Zhang Lin, Lin Tzu-Yu, Liu Wen-Tso, Ling Fangqiong
Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States.
Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, United States.
ACS Environ Au. 2024 Feb 23;4(3):127-141. doi: 10.1021/acsenvironau.3c00074. eCollection 2024 May 15.
Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, gene, and gene, and by genome-based approaches. Recent updates on the genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3-V4, V3-V5, V4, V4-V5, and V1-V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.
非结核分枝杆菌（NTM）是指任何不会导致结核病或麻风病的分枝杆菌。虽然大多数NTM是无害的，其中一些还被认为是益生菌，但越来越多的人被诊断出患有NTM感染。因此，临床医生、环境微生物学家和水质研究人员都对在环境中检测到它们很感兴趣。本综述提供了关于分类学基础方法的教程，重点关注16S rRNA基因、[此处原文缺失两个基因名称]基因以及基于基因组的方法所揭示的NTM之间的系统发育关系。还提供了[此处原文缺失菌属名称]菌属分类学的最新进展。在基于基因组的分类学框架内，对189种分枝杆菌的栖息地进行了综合分析，并关注了环境来源（如饮用水、水生环境和土壤）。评估了不同区域基于16S rRNA基因的分类准确性（V3、V3-V4、V3-V5、V4、V4-V5和V1-V9），结果表明在属水平上总体分类准确性极佳（高达100%），但在种水平上表现一般（高达63.5%）。未来的研究包括量化水系统中的NTM物种、确定水处理和管道条件对其变异的影响、开发用于环境的高通量物种水平表征工具以及在系统发育框架中纳入功能表征，这些研究可能会填补关键的知识空白。我们相信本教程将对环境微生物群落分子或基于基因组的分类分析领域的新手研究人员有用。专家们可能也会发现，就过去30年的选定关键发现、系统发育分析的最新进展以及在系统发育框架内对NTM生态学的综合而言，本综述是有用的。
