ArticleEnvironmental microbiology2026
Flush With Data (or) Optimizing and Validating the Efficacy of Free and Computationally Simple 16S Metabarcoding Approaches for Use in Wastewater Surveillance.
Article in Environmental microbiology, 2026. 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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Abstract
We propose free and low-computationally complex methods of 16S rRNA metabarcoding analysis, then optimized and validate their accuracy for wastewater bacterial surveillance. Three taxonomic analysis pipelines were augmented: NCBI BLAST subsampling, Kraken 2/Bracken and QIIME 2/DADA 2. Our optimization strategies for the high complexity of wastewater samples raised QIIME 2/DADA 2's sensitivity to species-level taxa by 240.5%, while they increased the species-level selectivity of Kraken 2/Bracken and NCBI BLAST subsampling by 18.7% and 79.1%, respectively. Optimization vastly lowered the read mapping error for BLAST subsampling and Kraken 2/Bracken, by 42.0% and 11.4%, respectively. Microbial community diversity estimates were also improved through our optimization strategies. Richness measurements for BLAST subsampling became 95.6% more accurate, while Kraken 2/Bracken and QIIME 2/DADA 2 improved by 2.2% and 37.8%. Shannon entropy estimates by BLAST subsampling increased in accuracy by 17.4%, while for Kraken 2/Bracken and QIIME 2/DADA 2 they increased by 19.7% and 41.4%. For beta diversity, Bray-Curtis dissimilarity estimates by QIIME 2/DADA 2 increased in accuracy by 8.5% and by Kraken 2/Bracken by 174.3%.
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