Flush With Data (or) Optimizing and Validating the Efficacy of Free and Computationally Simple 16S Metabarcoding Approaches for Use in Wastewater Surveillance.

IF 4 2区生物学 Q2 MICROBIOLOGY

Environmental microbiology Pub Date : 2026-05-01 DOI:10.1111/1462-2920.70276

Joe Berta, Lori A Rowe, Evan Multala, Robert F Garry

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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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用数据冲洗（或）优化和验证用于废水监测的免费和计算简单的16S元条形码方法的有效性。

我们提出了免费且计算复杂度低的16S rRNA元条形码分析方法，并对其进行了优化和验证，用于废水细菌监测。增加了NCBI BLAST亚采样、Kraken 2/Bracken和QIIME 2/DADA 2三个分类学分析管道。我们对高复杂性废水样品的优化策略使QIIME 2/DADA 2对物种水平分类群的敏感性提高了240.5%，而Kraken 2/Bracken和NCBI BLAST亚样的物种水平选择性分别提高了18.7%和79.1%。优化大大降低了BLAST子采样和Kraken 2/Bracken的读取映射误差，分别降低了42.0%和11.4%。通过我们的优化策略，微生物群落多样性估计也得到了改善。而Kraken 2/Bracken和QIIME 2/DADA 2分别提高了2.2%和37.8%，BLAST子样本的丰度测量精度提高了95.6%。BLAST子抽样的Shannon熵估计准确率提高了17.4%，而Kraken 2/Bracken和QIIME 2/DADA 2的准确率分别提高了19.7%和41.4%。对于beta多样性，采用QIIME 2/DADA 2进行的布雷-柯蒂斯差异估计准确率提高了8.5%，采用Kraken 2/Bracken进行的布雷-柯蒂斯差异估计准确率提高了174.3%。

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来源期刊

Environmental microbiology 环境科学-微生物学

CiteScore

9.90

自引率

3.90%

发文量

427

审稿时长

2.3 months

期刊介绍： Environmental Microbiology provides a high profile vehicle for publication of the most innovative, original and rigorous research in the field. The scope of the Journal encompasses the diversity of current research on microbial processes in the environment, microbial communities, interactions and evolution and includes, but is not limited to, the following: the structure, activities and communal behaviour of microbial communities microbial community genetics and evolutionary processes microbial symbioses, microbial interactions and interactions with plants, animals and abiotic factors microbes in the tree of life, microbial diversification and evolution population biology and clonal structure microbial metabolic and structural diversity microbial physiology, growth and survival microbes and surfaces, adhesion and biofouling responses to environmental signals and stress factors modelling and theory development pollution microbiology extremophiles and life in extreme and unusual little-explored habitats element cycles and biogeochemical processes, primary and secondary production microbes in a changing world, microbially-influenced global changes evolution and diversity of archaeal and bacterial viruses new technological developments in microbial ecology and evolution, in particular for the study of activities of microbial communities, non-culturable microorganisms and emerging pathogens