ArticleBioinformatics advances2025
Assessing accuracy and specificity of faecal source library for microbial source-tracking, using SourceTracker as case study.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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5 authors.
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Abstract
Motivation: Understanding the quality of the source library prior to undertaking library-dependent microbial source-tracking (MST) is an essential, but often overlooked, primary analysis step. Results: We propose an assessment approach to validate the quality of amplicon-derived faecal source libraries. This approach was demonstrated on a faecal source library consisting of 16S rRNA paired-end amplicon sequences, obtained from various animal types in Victoria, Australia. First, a leave-one-out (LOO) analysis was performed to assess the accuracy of source category groupings by identifying the number of samples incorrectly assigned to a different source category (i.e. animal type). Following a quality control procedure to decide retaining/removing/grouping incorrectly assigned samples, we then assessed if the sample sizes for each source type were sufficient to properly characterize the source fingerprints. Results from LOO demonstrated 15.5% of samples were incorrectly assigned, with high error rates in birds and wallabies within our source library. Increasing the sample size improved source identification accuracy. However, accuracy eventually plateaued in a source-specific manner. Importantly, this highlights the importance of conducting thorough assessments to understand the quality and limitations of the source library prior to library-dependent MST applications. Availability and implementation: QIIME2 is available via https://qiime2.org/; SourceTracker v2.0.1 is available via https://github.com/caporaso-lab/sourcetracker2; Pipeline for LOO is available via https://github.com/MonashOWL/Bioinformatics-IlluminaMGI/tree/main/16S/LOO; Pipeline for sample size assessment is available via https://github.com/MonashOWL/Bioinformatics-IlluminaMGI/tree/main/16S/Source%20variability.
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