Find research datasets worth reusing

opencc-by-4.0Jun 2024View details →

Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota

<div> Background: Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models.  </div> <div> Results: As expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra.  </div> <div> Conclusions: Shotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.  </div>

opencc-by-4.0Sep 2024View details →

Comparative Analysis of Gut Microbiota in Hepatocellular Carcinoma and Hepatitis

The differential abundance of flora was modeled using support vector machine (SVM) methodology. Predictive performance for hepatocellular carcinoma and hepatitis was assessed using the model. 3 genera including Paraprevotella, Pasteurellaceae, and Prevotellaceae showed superior predictive performance for HCC, whereas Oscillibacter, Clostridium_XVIII, while 5 genera including  Eggerthella exhibited better predictive ability for HBV.

opencc-by-4.0Sep 2024View details →

Influence of Nutritional Emulsifier (Egg lecithin) on growth, feed utilization and gut microbiota of Catla catla

Influence of Nutritional Emulsifier (Egg lecithin) on growth, feed utilization and gut microbiota of Catla catla

opencc-by-4.0Oct 2024View details →

Investigating the Casual Associations among the Gut Microbiota, Metabolites, and Bladder Cancer: A Mediation Mendelian Randomization Study

Open the record for dataset details and reuse information.

dryad32/100

Data from: Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.

Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, since the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery reared parrs.

opencc-zeroDec 2017View details →

dryad32/100

Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota

Background and objectives Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of resistance. On the other hand, antibiotic-mediated killing of susceptible genotypes can alleviate competition and allow resistant strains to thrive (competitive release). Here, by observing interactions both within and between species in microbial communities sampled from humans, we investigate the potential role for cross-protection and competitive release in driving the spread of ampicillin resistance in the ubiquitous gut commensal and opportunistic pathogen Escherichia coli. Methodology Using anaerobic gut microcosms comprising E. coli embedded within gut microbiota sampled from humans, we tested for cross-protection and competitive release both within and between species in response to the clinically important beta-lactam antibiotic ampicillin. Results While cross-protection gave an advantage to antibiotic-susceptible E. coli in standard laboratory conditions (well-mixed LB medium), competitive release instead drove the spread of antibiotic-resistant E. coli in gut microcosms (ampicillin boosted growth of resistant bacteria in the presence of susceptible strains). Conclusions and implications Competition between resistant strains and other members of the gut microbiota can restrict the spread of ampicillin resistance. If antibiotic therapy alleviates competition with resident microbes by killing susceptible strains, as here, microbiota-based interventions that restore competition could be key for slowing the spread of resistance.

opencc-zeroJul 2021View details →

dryad32/100

Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients

Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.

opencc-zeroJul 2021View details →

opencc-by-4.0May 2023View details →

Data from: Feeding and water temperature modulate the activity of gut microbiota in greater amberjack juveniles (Seriola dumerili)

Illumina (MiSeq v3) sequencing data for gut microbiota profiling in greater amberjack (Seriola dumerili) juveniles reared at three different water temperatures and sampled along a day cycle.

opencc-by-4.0Aug 2023View details →

Gut microbiota as mediator and moderator between hepatitis B virus and hepatocellular carcinoma

A STORMS (Strengthening The Organizing and Reporting of Microbiome Studies) checklist is available here.

The Gut Microbiota in Obsessive-Compulsive Disorder

ClinicalTrials.gov study NCT02285699. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Dietary Intervention and Gut Microbiota in Hepatocellular Carcinoma (HCC)

ClinicalTrials.gov study NCT07143955. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Low Grade Inflammation, Gut Microbiota and Barrier Function in Elderly Humans

ClinicalTrials.gov study NCT01218165. IPD Sharing: Not stated. Countries: 1. Publications: 24.

Impact of a Dried Vegetable on Bowel Function and Gut Microbiota

ClinicalTrials.gov study NCT05473793. IPD Sharing: NO. Countries: 1. Publications: 2.

Choline Source, Gut Microbiota and Trimethylamine-N-oxide Response

ClinicalTrials.gov study NCT04255368. IPD Sharing: NO. Countries: 1. Publications: 3.

Cranberry Flavan-3-ols Consumption and Gut Microbiota in Healthy Adults

ClinicalTrials.gov study NCT05931237. IPD Sharing: NO. Countries: 1. Publications: 0.

Effect of GOS Supplementation on Amoxicillin-treated Gut Microbiota From Healthy Adults

ClinicalTrials.gov study NCT01848535. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Traditional Chinese Medicine on Gut Microbiota and Allergic Diseases

ClinicalTrials.gov study NCT03033290. IPD Sharing: UNDECIDED. Countries: 1. Publications: 7.

controlledIPD-YESFeb 2026View details →

GutHeart: Targeting Gut Microbiota to Treat Heart Failure

ClinicalTrials.gov study NCT02637167. IPD Sharing: YES. Countries: 1. Publications: 16.

Pressure Ulcers in Patients Receiving Enteral Nutrition Therapy and Their Relationship With Gut Microbiota

ClinicalTrials.gov study NCT03627910. IPD Sharing: NO. Countries: 1. Publications: 10.

Fiber Intervention on Gut Microbiota in Children With Prader-Willi Syndrome

ClinicalTrials.gov study NCT04150991. IPD Sharing: Not stated. Countries: 1. Publications: 3.