The Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus, and biopesticide B. thuringiensis Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruences, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes (n = 2,231), we show that current species definitions lead to overlapping genomospecies clusters, in which 66.2% of genomes belong to multiple genomospecies at a conventional 95 average nucleotide identity (ANI) genomospecies threshold. A genomospecies threshold of ≈92.5 ANI is shown to reflect a natural gap in genome similarity for the B. cereus group, and medoid genomes identified at this threshold are shown to yield resolvable genomospecies clusters with minimal overlap (six of 2,231 genomes assigned to multiple genomospecies; 0.269%). We thus propose a nomenclatural framework for the B. cereus group which accounts for (i) genomospecies using resolvable genomospecies clusters obtained at ≈92.5 ANI, (ii) established lineages of medical importance using a formal collection of subspecies names, and (iii) heterogeneity of clinically and industrially important phenotypes using a formalized and extended collection of biovar terms. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance; early detection of emerging, high-risk genotypes; and outbreak preparedness.IMPORTANCE Historical species definitions for many prokaryotes, including pathogens, have relied on phenotypic characteristics that are inconsistent with genome evolution. This scenario forces microbiologists and clinicians to face a tradeoff between taxonomic rigor and clinical interpretability. Using the Bacillus cereus group as a model, a conceptual framework for the taxonomic delineation of prokaryotes which reconciles genomic definitions of species with clinically and industrially relevant phenotypes is presented. The nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy that moves beyond arbitrarily set genomospecies thresholds while maintaining congruence with phenotypes and historically important species names.

中文翻译：

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蜡样芽孢杆菌群的分类学名称的提议，该分类学名称使具有临床和工业表型的细菌物种的基因组定义相一致。

蜡状芽孢杆菌组包括许多密切相关的物种，包括生物恐怖因子B.炭疽杆菌，食源性致病菌蜡状芽孢杆菌和苏云金芽孢杆菌B.能与疾病相关的能够引起疾病或死亡的生物对于风险评估和疾病爆发的预防至关重要。但是，当前的物种定义促进了物种-表型的不一致，特别是当水平获取的基因负责表型时。使用所有公开可获得的蜡状芽孢杆菌组基因组（n = 2,231），我们显示当前的物种定义导致重叠的基因组簇，其中在常规的95个平均核苷酸同一性（ANI）基因组阈值下，66.2％的基因组属于多个基因组。基因组的阈值约为92。显示5个ANI反映了蜡状芽孢杆菌组的基因组相似性的自然差距，并且在此阈值处鉴定的类固醇基因组显示产生了具有最小重叠的可分辨基因组簇（2,231个基因组中的六个分配给多个基因组; 0.269％）。因此，我们提出了蜡状芽孢杆菌组的命名法框架，该框架说明了（i）使用可分辨的基因组簇以≈92.5ANI获得的基因组，（ii）使用正式的亚种名称集合建立了具有医学重要性的谱系，以及（iii）异质性通过形式化和扩展的biovar术语集合来确定具有临床和工业重要性的表型。我们预计拟议的命名法将在不牺牲基因组物种定义的前提下仍可为临床医生解释，从而有助于病原体的监测。及早发现新兴的高风险基因型；重要信息许多原核生物（包括病原体）的历史物种定义都依赖于与基因组进化不一致的表型特征。这种情况迫使微生物学家和临床医生要在分类严谨性和临床可解释性之间进行权衡。以蜡状芽孢杆菌为模型，提出了用于原核生物分类学描述的概念框架，该框架与临床和工业相关的表型协调了物种的基因组定义。此处概述的命名法框架可作为基于基因组学的细菌分类学的模型，该模型超越了任意设置的基因组阈值，同时保持了与表型和历史上重要的物种名称的一致性。