sporadic constipation) also varied widely from 2.6% to 31.0% in general adult populations and from 4.4% to 44.5% in older adult populations. Apart from any country or regional differences, this wide range of estimated prevalence may be attributed to different definitions used for both chronic and any constipation as well as different data collection methods and sampling differences. Sampling issues include sample size, representativeness and age range of populations sampled. Further research is required to examine the impact of different definitions on prevalence estimates to help determine the best definitions for use in future epidemiological studies. If standard definitions can be universally agreed and used, along with appropriate sampling and data collection methods, more precise estimates of constipation prevalence should be attained. This would allow more meaningful comparisons between countries and may also provide the ability to pool results.

scholarly journals A Systematic Review of Collection and Analysis of Human Milk for Macronutrient Composition

2020 ◽  
Vol 150 (6) ◽  
pp. 1652-1670 ◽  
Author(s):  
Gabriela E Leghi ◽  
Philippa F Middleton ◽  
Merryn J Netting ◽  
Mary E Wlodek ◽  
Donna T Geddes ◽  
...  
Keyword(s):  
Human Milk ◽  
Data Extraction ◽  
The Body ◽  
Systematic Evaluation ◽  
Cochrane Library ◽  
Sample Collection ◽  
Macronutrient Composition ◽  
Lactation Stage ◽  
Wide Range ◽  
Collection Methods

ABSTRACT Background As human milk (HM) composition varies by time and across even a single feed, methods of sample collection can significantly affect the results of compositional analyses and complicate comparisons between studies. Objective The aim was to compare the results obtained for HM macronutrient composition between studies utilizing different sampling methodologies. The results will be used as a basis to identify the most reliable HM sampling approach. Methods EMBASE, MEDLINE/PubMed, Cochrane Library, Scopus, Web of Science, and ProQuest databases were searched for relevant articles. Observational and interventional studies were included, and at least 2 authors screened studies and undertook data extraction. Quality assessment was conducted using the Newcastle-Ottawa scale and previously published pragmatic score. Results A total of 5301 publications were identified from our search, of which 101 studies were included (n = 5049 breastfeeding women). Methods used for HM collection were divided into 3 categories: collection of milk from all feeds over 24 h (32 studies, n = 1309 participants), collection at one time point (62 studies, n = 3432 participants), and “other methods” (7 studies, n = 308 participants). Fat and protein concentrations varied between collection methods within lactation stage, but there were no obvious differences in lactose concentrations. There was substantial variability between studies in other factors potentially impacting HM composition, including stage of lactation, gestational age, and analytical method, which complicated direct comparison of methods. Conclusions This review describes the first systematic evaluation of sampling methodologies used in studies reporting HM composition and highlights the wide range of collection methods applied in the field. This information provides an important basis for developing recommendations for best practices for HM collection for compositional analysis, which will ultimately allow combination of information from different studies and thus strengthen the body of evidence relating to contemporary HM composition. This trial was registered at PROSPERO as CRD42017072563, https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42017072563

scholarly journals Approaches to minimising the epidemiological impact of sources of systematic and random variation that may affect biochemistry assay data in UK Biobank

2021 ◽  
Vol 5 ◽  
pp. 222
Author(s):  
Naomi E. Allen ◽  
Matthew Arnold ◽  
Sarah Parish ◽  
Michael Hill ◽  
Simon Sheard ◽  
...  
Keyword(s):  
Uk Biobank ◽  
Sample Collection ◽  
Sodium Potassium ◽  
Reactive Protein ◽  
Serum Assay ◽  
Wide Range ◽  
Epidemiological Impact ◽  
The Uk ◽  
The Impact ◽  
Random Variation

Background: UK Biobank is a large prospective study that recruited 500,000 participants aged 40 to 69 years, between 2006-2010.The study has collected (and continues to collect) extensive phenotypic and genomic data about its participants. In order to enhance further the value of the UK Biobank resource, a wide range of biochemistry markers were measured in all participants with an available biological sample. Here, we describe the approaches UK Biobank has taken to minimise error related to sample collection, processing, retrieval and assay measurement. Methods: During routine quality control checks, the laboratory team observed that some assay results were lower than expected for samples acquired during certain time periods. Analyses were undertaken to identify and correct for the unexpected dilution identified during sample processing, and for expected error caused by laboratory drift of assay results. Results: The vast majority (92%) of biochemistry serum assay results were assessed to be not materially affected by dilution, with an estimated difference in concentration of less than 1% (i.e. either lower or higher) than that expected if the sample were unaffected; 8.3% were estimated to be diluted by up to 10%; very few samples appeared to be diluted more than this. Biomarkers measured in urine (creatinine, microalbumin, sodium, potassium) and red blood cells (HbA1c) were not affected. In order to correct for laboratory variation over the assay period, all assay results were adjusted for date of assay, with the exception of those that had a high biological coefficient of variation or evident seasonal variability: vitamin D, lipoprotein (a), gamma glutamyltransferase, C-reactive protein and rheumatoid factor. Conclusions: Rigorous approaches related to sample collection, processing, retrieval, assay measurement and data analysis have been taken to mitigate the impact of both systematic and random variation in epidemiological analyses that use the biochemistry assay data in UK Biobank.

scholarly journals Approaches to minimising the epidemiological impact of sources of systematic and random variation that may affect biochemistry assay data in UK Biobank

2020 ◽  
Vol 5 ◽  
pp. 222
Author(s):  
Naomi E. Allen ◽  
Matthew Arnold ◽  
Sarah Parish ◽  
Michael Hill ◽  
Simon Sheard ◽  
...  
Keyword(s):  
Uk Biobank ◽  
Sample Collection ◽  
Sodium Potassium ◽  
Reactive Protein ◽  
Serum Assay ◽  
Wide Range ◽  
Epidemiological Impact ◽  
The Uk ◽  
The Impact ◽  
Random Variation

Background: UK Biobank is a large prospective study that recruited 500,000 participants aged 40 to 69 years, between 2006-2010.The study has collected (and continues to collect) extensive phenotypic and genomic data about its participants. In order to enhance further the value of the UK Biobank resource, a wide range of biochemistry markers were measured in all participants with an available biological sample. Here, we describe the approaches UK Biobank has taken to minimise error related to sample collection, processing, retrieval and assay measurement. Methods: During routine quality control checks, the laboratory team observed that some assay results were lower than expected for samples acquired during certain time periods. Analyses were undertaken to identify and correct for the unexpected dilution identified during sample processing, and for expected error caused by laboratory drift of assay results. Results: The vast majority (92%) of biochemistry serum assay results were assessed to be not materially affected by dilution, with an estimated difference in concentration of less than 1% (i.e. either lower or higher) than that expected if the sample were unaffected; 8.3% were estimated to be diluted by up to 10%; very few samples appeared to be diluted more than this. Biomarkers measured in urine (creatinine, microalbumin, sodium, potassium) and red blood cells (HbA1c) were not affected. In order to correct for laboratory variation over the assay period, all assay results were adjusted for date of assay, with the exception of those that had a high biological coefficient of variation or evident seasonal variability: vitamin D, lipoprotein (a), gamma glutamyltransferase, C-reactive protein and rheumatoid factor. Conclusions: Rigorous approaches related to sample collection, processing, retrieval, assay measurement and data analysis have been taken to mitigate the impact of both systematic and random variation in epidemiological analyses that use the biochemistry assay data in UK Biobank.

scholarly journals Mobilizing COVID-19 Testing: Impact and Challenges

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S110-S110
Author(s):  
R Odenbrett ◽  
D Ingemansen ◽  
T Baumgart ◽  
V Hieb ◽  
A Ross ◽  
...  
Keyword(s):  
Inventory Management ◽  
Successful Implementation ◽  
Sample Collection ◽  
Site Testing ◽  
Testing Program ◽  
Result Verification ◽  
Public Health Reporting ◽  
Percent Positivity ◽  
Wide Range ◽  
The Impact

Abstract Introduction/Objective In response to the rapidly evolving COVID-19 pandemic, Sanford Health developed a mobile diagnostic testing program capable of reaching geographically dispersed sites and communities. These mobile laboratories provided on-site testing and sensitive detection of SARS-CoV-2 by leveraging Cepheid’s GeneXpert platform, enabling rapid reporting of results directly to the patient and physician. Aggregation of these results allowed monitoring population infection rates and public health reporting. Methods/Case Report Within 3 weeks of conception, the first mobile unit was designed, engineered and deployed. Key requirements for successful implementation included mobile lab licensure, CLIA certification, COLA enrollment, Quality and Risk assessments, inventory management, lab maintenance and ongoing monitoring. Testing was performed using the Xpert Xpress SARS-CoV-2 test and the population tested were primarily asymptomatic individuals. Results (if a Case Study enter NA) Between May 3rd, 2020 and June 23rd, 2021, a total of 31,148 Xpert Xpress SARS-CoV-2 tests were run across 3 mobile laboratories, with an average of 600 tests performed per week. The percent positivity ranged from 0% to 5.8%, reaching highest positivity in week beginning May 10th, 2020. The average turnaround time from sample collection to result verification was 2.0 hours, and the average time from sample receipt to result verification was under 1 hour. Conclusion Sanford Health’s mobile testing program brings SARS-CoV-2 PCR testing to the community and dramatically reduces the time from sample collection to result reporting compared with traditional testing labs, enabling rapid intervention following a positive result. The flexibility of the GeneXpert platform, including the instrument’s robustness, the independently functioning analyzers, and the wide range of tests available, makes it particularly well suited to mobile laboratories. This program demonstrates the impact of on-site testing and highlights the challenges that were overcome for successful implementation, providing a blueprint to support the development of other mobile laboratories in the US.

scholarly journals Data on the impact of the blood sample collection methods on blood protein profiling studies

Data in Brief ◽  
2017 ◽  
Vol 14 ◽  
pp. 313-319 ◽  
Author(s):  
Maria Ilies ◽  
Cristina Adela Iuga ◽  
Felicia Loghin ◽  
Vishnu Mukund Dhople ◽  
Thomas Thiele ◽  
...  
Keyword(s):  
Blood Sample ◽  
Protein Profiling ◽  
Blood Protein ◽  
Sample Collection ◽  
The Impact ◽  
Collection Methods

scholarly journals Impact of Blood Sample Collection and Processing Methods on Glucose Levels in Community Outreach Studies

2013 ◽  
Vol 2013 ◽  
pp. 1-4 ◽  
Author(s):  
Michael Turchiano ◽  
Cuong Nguyen ◽  
Arthur Fierman ◽  
Mark Lifshitz ◽  
Antonio Convit
Keyword(s):  
Clinical Laboratory ◽  
Community Outreach ◽  
Working Environment ◽  
Sample Collection ◽  
Blood Draw ◽  
Blood Samples ◽  
Glucose Levels ◽  
The Impact ◽  
Average Glucose ◽  
Collection Methods

Glucose obtained from unprocessed blood samples can decrease by 5%–7% per hour due to glycolysis. This study compared the impact of glucose degradation on measured glucose values by examining two different collection methods. For the first method, blood samples were collected in tubes containing sodium fluoride (NaF), a glycolysis inhibitor. For the second method, blood samples were collected in tubes containing a clot activator and serum gel separator and were centrifuged to separate the serum and plasma 20 minutes after sample collection. The samples used in the two methods were collected during the same blood draw and were assayed by the clinical laboratory 2–4 hours after the samples were obtained. A total of 256 pairs of samples were analyzed. The average glucose reading for the centrifuged tubes was significantly higher than the NaF tubes by0.196±0.159 mmol/L (P<0.01) or 4.2%. This study demonstrates the important role collection methods play in accurately assessing glucose levels of blood samples collected in the field, where working environment may be suboptimal. Therefore, blood samples collected in the field should be promptly centrifuged before being transported to clinical labs to ensure accurate glucose level measurements.

scholarly journals Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zeni Wu ◽  
Autumn G. Hullings ◽  
Reza Ghanbari ◽  
Arash Etemadi ◽  
Yunhu Wan ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Room Temperature ◽  
Temperature Stability ◽  
Occult Blood ◽  
Shannon Index ◽  
Fecal Occult Blood ◽  
Sample Collection ◽  
Human Microbiota ◽  
The Impact ◽  
Collection Methods

Abstract Background To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities. This study aimed to investigate the impact of fecal and oral sample collection methods and room temperature storage on collection samples for studies of the human microbiota. Results We collected fecal and oral samples from participants in two Iranian cohorts located in rural Yazd (n = 46) and urban Gonbad (n = 38) and investigated room temperature stability over 4 days of fecal (RNAlater and fecal occult blood test [FOBT] cards) and comparability of fecal and oral (OMNIgene ORAL kits and Scope mouthwash) collection methods. We calculated interclass correlation coefficients (ICCs) based on 3 alpha and 4 beta diversity metrics and the relative abundance of 3 phyla. After 4 days at room temperature, fecal stability ICCs and ICCs for Scope mouthwash were generally high for all microbial metrics. Similarly, the fecal comparability ICCs for RNAlater and FOBT cards were high, ranging from 0.63 (95% CI: 0.46, 0.75) for the relative abundance of Firmicutes to 0.93 (95% CI: 0.89, 0.96) for unweighted Unifrac. Comparability ICCs for OMNIgene ORAL and Scope mouthwash were lower than fecal ICCs, ranging from 0.55 (95% CI: 0.36, 0.70) for the Shannon index to 0.79 (95% CI: 0.69, 0.86) for Bray-Curtis. Overall, RNAlater, FOBT cards and Scope mouthwash were stable up to 4 days at room temperature. Samples collected using FOBT cards were generally comparable to RNAlater while the OMNIgene ORAL were less similar to Scope mouthwash. Conclusions As microbiome measures for feces samples collected using RNAlater, FOBT cards and oral samples collected using Scope mouthwash were stable over four days at room temperature, these would be most appropriate for microbial analyses in these populations. However, one collection method should be consistently since each method may induce some differences.

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