Isolates within the Clostridium estertheticum complex (CEC) have routinely been identified through the 16S rRNA sequence, but the high interspecies sequence similarity reduces the resolution necessary for species level identification and often results in ambiguous taxonomic classification. The current study identified CEC isolates from meat juice (MJS) and bovine fecal samples (BFS) and determined the phylogeny of species within the CEC through whole genome sequence (WGS)-based analyses. About 1,054 MJS were screened for CEC using quantitative real-time PCR (qPCR). Strains were isolated from 33 MJS and 34 BFS qPCR-positive samples, respectively. Pan- and core-genome phylogenomics were used to determine the species identity of the isolates. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were used to validate the species identity. The phylogeny of species within the CEC was determined through a combination of these methods. Twenty-eight clostridia strains were isolated from MJS and BFS samples out of which 13 belonged to CEC. At 95% ANI and 70% dDDH thresholds for speciation, six CEC isolates were identified as genomospecies2 (n=3), Clostridium tagluense (n=2) and genomospecies3 (n=1). Lower thresholds of 94% ANI and 58% dDDH were required for the classification of seven CEC isolates into species C. estertheticum and prevent an overlap between species C. estertheticum and Clostridium frigoriphilum. Combination of the two species and abolishment of current subspecies classification within the species C. estertheticum are proposed. These data demonstrate the suitability of phylogenomics to identify CEC isolates and determine the phylogeny within CEC.

隔离在 酯化梭菌复合体 (CEC) 通常通过 16S rRNA 序列进行鉴定，但高的种间序列相似性降低了物种水平鉴定所需的分辨率，并经常导致分类学分类不明确。目前的研究从肉汁 (MJS) 和牛粪便样本 (BFS) 中鉴定了 CEC 分离株，并通过基于全基因组序列 (WGS) 的分析确定了 CEC 内物种的系统发育。使用定量实时 PCR (qPCR) 筛选了大约 1,054 个 MJS 的 CEC。菌株分别从 33 个 MJS 和 34 个 BFS qPCR 阳性样品中分离出来。泛基因组和核心基因组系统基因组学用于确定分离株的物种身份。平均核苷酸同一性 (ANI) 和数字 DNA-DNA 杂交 (dDDH) 用于验证物种同一性。CEC 内物种的系统发育是通过这些方法的组合确定的。从 MJS 和 BFS 样品中分离出 28 株梭菌菌株，其中 13 株属于 CEC。在物种形成的 95% ANI 和 70% dDDH 阈值下，6 个 CEC 分离株被鉴定为基因物种2（n=3), 梭菌 (n=2) 和基因物种 3 (n=1）。将 7 个 CEC 分离株分类为物种需要 94% ANI 和 58% dDDH 的较低阈值C. 酯类 并防止物种之间的重叠 C. 酯类 和 嗜冷梭菌. 两个物种的组合和物种内现有亚种分类的废除C. 酯类被提议。这些数据表明系统基因组学适用于鉴定 CEC 分离株并确定 CEC 内的系统发育。