Evaluating intestinal biopsy tissue preservation methods to facilitate large-scale microbiome research
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PROVIDER: PRJEB74359 | ENA |
REPOSITORIES: ENA
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Project description:BackgroundLarge-scale multicentre studies are needed to understand complex relationships between the gut microbiota, health and disease. Interrogating the mucosal microbiota may identify important biology not captured by stool analysis. Gold standard tissue cryopreservation ('flash freezing') limits large-scale study feasibility. We aimed to compare gut microbiota in gold standard and pragmatic mucosal biopsy storage conditions.MethodsWe collected endoscopic recto-sigmoid biopsies from 20 adults with inflammatory bowel disease. Biopsies were preserved using three methods: (i) flash freezing (most proximal and distal biopsy sites); (ii) nucleic acid preservative reagents (QIAGEN Allprotect®, Invitrogen RNAlater™, and Zymo DNA/RNA Shield™); and (iii) formalin fixation with paraffin embedding (FFPE), which is used to preserve tissue for clinical histopathology within healthcare settings. Microbiota were sequenced on the MiSeq platform (V4 region, 16S rRNA gene).FindingsTissue microbiota were consistent between most proximal and distal tissue suggesting any within-patient variation observed reflected storage condition, not biopsy location. There was no significant difference in alpha-diversity or microbial community profiles of reagent-preserved versus gold standard tissue. FFPE community structure was significantly dissimilar to other tissue samples, driven by differential relative abundance of obligate gut anaerobes; Faecalibacterium, Anaerostipes and Lachnospiraceae. Despite these differences, tissue microbiota grouped by participant regardless of preservation and storage conditions.InterpretationPreservative reagents offer a convenient alternative to flash freezing tissue in prospective large-scale mucosal microbiota studies. Whilst less comparable, FFPE provides potential for retrospective microbiota studies using historical samples.FundingMedical Research Council (MR/T032162/1) and The Leona M. and Harry B. Helmsley Charitable Trust (G-2002-04255).
| S-EPMC11751561 | biostudies-literature
Project description:The investigation of wildlife gastrointestinal microbiomes by next-generation sequencing approaches is a growing field in microbial ecology and conservation. Such studies often face difficulties in sample preservation if neither freezing facilities nor liquid nitrogen (LQN) are readily available. Thus, in order to prevent microbial community changes because of bacterial growth after sampling, preservation buffers need to be applied to samples. However, the amount of microbial community variation attributable to the different preservation treatments and potentially affecting biological interpretation is hardly known. Here, we sampled feces of 11 sheep (Ovis aries sp.) by using swabs and analyzed the effect of air-drying, an inexpensive self-made nucleic acid preservation buffer (NAP), DNA/RNA Shield™, and RNAlater®, each together with freezing (for 10 days) or storing at room temperature (for 10 days) prior to 16S rRNA gene high-throughput sequencing to determine bacterial communities. Results revealed that the proportions of operational taxonomic units (OTUs) belonging to a bacterial phylum were affected by the preservation treatments, and that alpha diversities [observed OTUs, Shannon index, and phylogenetic diversity (PD)] were lower in all preservation treatments than in samples taken by forensic swabs and immediately frozen which is considered as the favored preservation treatment in the absence of any logistic constraints. Overall, NAP had better preservation qualities than RNAlater® and DNA/RNA Shield™ making this self-made buffer a valuable solution in wildlife microbiome studies.
| S-EPMC5281576 | biostudies-literature
Project description:Deficiency in the X-linked inhibitor of apoptosis protein (XIAP) is the cause for the X-linked lymphoproliferative syndrome 2 (XLP2). About one third of all patients suffers from severe and therapy refractory inflammatory bowel disease (IBD), but the exact pathogenesis remains undefined. We examined the differences in gene expression of pediatric XLP2 patients with IBD to healthy controls and pediatric IBD patients.
2021-09-20 | GSE183069 | GEO
Project description:Inflammatory Bowel Disease (IBD) is a progressive disease of the gut and consists of two types, Crohn’s Disease (CD) and Ulcerative Colitis (UC). It is a complex disease involving genetic, microbial, and environmental factors. The incidence of IBD is steadily increasing and current therapeutic options are plateauing. Thus treatments are evolving to 1. deeper levels of remission from clinical to endoscopic and histologic normalization and 2. Embrace novel targets or drug combinations. We explored whole transcriptome data generated in biopsy specimens sampled from a large cohort of adult IBD and control subjects to provide 1. a granular, objective and sensitive molecular measures of disease activity in the gut and 2. Novel molecular mechanisms and biomarkers underlying IBD pathology.
2022-09-16 | GSE193677 | GEO
Project description:A significant challenge for fMRI research is statistically controlling for false positives without omitting true effects. Although a number of traditional methods for multiple comparison correction exist, several alternative tools have been developed that do not rely on strict parametric assumptions, but instead implement alternative methods to correct for multiple comparisons. In this study, we evaluated three of these methods, Statistical non-Parametric Mapping (SnPM), 3DClustSim, and Threshold Free Cluster Enhancement (TFCE), by examining which method produced the most consistent outcomes even when spatially-autocorrelated noise was added to the original images. We assessed the false alarm rate and hit rate of each method after noise was applied to the original images.
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Project description:Human pluripotent stem cells have been employed in generating organoids, yet their immaturity compared to fetal organs and the limited induction of all constituent cell types remain challenges. Porcine fetal progenitor cells have emerged as promising candidates for co-culturing with human progenitor cells in regeneration and xenotransplantation research. This study focused on identifying proper preservation methods for porcine fetal kidneys, hearts, and livers, aiming to optimize their potential as cell sources. Extracted from fetal microminiature pigs, these organs were dissociated before and after cryopreservation-thawing, with subsequent cell quality evaluations. Kidney cells, dissociated and aggregated after vitrification in a whole-organ form, were successfully differentiated into glomeruli and tubules in vivo. In contrast, freezing hearts and livers before dissociation yielded suboptimal results. Heart cells, frozen after dissociation, exhibited pulsating heart muscle cells similar to non-frozen hearts. As for liver cells, we developed a direct tissue perfusion technique and successfully obtained highly viable liver parenchymal cells. Freezing dissociated liver cells, although inferior to their non-frozen counterparts, maintained the ability for colony formation. The findings of this study provide valuable insights into suitable preservation methods for porcine fetal cells from kidneys, hearts, and livers, contributing to the advancement of regeneration and xenotransplantation research.
| S-EPMC10854901 | biostudies-literature
Project description:Population health researchers from different fields often address similar substantive questions but rely on different study designs, reflecting their home disciplines. This is especially true in studies involving causal inference, for which semantic and substantive differences inhibit interdisciplinary dialogue and collaboration. In this paper, we group nonrandomized study designs into two categories: those that use confounder-control (such as regression adjustment or propensity score matching) and those that rely on an instrument (such as instrumental variables, regression discontinuity, or differences-in-differences approaches). Using the Shadish, Cook, and Campbell framework for evaluating threats to validity, we contrast the assumptions, strengths, and limitations of these two approaches and illustrate differences with examples from the literature on education and health. Across disciplines, all methods to test a hypothesized causal relationship involve unverifiable assumptions, and rarely is there clear justification for exclusive reliance on one method. Each method entails trade-offs between statistical power, internal validity, measurement quality, and generalizability. The choice between confounder-control and instrument-based methods should be guided by these tradeoffs and consideration of the most important limitations of previous work in the area. Our goals are to foster common understanding of the methods available for causal inference in population health research and the tradeoffs between them; to encourage researchers to objectively evaluate what can be learned from methods outside one's home discipline; and to facilitate the selection of methods that best answer the investigator's scientific questions.
| S-EPMC6926350 | biostudies-literature
Project description:BackgroundVariable selection for regression models plays a key role in the analysis of biomedical data. However, inference after selection is not covered by classical statistical frequentist theory, which assumes a fixed set of covariates in the model. This leads to over-optimistic selection and replicability issues.MethodsWe compared proposals for selective inference targeting the submodel parameters of the Lasso and its extension, the adaptive Lasso: sample splitting, selective inference conditional on the Lasso selection (SI), and universally valid post-selection inference (PoSI). We studied the properties of the proposed selective confidence intervals available via R software packages using a neutral simulation study inspired by real data commonly seen in biomedical studies. Furthermore, we present an exemplary application of these methods to a publicly available dataset to discuss their practical usability.ResultsFrequentist properties of selective confidence intervals by the SI method were generally acceptable, but the claimed selective coverage levels were not attained in all scenarios, in particular with the adaptive Lasso. The actual coverage of the extremely conservative PoSI method exceeded the nominal levels, and this method also required the greatest computational effort. Sample splitting achieved acceptable actual selective coverage levels, but the method is inefficient and leads to less accurate point estimates. The choice of inference method had a large impact on the resulting interval estimates, thereby necessitating that the user is acutely aware of the goal of inference in order to interpret and communicate the results.ConclusionsDespite violating nominal coverage levels in some scenarios, selective inference conditional on the Lasso selection is our recommended approach for most cases. If simplicity is strongly favoured over efficiency, then sample splitting is an alternative. If only few predictors undergo variable selection (i.e. up to 5) or the avoidance of false positive claims of significance is a concern, then the conservative approach of PoSI may be useful. For the adaptive Lasso, SI should be avoided and only PoSI and sample splitting are recommended. In summary, we find selective inference useful to assess the uncertainties in the importance of individual selected predictors for future applications.
| S-EPMC9316707 | biostudies-literature
Project description:The development and scope of using various food preservation methods depends on the level of consumers' acceptance. Despite their advantages, in the case of negative attitudes, producers may limit their use if it determines the level of sales. The aim of this study was to evaluate the perception of seven different food processing methods and to identify influencing factors, such as education as well as living area and, at the same time, to consider whether consumers verify this type of information on the labels. Additionally, the study included the possibility of influencing consumer attitudes by using alternative names for preservation methods, on the example of microwave treatment. The results showed that conventional heat treatments were the most preferred preservation methods, whereas preservatives, irradiation, radio waves and microwaves were the least favored, suggesting that consumers dislike methods connected with "waves" to a similar extent as their dislike for preservatives. The control factors proved to significantly modify the evaluation of the methods. The analysis of alternative names for microwave treatment showed that "dielectric heating" was significantly better perceived. These research findings are important as the basis for understanding consumer attitudes. Implications for business and directions of future research are also indicated.
| S-EPMC9099755 | biostudies-literature
Project description:Genomics and molecular imaging, along with clinical and translational research have transformed biomedical science into a data-intensive scientific endeavor. For researchers to benefit from Big Data sets, developing long-term biomedical digital data preservation strategy is very important. In this opinion article, we discuss specific actions that researchers and institutions can take to make research data a continued resource even after research projects have reached the end of their lifecycle. The actions involve utilizing an Open Archival Information System model comprised of six functional entities: Ingest, Access, Data Management, Archival Storage, Administration and Preservation Planning. We believe that involvement of data stewards early in the digital data life-cycle management process can significantly contribute towards long term preservation of biomedical data. Developing data collection strategies consistent with institutional policies, and encouraging the use of common data elements in clinical research, patient registries and other human subject research can be advantageous for data sharing and integration purposes. Specifically, data stewards at the onset of research program should engage with established repositories and curators to develop data sustainability plans for research data. Placing equal importance on the requirements for initial activities (e.g., collection, processing, storage) with subsequent activities (data analysis, sharing) can improve data quality, provide traceability and support reproducibility. Preparing and tracking data provenance, using common data elements and biomedical ontologies are important for standardizing the data description, making the interpretation and reuse of data easier. The Big Data biomedical community requires scalable platform that can support the diversity and complexity of data ingest modes (e.g. machine, software or human entry modes). Secure virtual workspaces to integrate and manipulate data, with shared software programs (e.g., bioinformatics tools), can facilitate the FAIR (Findable, Accessible, Interoperable and Reusable) use of data for near- and long-term research needs.
| S-EPMC6144948 | biostudies-other