Dataset Information

What Can Be Learned From Crowdsourced Population Asparagus Urinary Odor Kinetics?

ABSTRACT: Asparagus consumption is associated with the production of malodorous urine. Interindividual variability was previously characterized by an American Society for Clinical Pharmacology and Therapeutics crowdsourced study. To further characterize urinary odor kinetics, we conducted a study with consenting participants from Takeda Pharmaceutical International Company. The participants were randomized to consume a specified number of asparagus spears and asked to record urine odor. A kinetic-pharmacodynamic model characterized the data from both the newly conducted Takeda study (N = 42) and the previously analyzed American Society for Clinical Pharmacology and Therapeutics studies (total N = 139). The updated model included the identification of an absorption process with a half-life of 25 minutes. We estimated the elimination half-life of the asparagus effect on malodorous urine to be 7.2 hours, which was 44% longer in our study. We built on previous experience using an improved R-Shiny app for conducting the crowdsourcing experiment, further demonstrating the utility of this population kinetics approach in organizational and educational settings.

SUBMITTER: Facius A

PROVIDER: S-EPMC6617763 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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What Can Be Learned From Crowdsourced Population Asparagus Urinary Odor Kinetics?

Facius Axel A Atkinson Linda A LA Hanna Kelly K Coombes Mai Chi MC Lahu Gezim G Wagner John A JA

CPT: pharmacometrics & systems pharmacology 20190423 6

Asparagus consumption is associated with the production of malodorous urine. Interindividual variability was previously characterized by an American Society for Clinical Pharmacology and Therapeutics crowdsourced study. To further characterize urinary odor kinetics, we conducted a study with consenting participants from Takeda Pharmaceutical International Company. The participants were randomized to consume a specified number of asparagus spears and asked to record urine odor. A kinetic-pharmaco ...[more]

PMID: 31016886

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Project description:BackgroundSelection of optimal computational strategies for analyzing metagenomics data is a decisive step in determining the microbial composition of a sample, and this procedure is complex because of the numerous tools currently available. The aim of this research was to summarize the results of crowdsourced sbv IMPROVER Microbiomics Challenge designed to evaluate the performance of off-the-shelf metagenomics software as well as to investigate the robustness of these results by the extended post-challenge analysis. In total 21 off-the-shelf taxonomic metagenome profiling pipelines were benchmarked for their capacity to identify the microbiome composition at various taxon levels across 104 shotgun metagenomics datasets of bacterial genomes (representative of various microbiome samples) from public databases. Performance was determined by comparing predicted taxonomy profiles with the gold standard.ResultsMost taxonomic profilers performed homogeneously well at the phylum level but generated intermediate and heterogeneous scores at the genus and species levels, respectively. kmer-based pipelines using Kraken with and without Bracken or using CLARK-S performed best overall, but they exhibited lower precision than the two marker-gene-based methods MetaPhlAn and mOTU. Filtering out the 1% least abundance species-which were not reliably predicted-helped increase the performance of most profilers by increasing precision but at the cost of recall. However, the use of adaptive filtering thresholds determined from the sample's Shannon index increased the performance of most kmer-based profilers while mitigating the tradeoff between precision and recall.Conclusionskmer-based metagenomic pipelines using Kraken/Bracken or CLARK-S performed most robustly across a large variety of microbiome datasets. Removing non-reliably predicted low-abundance species by using diversity-dependent adaptive filtering thresholds further enhanced the performance of these tools. This work demonstrates the applicability of computational pipelines for accurately determining taxonomic profiles in clinical and environmental contexts and exemplifies the power of crowdsourcing for unbiased evaluation.

Dataset Information

What Can Be Learned From Crowdsourced Population Asparagus Urinary Odor Kinetics?

Publications

What Can Be Learned From Crowdsourced Population Asparagus Urinary Odor Kinetics?

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